# HG changeset patch
# User iuc
# Date 1706398195 0
# Node ID 92b9fd5f1f9feec34b624bf57cf6309c794593c9
# Parent  9f23fe0cb70b00a7a090db40428a5b7ab77e0347
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit commit 58fa50696846c7f6a5bcfc22a59243c80107e41a

diff -r 9f23fe0cb70b -r 92b9fd5f1f9f snipit.xml
--- a/snipit.xml	Fri Oct 28 20:58:45 2022 +0000
+++ b/snipit.xml	Sat Jan 27 23:29:55 2024 +0000
@@ -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 -r 9f23fe0cb70b -r 92b9fd5f1f9f test-data/snps.csv
--- a/test-data/snps.csv	Fri Oct 28 20:58:45 2022 +0000
+++ b/test-data/snps.csv	Sat Jan 27 23:29:55 2024 +0000
@@ -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