From 58fa50696846c7f6a5bcfc22a59243c80107e41a Mon Sep 17 00:00:00 2001
From: Wolfgang Maier <maierw@informatik.uni-freiburg.de>
Date: Sun, 28 Jan 2024 00:19:08 +0100
Subject: [PATCH] Update snipit to v1.2 (#4971)

* Implement version command through snipit's new -v/--version command line flag

* Implement new --show-indels option

* Handle matplotlib config dir transparently

Moved setting of the corresponding environment variable out of the
command section.

* Document new ref requirement

* Add bio.tools xref

* Add long_description to .shed.yml
---
 tools/snipit/.shed.yml          |  4 +++-
 tools/snipit/snipit.xml         | 20 +++++++++++++++++---
 tools/snipit/test-data/snps.csv | 10 +++++-----
 3 files changed, 25 insertions(+), 9 deletions(-)

diff --git a/tools/snipit/.shed.yml b/tools/snipit/.shed.yml
index e267b9b927c..98f39be06e1 100644
--- a/tools/snipit/.shed.yml
+++ b/tools/snipit/.shed.yml
@@ -2,8 +2,10 @@ categories:
   - Variant Analysis
   - Sequence Analysis
 description: Summarise snps relative to a reference sequence
+long_description: |
+    Snipit finds SNPs relative to a reference in a multiple sequence alignment and produces a plot highlighting these changes.
 homepage_url: https://github.com/aineniamh/snipit
-remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/snipit
+remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit
 name: snipit
 owner: iuc
 type: unrestricted
diff --git a/tools/snipit/snipit.xml b/tools/snipit/snipit.xml
index 47621ed06aa..eb1f5d48204 100644
--- a/tools/snipit/snipit.xml
+++ b/tools/snipit/snipit.xml
@@ -1,18 +1,22 @@
 <tool id="snipit" name="snipit" version="@TOOL_VERSION@+galaxy0">
     <description>Summarise snps relative to a reference sequence</description>
     <macros>
-        <token name="@TOOL_VERSION@">1.0.7</token>
+        <token name="@TOOL_VERSION@">1.2</token>
         <xml name="handle_background" tokens="format">
             <when value="@FORMAT@">
                 <param argument="--solid-background" name="transparent_background" type="boolean" truevalue="" falsevalue="--solid-background" label="Plot on transparent background?" />
             </when>
         </xml>
     </macros>
+    <xrefs>
+        <xref type="bio.tools">snipit</xref>
+    </xrefs>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">snipit</requirement>
     </requirements>
+    <version_command>snipit -v</version_command>
     <command detect_errors="exit_code"><![CDATA[
-        MPLCONFIGDIR=.matplotlib snipit '$alignment'
+        snipit '$alignment'
             #if str($ref.select) == 'by_id'
                 -r '$ref.id'
             #end if
@@ -35,6 +39,7 @@
             #end if
             $dims.size_option
             $style.flip_vertical
+            $show_indels
             #if len($pos_restrict.include_positions)
                 --include-positions
                 #for $p in $pos_restrict.include_positions
@@ -61,10 +66,14 @@
                 -c $style.colouring.palette
             #end if
     ]]></command>
+    <environment_variables>
+        <environment_variable name="MPLCONFIGDIR">.matplotlib</environment_variable>
+    </environment_variables>
     <inputs>
         <param name="alignment" format="fasta" type="data" label="Input alignment fasta file" />
         <conditional name="ref">
-            <param name="select" type="select" label="The reference sequence ...">
+            <param name="select" type="select" label="The reference sequence ..."
+            help="Please note that you will HAVE to specify the reference explicitly via its ID if you choose the 'recombinant mutations colouring' scheme and in this case the reference can NOT be one of the recombinant parents.">
                 <option value="first">is the first sequence in the input</option>
                 <option value="by_id">should be picked via its ID</option>
             </param>
@@ -167,6 +176,7 @@
                 <option value="" selected="true">scale</option>
             </param>
         </section>
+        <param argument="--show-indels" type="boolean" truevalue="--show-indels" falsevalue="" label="Try to plot indels" help="This is newly introduced functionality for which you may encounter bugs still." />
         <param argument="--write-snps" type="boolean" truevalue="-s" falsevalue="" label="Write out SNPs?" help="Produces extra CSV output with lists of SNPs per sequence in the alignment if enabled." />
     </inputs>
     <outputs>
@@ -279,6 +289,10 @@
         </test>
         <test expect_num_outputs="1">
             <param name="alignment" value="input.fasta" />
+            <conditional name="ref">
+                <param name="select" value="by_id" />
+                <param name="id" value="reference" />
+            </conditional>
             <section name="style">
                 <conditional name="colouring">
                     <param name="palette" value="" />
diff --git a/tools/snipit/test-data/snps.csv b/tools/snipit/test-data/snps.csv
index 2649524641d..db9e4479e09 100644
--- a/tools/snipit/test-data/snps.csv
+++ b/tools/snipit/test-data/snps.csv
@@ -1,6 +1,6 @@
 record,snps,num_snps
-USA_1,1059CT;3037CT;8782TC;14408CT;23403AG;25563GT;28144CT,52
-USA_2,15240CT;17747CT;17858AG;18060CT;21774CT,39
-USA_3,1059CT;3037CT;8782TC;13006TC;14408CT;23403AG;25563GT;25688CT;28144CT,68
-USA_4,2005CA;2749CA;3037CT;8782TC;14408CT;20268AG;23403AG;28144CT,59
-USA_5,17747CT;17858AG;18060CT;20281TC,31
+USA_1,1059:CT;3037:CT;8782:TC;14408:CT;23403:AG;25563:GT;28144:CT,7
+USA_2,15240:CT;17747:CT;17858:AG;18060:CT;21774:CT,5
+USA_3,1059:CT;3037:CT;8782:TC;13006:TC;14408:CT;23403:AG;25563:GT;25688:CT;28144:CT,9
+USA_4,2005:CA;2749:CA;3037:CT;8782:TC;14408:CT;20268:AG;23403:AG;28144:CT,8
+USA_5,17747:CT;17858:AG;18060:CT;20281:TC,4