Update HiCExplorer to 3.7.5 (galaxyproject#6112)

* add dbkey to build matrix. Tests failed because of prepareqc upstream? * fails - upstream module error. * update label help * bump version just for hicbuildmatrix * bump hicexplorer version to fix pandas and other dependency issues * remove redundant fake version suffix - already bumped to 3.7.3 * Update tools/hicexplorer/hicBuildMatrix.xml Co-authored-by: Björn Grüning <[email protected]> * add profile version * upgrade samtools and a few test datasets * more fixes for tests * update plotmatrix test outputs and passing hicbuildmatrix outputs are here - will see where they got to. * adding the fixed output for hicbuildmatrix * updating hicbuildmatrix test outputs again again. * bump hicexplorer version * fix wrappers that modify input dataset * change space to tabs in bed file * fix input matrix and update output * remove hicTADClassifier and hicTrainTADClassifier * use 3.7.5 * fix version number * update filetype input + diff test --------- Co-authored-by: fubar2 <[email protected]> Co-authored-by: Ross Lazarus <[email protected]> Co-authored-by: Björn Grüning <[email protected]> Co-authored-by: Bjoern Gruening <[email protected]>
pavanvidem · Jul 1, 2024 · 8586409 · 8586409
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diff --git a/tools/hicexplorer/chicAggregateStatistic.xml b/tools/hicexplorer/chicAggregateStatistic.xml
@@ -1,4 +1,4 @@
-<tool id="hicexplorer_chicaggregatestatistic" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+<tool id="hicexplorer_chicaggregatestatistic" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>computes with a target file the to be tested regions for chicDifferentialTest</description>
     <macros>
         <token name="@BINARY@">chicAggregateStatistic</token>

diff --git a/tools/hicexplorer/chicDifferentialTest.xml b/tools/hicexplorer/chicDifferentialTest.xml
@@ -1,4 +1,4 @@
-<tool id="hicexplorer_chicdifferentialtest" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+<tool id="hicexplorer_chicdifferentialtest" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>computes differential interactions of viewpoints</description>
     <macros>
         <token name="@BINARY@">chicDifferentialTest</token>

diff --git a/tools/hicexplorer/chicExportData.xml b/tools/hicexplorer/chicExportData.xml
@@ -1,4 +1,4 @@
-<tool id="hicexplorer_chicexportdata" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+<tool id="hicexplorer_chicexportdata" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>exports data of hdf to txt based files</description>
     <macros>
         <token name="@BINARY@">chicExportData</token>
@@ -7,7 +7,7 @@
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
         #import re
-        mkdir exportFolder && 
+        mkdir exportFolder &&
         @BINARY@
             --file '$file'
 
@@ -33,13 +33,11 @@
                 --outputModeName $outputMode_conditional.outputModeName
             #end if
             --decimalPlaces $decimalPlaces
-            
             --outFileName exportFolder/export.tar.gz
             --threads @THREADS@
 
-    ]]>    </command>
+    ]]></command>
     <inputs>
-
         <param name="file" type="data" format="h5" label="" />
         <conditional name="fileType_conditional">
 
