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Merge pull request #1 from wm75/more_suggestions
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Treat and test GFF and GTF separately
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@drosofff
drosofff authored Jan 31, 2024
2 parents 26de736 + 3dd0e69 commit 49ea1b8
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66 changes: 39 additions & 27 deletions tools/htseq_count/htseq-count.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@
<xref type="bio.tools">htseq</xref>
</xrefs>
<requirements>
<requirement type="package" version="2.0.5">htseq</requirement>
<requirement type="package" version="@TOOL_VERSION@">htseq</requirement>
<requirement type="package" version="1.19.2">samtools</requirement>
<requirement type="package" version="5.3.0">gawk</requirement>
<requirement type="package" version="9.4">coreutils</requirement>
Expand All @@ -24,30 +24,36 @@
<regex match="Error" source="stderr" level="fatal" description="Unknown error occured" />
</stdio>

<version_command>htseq-count -h | grep version | sed 's/^\(.*\)*\(version .*\)\./\2/'</version_command>
<version_command>htseq-count --version</version_command>

<command><![CDATA[
##set up input files
#set $reference_fasta_filename = "localref.fa"
#set $name_sorted_alignment_filename = "name_sorted_alignment.sam"
#set $name_sorted_alignment_filename = "name_sorted.bam"
#set $ref_index = "ref.fai"
#if str( $advanced_options.advanced_options_selector ) == "advanced":
#if str( $advanced_options.samout_conditional.samout ) == "Yes":
#if str( $advanced_options.samout_conditional.reference_source.reference_source_selector ) == "history":
ln -s "${advanced_options.samout_conditional.reference_source.ref_file}" "${reference_fasta_filename}" &&
samtools faidx '${reference_fasta_filename}' 2>&1 || echo "Error running samtools faidx for htseq-count" >&2 &&
samtools faidx --fai-idx $ref_index '${advanced_options.samout_conditional.reference_source.ref_file}' 2>&1 || echo "Error running samtools faidx for htseq-count" >&2 &&
#else:
#set $reference_fasta_filename = str( $advanced_options.samout_conditional.reference_source.ref_file.fields.path )
ln -s '${advanced_options.samout_conditional.reference_source.ref_file.fields.path}.fai' $ref_index
#end if
#end if
#end if
#if $samfile.extension == 'bam':
samtools sort -n -T "\${TMPDIR:-.}" --output-fmt=BAM -o '$name_sorted_alignment_filename' '$samfile' &&
#else
samtools view -Su -t '${reference_fasta_filename}.fai' '$samfile' | samtools sort -n -T "\${TMPDIR:-.}" --output-fmt=BAM -o '$name_sorted_alignment_filename' - &&
samtools sort -n -T "\${TMPDIR:-.}" -o $name_sorted_alignment_filename '$samfile' &&
#else:
samtools view -Su -t $ref_index '$samfile' | samtools sort -n -T "\${TMPDIR:-.}" -o $name_sorted_alignment_filename - &&
#end if
ln -s '$gfffile' reference.gtf &&
#if $gfffile.is_of_type('gtf'):
## htseq-count requires .gtf suffix to recognize GTF-formatted feature files
## and to handle textual attributes should surrounded by doublequotes correctly
#set $genomic_features = 'features.gtf'
ln -s '$gfffile' $genomic_features &&
#else:
#set $genomic_features = $gfffile
#end if
htseq-count
--mode=$mode
Expand All @@ -66,24 +72,26 @@
#end if
--order=name
'$name_sorted_alignment_filename'
$name_sorted_alignment_filename
'$genomic_features' | csplit -q - /^__/ &&
reference.gtf | csplit -q - /^__/ &&
mv xx00 '$counts' && mv xx01 '$allcounts' &&
echo -e "__aligned\t\$(cut -f2 '$counts' | awk '{s+=$1}END{print s}' -)" >> '$allcounts'
## csplit above creates two files,
## xx00 with the feature counts and xx01 with category counts.
## Now we calculate the sum over all feature counts in xx00 and append that
## sum as the __aligned count to xx01.
echo -e "__aligned\t\$(cut -f2 xx00 | awk '{s+=$1}END{print s}' -)" >> xx01
#if str( $advanced_options.advanced_options_selector ) == "advanced":
#if $advanced_options.samout_conditional.samout == "Yes":
&& samtools view -Su
-t '${reference_fasta_filename}.fai'
-t $ref_index
samout.sam
| samtools sort -T "\${TMPDIR:-.}" -o '$samoutfile' -
| samtools sort -T "\${TMPDIR:-.}" -o out.bam -
#end if
#end if
]]>
</command>

<inputs>
<param format="sam,bam" name="samfile" type="data" label="Aligned SAM/BAM File"/>
<param format="gff" name="gfffile" type="data" label="GFF/GTF File"/>
Expand Down Expand Up @@ -116,8 +124,7 @@
<option value="simple" selected="true">Default settings</option>
<option value="advanced">Set advanced options</option>
</param>
<when value="simple">
</when>
<when value="simple" />
<when value="advanced">
<param argument="--nonunique" type="select" label="How to count nonunique or ambiguous mapping reads">
<option value="none" selected="true">None - do not count nonuniquely or ambiguously mapped reads for any features</option>
Expand Down Expand Up @@ -150,32 +157,37 @@
</when>
</conditional>
</when>
<when value="No">
<!-- Do nothing -->
</when>
<when value="No" />
</conditional>
</when>
</conditional>
</inputs>

<outputs>
<data format="tabular" name="counts" metadata_source="samfile" label="${tool.name} on ${on_string}">
<data name="counts" format="tabular" metadata_source="samfile" from_work_dir="xx00" label="${tool.name} on ${on_string}">
<actions>
<action name="column_names" type="metadata" default="Geneid,${samfile.element_identifier}" />
</actions>
</data>
<data format="tabular" name="allcounts" metadata_source="samfile" label="${tool.name} on ${on_string}: summary">
<data name="allcounts" format="tabular" metadata_source="samfile" from_work_dir="xx01" label="${tool.name} on ${on_string}: summary">
<actions>
<action name="column_names" type="metadata" default="Category,${samfile.element_identifier}" />
</actions>
</data>
<data format="bam" name="samoutfile" metadata_source="samfile" label="${tool.name} on ${on_string} (BAM)">
<data name="samoutfile" format="bam" metadata_source="samfile" from_work_dir="out.bam" label="${tool.name} on ${on_string} (BAM)">
<filter>advanced_options['advanced_options_selector'] == 'advanced' and advanced_options['samout_conditional']['samout'] == "Yes"</filter>
</data>
</outputs>

<tests>
<test expect_num_outputs="2">
<param name="samfile" value="htseq-test.sam" />
<param name="gfffile" value="htseq-test.gtf" />
<output name="counts" file="htseq-test_counts.tsv" />
<output name="allcounts" file="htseq-test_allcounts.tsv" />
</test>
<test expect_num_outputs="2">
<!-- same as before, but with gff3 input instead of gtf -->
<param name="samfile" value="htseq-test.sam" />
<param name="gfffile" value="htseq-test.gff" />
<output name="counts" file="htseq-test_counts.tsv" />
Expand Down
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