diff discosnp_pp.xml @ 5:fd98c5af5a6c draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 8d37fef93da141323cc120b5fec737432e497dcf"

--- a/discosnp_pp.xml	Mon Aug 17 10:39:36 2020 -0400
+++ b/discosnp_pp.xml	Thu May 06 12:45:52 2021 +0000
@@ -1,56 +1,49 @@
-<?xml version='1.0' encoding='utf-8'?>
-<tool profile="16.04" id="discosnp_pp" name="DiscoSnp++" version="@DISCOSNP_VERSION@">
+<tool id="discosnp_pp" name="DiscoSnp++" version="@DISCOSNP_VERSION@+galaxy0" profile="@PROFILE@">
     <description>is an efficient tool for detecting SNPs without a reference genome.</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="discosnp_requirements" />
-    <command><![CDATA[
-        ## simple option
-        #if str( $input_type_options.input_type) == "single"
-            @discosnp_single_reads@
-        ## paired option
-        #else if str( $input_type_options.input_type) == "paired"
-            @discosnp_paired_reads@
-        ## mix option
-        #else
-            @discosnp_single_reads@
-            @discosnp_paired_reads@
+    <command detect_errors="exit_code"><![CDATA[
+        #if str($input_type_options.input_type) == "single":
+            @discosnp_single_for@
+            @single_reads@
+            @discosnp_single_end_for@
+        #else if str($input_type_options.input_type) == "paired":
+            @discosnp_paired_for@
+            @paired_reads@
+            @discosnp_paired_end_for@
+        #else:
+            @discosnp_single_for@
+            @single_reads@
+            @discosnp_single_end_for@
+            @discosnp_paired_for@
+            @paired_reads@
+            @discosnp_paired_end_for@
         #end if
-
-        #if str($VCF_option.mapping) == 'reference'
+        #if str($VCF_option.mapping) == 'reference':
             #set $reference_file = os.path.basename(str($VCF_option.G)) + "." + $VCF_option.G.ext
             ln -sf '${VCF_option.G}' '${reference_file}' &&
         #end if
-
         run_discoSnp++.sh
         @discosnp_inputs@
         ${T}
         -b ${b}
-        #if str($VCF_option.mapping) == 'reference'
+        #if str($VCF_option.mapping) == 'reference':
             -G '${reference_file}'
             ${VCF_option.R}
         #end if
-
         --max_threads \${GALAXY_SLOTS:-1}
-
   ]]></command>
-
   <inputs>
-
-
       <expand macro="discosnp_inputs" />
-
       <param argument="-b" type="select" label="Branching strategy">
           <option value="0">variants for which any of the two paths is branching are discarded</option>
           <option value="1">forbid SNPs for wich the two paths are branching</option>
           <option value="2">No limitation on branching</option>
       </param>
-
       <expand macro="discosnp_options" />
-
       <param argument="-T" type="boolean" checked="false" truevalue="-T" falsevalue="" label="Extends each polymorphism with left and right contigs" />
-
       <conditional name="VCF_option" >
           <param name="mapping" type="select" label="VCF option">
               <option value="default">Do not use reference genome</option>
@@ -58,23 +51,20 @@
           </param>
           <when value="default"></when>
           <when value="reference">
-              <param argument="-G" type="data" format="fasta,fastq" label="Reference genome file" />
+              <param argument="-G" type="data" format="fasta,fasta.gz,fastq,fastq.gz" label="Reference genome file" />
               <param argument="-R" type="boolean" truevalue="-R" falsevalue="" checked="false" label="Use the reference genome also in the variant calling, not only for mapping results" />
           </when>
       </conditional>
-
   </inputs>
-
   <outputs>
       <data name="vcf" from_work_dir="*_coherent.vcf" format="vcf" label="VCF with ${tool.name} on $on_string"/>
       <data name="fasta" from_work_dir="*_coherent.fa" format="fasta" label="Multifasta with ${tool.name} on $on_string"/>
   </outputs>
-
   <tests>
       <test>
           <conditional name="input_type_options">
               <param name="input_type" value="single"/>
-              <param name="list_reads" value="discosnp/reads1,discosnp/reads2" ftype="fasta" />
+              <param name="list_reads" value="discosnp/reads1.gz,discosnp/reads2.gz" ftype="fasta.gz" />
           </conditional>
           <param name="k" value="25"/>
           <output name="fasta" file="discosnp/multifasta.fa"/>
@@ -87,8 +77,8 @@
                   <collection type="list:paired">
                       <element name="Pair1">
                           <collection type="paired">
-                              <element name="forward" value="discosnp/reads1" ftype="fasta"/>
-                              <element name="reverse" value="discosnp/reads2" ftype="fasta"/>
+                              <element name="forward" value="discosnp/reads1.gz" ftype="fasta.gz"/>
+                              <element name="reverse" value="discosnp/reads2.gz" ftype="fasta.gz"/>
                           </collection>
                       </element>
                   </collection>
@@ -96,13 +86,12 @@
           </conditional>
           <conditional name="VCF_option">
               <param name="mapping" value="reference"/>
-              <param name="G" value="discosnp/reads1" ftype="fasta"/>
+              <param name="G" value="discosnp/reads1.gz" ftype="fasta.gz"/>
           </conditional>
           <output name="fasta" file="discosnp/multifasta_paired.fa"/>
           <output name="vcf" file="discosnp/vcf_file_paired.vcf" compare="diff" lines_diff="2"/>
       </test>
   </tests>
-
   <help><![CDATA[
 
 **Description**