@@ -59,16 +57,20 @@
                     <when value="txt" >
                     </when>
                     <when value="bigwig" >
-                        <param name="rangeUpstream" type="integer" value="500000" label="Upstream range" help="Defines the region upstream of a reference point which should be considered in the analysis." />
-                        <param name="rangeDownstream" type="integer" value="500000" label="Downstream range" help="Defines the region upstream of a reference point which should be considered in the analysis." />
+                        <param name="rangeUpstream" type="integer" value="500000" label="Upstream range"
+                            help="Defines the region upstream of a reference point which should be considered in the analysis." />
+                        <param name="rangeDownstream" type="integer" value="500000" label="Downstream range"
+                            help="Defines the region upstream of a reference point which should be considered in the analysis." />
                         <param name="column_selector" type="select" label="Datatrack output type">
                             <option value="relative-interactions" selected="True">relative interactions</option>
                             <option value="p-value">p-value</option>
                             <option value="x-fold" >x-fold</option>
                             <option value="raw" >raw</option>
                         </param>
-                        <param name="backgroundModelFile" type="data" format="tabular" label="Background model" help="The background file computed by chicViewpointBackgroundModel" />
-                        <param name="chromosomeSize" type="data" format="tabular" label="Chromosome size" help="Chromosome size as tabular file. One chromosome per line" />
+                        <param name="backgroundModelFile" type="data" format="tabular" label="Background model"
+                            help="The background file computed by chicViewpointBackgroundModel" />
+                        <param name="chromosomeSize" type="data" format="tabular" label="Chromosome size"
+                            help="Chromosome size as tabular file. One chromosome per line" />
                     </when>
                 </conditional>
             </when>
@@ -136,10 +138,10 @@
                 <param name="outputModeName" value="Eya1" />
             </conditional>
             <output_collection name="oneGeneCollectionBigwig" type="list" count="4">
-                <element name="background_FL-E13-5_chr1_genes_Eya1_interactions.bigwig" file="cHi-C/chicExportData/oneGene/background_FL-E13-5_chr1_genes_Eya1_interactions.bigwig" ftype="bigwig" compare="sim_size" />
-                <element name="background_MB-E10-5_chr1_genes_Eya1_interactions.bigwig" file="cHi-C/chicExportData/oneGene/background_MB-E10-5_chr1_genes_Eya1_interactions.bigwig" ftype="bigwig" compare="sim_size" />
                 <element name="FL-E13-5_chr1_genes_Eya1.bigwig" file="cHi-C/chicExportData/oneGene/FL-E13-5_chr1_genes_Eya1.bigwig" ftype="bigwig" compare="sim_size" />
                 <element name="MB-E10-5_chr1_genes_Eya1.bigwig" file="cHi-C/chicExportData/oneGene/MB-E10-5_chr1_genes_Eya1.bigwig" ftype="bigwig" compare="sim_size" />
+                <element name="background_FL-E13-5_chr1_genes_Eya1_interactions.bigwig" file="cHi-C/chicExportData/oneGene/background_FL-E13-5_chr1_genes_Eya1_interactions.bigwig" ftype="bigwig" compare="sim_size" />
+                <element name="background_MB-E10-5_chr1_genes_Eya1_interactions.bigwig" file="cHi-C/chicExportData/oneGene/background_MB-E10-5_chr1_genes_Eya1_interactions.bigwig" ftype="bigwig" compare="sim_size" />
             </output_collection>
         </test>
         <test expect_num_outputs="2">

diff --git a/tools/hicexplorer/chicPlotViewpoint.xml b/tools/hicexplorer/chicPlotViewpoint.xml
@@ -1,4 +1,4 @@
-<tool id="hicexplorer_chicplotviewpoint" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+<tool id="hicexplorer_chicplotviewpoint" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>creates plots for viewpoints</description>
     <macros>
         <token name="@BINARY@">chicPlotViewpoint</token>

diff --git a/tools/hicexplorer/chicQualityControl.xml b/tools/hicexplorer/chicQualityControl.xml
@@ -1,4 +1,4 @@
-<tool id="hicexplorer_chicqualitycontrol" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+<tool id="hicexplorer_chicqualitycontrol" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>generates an estimate of the quality of each viewpoint</description>
     <macros>
         <token name="@BINARY@">chicQualityControl</token>

diff --git a/tools/hicexplorer/hicBuildMatrix.xml b/tools/hicexplorer/hicBuildMatrix.xml
@@ -5,7 +5,7 @@
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements">
-        <requirement type="package" version="1.9">samtools</requirement>
+        <requirement type="package" version="1.19">samtools</requirement>
     </expand>
     <command detect_errors="exit_code"><![CDATA[
 
@@ -18,7 +18,7 @@
             #end for
 
             --restrictionCutFile '$restrictionCutFile'
-            
+
             #if $restrictionSequence:
                 --restrictionSequence '$restrictionSequence'
             #end if
@@ -31,21 +31,28 @@
             #if $maxLibraryInsertSize:
                 --maxLibraryInsertSize $maxLibraryInsertSize
             #end if
-           
+
             #if $binSizes:
                 --binSize
                 #for $repeat in $binSizes
                     '${repeat.binSize}'
                 #end for
             #end if
 
-            --genomeAssembly $samFiles[0].samFile.metadata.dbkey
+            #if $chromosomeSizes:
+                --chromosomeSizes '$chromosomeSizes'
+            #end if
+            #if $dbKey:
+                --genomeAssembly '$dbKey'
+            #else
+                --genomeAssembly '$samFiles[0].samFile.metadata.dbkey'
+            #end if
 
             #if $region:
                 --region '$region'
             #end if
 
-            --outFileName matrix.$outputFormat
+            --outFileName 'matrix.$outputFormat'
 
             #if $outBam:
                 $outBam ./unsorted.bam
@@ -59,10 +66,6 @@
                 --minMappingQuality $minMappingQuality
             #end if
 
-            #if $chromosomeSizes:
-                --chromosomeSizes '$chromosomeSizes'
-            #end if
-
             --threads @THREADS@
 
             --QCfolder ./QCfolder
@@ -81,7 +84,6 @@
         <!-- can we use multiple=True here with min="2" and max="2" ? -->
         <repeat max="2" min="2" name="samFiles" title="Sam/Bam files to process (forward/reverse)" help="Please use the special BAM datatype: qname_input_sorted.bam and use for 'bowtie2' the '--reorder' option to create a BAM file.">
             <param name="samFile" type="data" format="sam,qname_input_sorted.bam">
-                <validator type="unspecified_build" />
             </param>
         </repeat>
 
@@ -107,11 +109,13 @@
         <expand macro="minMappingQuality" />
         <param argument="--skipDuplicationCheck" type="boolean" truevalue="--skipDuplicationCheck" falsevalue="" label="Skip duplication check" help="Identification of duplicated read pairs is memory consuming. Thus, in case of memory errors this check can be skipped." />
         <param argument="--chromosomeSizes" type="data" format="tabular" optional="true" label="Chromosome sizes for your genome" help="File with the chromosome sizes for your genome. A tab-delimited two column layout 'chr_name size' is expected
-                    Usually the sizes can be determined from the SAM/BAM input files, however, 
-                    for cHi-C or scHi-C it can be that at the start or end no data is present. 
+                    Usually the sizes can be determined from the SAM/BAM input files, however,
+                    for cHi-C or scHi-C it can be that at the start or end no data is present.
                     Please consider that this option causes that only reads are considered which are on the listed chromosomes.
-                    Use this option to guarantee fixed sizes. An example file is available via UCSC: 
+                    Use this option to guarantee fixed sizes. An example file is available via UCSC:
                     http://hgdownload.soe.ucsc.edu/goldenPath/dm3/bigZips/dm3.chrom.sizes" />
+        <param name="dbKey" type="text" optional="true" label="Use this dbkey for your history genome"
+        help="You can set the reference genome in your history as metadata. In case you have not you can specify it here." />
 
         <param argument="--outBam" type="boolean" truevalue="--outBam" falsevalue="" checked="false" label="Save valid Hi-C reads in BAM file" help="A bam
                     file containing all valid Hi-C reads can be created
@@ -154,7 +158,7 @@
             <param name="restrictionSequence" value="GATC" />
             <param name="danglingSequence" value="GATC" />
             <param name="outBam" value="True" />
-            <output name="outfileBam" file="small_test_matrix_result_sorted.bam" ftype="bam" />
+            <output name="outfileBam" file="small_test_matrix_result_sorted.bam" compare="diff" lines_diff="2" ftype="bam" />
             <output name="outFileName" ftype="h5">
                 <assert_contents>
                     <has_h5_keys keys="intervals,matrix" />
@@ -177,7 +181,7 @@
             <param name="danglingSequence" value="GATC" />
             <param name="outputFormat" value="cool" />
             <param name="outBam" value="True" />
-            <output name="outfileBam" file="small_test_matrix_result_sorted.bam" ftype="bam" />
+            <output name="outfileBam" file="small_test_matrix_result_sorted.bam" compare="diff" lines_diff="2" ftype="bam" />
             <output name="outFileName" ftype="cool">
                 <assert_contents>
                     <has_h5_keys keys="bins,chroms,indexes,pixels" />

diff --git a/tools/hicexplorer/hicCompareMatrices.xml b/tools/hicexplorer/hicCompareMatrices.xml
@@ -1,4 +1,4 @@
-<tool id="hicexplorer_hiccomparematrices" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+<tool id="hicexplorer_hiccomparematrices" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>normalize and compare two Hi-C contact matrices</description>
     <macros>
         <token name="@BINARY@">hicCompareMatrices</token>

diff --git a/tools/hicexplorer/hicCompartmentalization.xml b/tools/hicexplorer/hicCompartmentalization.xml
@@ -1,4 +1,4 @@
-<tool id="hicexplorer_hiccompartmentspolarization" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+<tool id="hicexplorer_hiccompartmentspolarization" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>compute pairwise correlations between multiple Hi-C contact matrices</description>
     <macros>
         <token name="@BINARY@">hicCompartmentalization</token>

diff --git a/tools/hicexplorer/hicConvertFormat.xml b/tools/hicexplorer/hicConvertFormat.xml
@@ -1,4 +1,4 @@
-<tool id="hicexplorer_hicconvertformat" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+<tool id="hicexplorer_hicconvertformat" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>Convert between different file formats</description>
     <macros>
         <token name="@BINARY@">hicConvertFormat</token>

diff --git a/tools/hicexplorer/hicCorrectMatrix.xml b/tools/hicexplorer/hicCorrectMatrix.xml
@@ -1,4 +1,4 @@
-<tool id="hicexplorer_hiccorrectmatrix" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+<tool id="hicexplorer_hiccorrectmatrix" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>run a Hi-C matrix correction algorithm</description>
     <macros>
         <token name="@BINARY@">hicCorrectMatrix</token>

diff --git a/tools/hicexplorer/hicCorrelate.xml b/tools/hicexplorer/hicCorrelate.xml
@@ -1,4 +1,4 @@
-<tool id="hicexplorer_hiccorrelate" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+<tool id="hicexplorer_hiccorrelate" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>compute pairwise correlations between multiple Hi-C contact matrices</description>
     <macros>
         <token name="@BINARY@">hicCorrelate</token>

diff --git a/tools/hicexplorer/hicDetectLoops.xml b/tools/hicexplorer/hicDetectLoops.xml
@@ -1,4 +1,4 @@
-<tool id="hicexplorer_hicdetectloops" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+<tool id="hicexplorer_hicdetectloops" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>searches for enriched regions</description>
     <macros>
         <token name="@BINARY@">hicDetectLoops</token>

diff --git a/tools/hicexplorer/hicDifferentialTAD.xml b/tools/hicexplorer/hicDifferentialTAD.xml
@@ -1,4 +1,4 @@
-<tool id="hicexplorer_hicdifferentialtad" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+<tool id="hicexplorer_hicdifferentialtad" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>searches for differential TADs</description>
     <macros>
         <token name="@BINARY@">hicDifferentialTAD</token>

diff --git a/tools/hicexplorer/hicFindRestrictionSites.xml b/tools/hicexplorer/hicFindRestrictionSites.xml
@@ -1,4 +1,4 @@
-<tool id="hicexplorer_hicfindrestrictionsites" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+<tool id="hicexplorer_hicfindrestrictionsites" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>identify restriction enzyme sites</description>
     <macros>
         <token name="@BINARY@">hicFindRestSite</token>

diff --git a/tools/hicexplorer/hicFindTADs.xml b/tools/hicexplorer/hicFindTADs.xml
@@ -1,4 +1,4 @@
-<tool id="hicexplorer_hicfindtads" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+<tool id="hicexplorer_hicfindtads" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>identify TAD boundaries by computing the degree of separation of each Hi-C matrix bin</description>
     <macros>
         <token name="@BINARY@">hicFindTADs</token>

diff --git a/tools/hicexplorer/hicHyperoptDetectLoops.xml b/tools/hicexplorer/hicHyperoptDetectLoops.xml
@@ -1,4 +1,4 @@
-<tool id="hicexplorer_hichyperoptDetectLoops" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+<tool id="hicexplorer_hichyperoptDetectLoops" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>optimizes parameters for hicDetectLoops</description>
     <macros>
         <token name="@BINARY@">hicHyperoptDetectLoops</token>

diff --git a/tools/hicexplorer/hicInfo.xml b/tools/hicexplorer/hicInfo.xml
@@ -1,4 +1,4 @@
-<tool id="hicexplorer_hicinfo" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+<tool id="hicexplorer_hicinfo" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>get information about the content of a Hi-C matrix</description>
     <macros>
         <token name="@BINARY@">hicInfo</token>

diff --git a/tools/hicexplorer/hicInterIntraTAD.xml b/tools/hicexplorer/hicInterIntraTAD.xml
@@ -1,4 +1,4 @@
-<tool id="hicexplorer_hicinterintratad" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+<tool id="hicexplorer_hicinterintratad" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>computes the ratio of inter TAD-scores vs. intra TADs</description>
     <macros>
         <token name="@BINARY@">hicInterIntraTAD</token>
@@ -54,11 +54,11 @@
     <tests>
         <test>
             <param name="matrix_h5_cooler" value="hicInterIntraTAD/matrix.cool" />
-            <param name="tadDomains" value="hicInterIntraTAD/untreated_R1_domains_chr1_chr2.bed" />
+            <param name="tadDomains" value="hicInterIntraTAD/untreated_R1_domains_chr1_chr2.bed" ftype="bed" />
 
             <output name="output_txt" file="hicInterIntraTAD/output.txt" ftype="txt" />
 
-            <output name="output_plot" file="hicInterIntraTAD/plot.png" ftype="png" />
+            <output name="output_plot" file="hicInterIntraTAD/plot.png" ftype="png" compare="sim_size" delta="10000"/>
 
         </test>
 

diff --git a/tools/hicexplorer/hicMergeDomains.xml b/tools/hicexplorer/hicMergeDomains.xml
@@ -1,4 +1,4 @@
-<tool id="hicexplorer_hicmergedomains" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+<tool id="hicexplorer_hicmergedomains" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>Merges TAD domains</description>
     <macros>
         <token name="@BINARY@">hicMergeDomains</token>

diff --git a/tools/hicexplorer/hicMergeLoops.xml b/tools/hicexplorer/hicMergeLoops.xml
@@ -1,4 +1,4 @@
-<tool id="hicexplorer_hicmergeloops" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+<tool id="hicexplorer_hicmergeloops" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>merge detected loops of different resolutions.</description>
     <macros>
         <token name="@BINARY@">hicMergeLoops</token>

diff --git a/tools/hicexplorer/hicMergeMatrixBins.xml b/tools/hicexplorer/hicMergeMatrixBins.xml
@@ -1,4 +1,4 @@
-<tool id="hicexplorer_hicmergematrixbins" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+<tool id="hicexplorer_hicmergematrixbins" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>merge adjacent bins from a Hi-C contact matrix to reduce its resolution</description>
     <macros>
         <token name="@BINARY@">hicMergeMatrixBins</token>
@@ -11,8 +11,8 @@
             --matrix 'matrix.$matrix_h5_cooler.ext'
             --numBins $numBins
             $runningWindow
-            --outFileName 'matrix.$matrix_h5_cooler.ext'
-        && mv 'matrix.$matrix_h5_cooler.ext' matrix
+            --outFileName 'out_matrix.$matrix_h5_cooler.ext'
+        && mv 'out_matrix.$matrix_h5_cooler.ext' matrix
 ]]>
     </command>
     <inputs>

diff --git a/tools/hicexplorer/hicNormalize.xml b/tools/hicexplorer/hicNormalize.xml
@@ -1,4 +1,4 @@
-<tool id="hicexplorer_hicnormalize" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+<tool id="hicexplorer_hicnormalize" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>normalizes a matrix to norm range or smallest read count</description>
     <macros>
         <token name="@BINARY@">hicNormalize</token>

diff --git a/tools/hicexplorer/hicPCA.xml b/tools/hicexplorer/hicPCA.xml
@@ -1,4 +1,4 @@
-<tool id="hicexplorer_hicpca" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+<tool id="hicexplorer_hicpca" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>compute the principal components for A / B compartment analysis</description>
     <macros>
         <token name="@BINARY@">hicPCA</token>

diff --git a/tools/hicexplorer/hicPlotAverageRegions.xml b/tools/hicexplorer/hicPlotAverageRegions.xml
@@ -1,4 +1,4 @@
-<tool id="hicexplorer_hicplotaverageregions" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+<tool id="hicexplorer_hicplotaverageregions" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>plot the average regions from hicAverageRegions</description>
     <macros>
         <token name="@BINARY@">hicPlotAverageRegions</token>