diff mapsembler2.xml @ 5:c5371f68db91 draft default tip

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

--- a/mapsembler2.xml	Mon Aug 17 10:40:05 2020 -0400
+++ b/mapsembler2.xml	Thu May 06 12:46:55 2021 +0000
@@ -1,5 +1,4 @@
-<?xml version='1.0' encoding='utf-8'?>
-<tool profile="16.04" id="mapsembler2" name="Mapsembler2" version="2.2.4">
+<tool id="mapsembler2" name="Mapsembler2" version="2.2.4+galaxy0" profile="@PROFILE@">
     <description>is a targeted assembly software</description>
     <macros>
         <import>macros.xml</import>
@@ -8,17 +7,19 @@
         <requirement type="package" version="2.2.4">mapsembler2</requirement>
     </requirements>
     <command><![CDATA[
-
-        #set $starter_filename = os.path.basename(str($s)) + "." + $s.ext
-        ln -sf '${s}' '${starter_filename}' &&
-
+        #import re
+        #set $starter_filename = re.sub('[^\w_]', '_', $s.element_identifier) + ".fasta"
+        #if $s.ext.endswith('.gz'):
+            gunzip -c '${s}' > '${starter_filename}' &&
+        #else:
+            ln -sf '${s}' '${starter_filename}' &&
+        #end if
         #set $samples = []
-        #for $read in $r
-            #set $filename = os.path.basename(str($read)) + "." + $read.ext
-            ln -sf '${read}' '${filename}' &&
+        #for $input in $r
+            #set $base_filename = re.sub('[^\w_]', '_', $input.element_identifier)
+            @single_reads@
             #silent $samples.append($filename)
         #end for
-
         run_mapsembler2_pipeline.sh
         -s '${starter_filename}'
         -r "${ ' '.join(['%s' % read for read in $samples]) }"
@@ -31,11 +32,10 @@
         -x ${x}
         -y ${y}
     ]]></command>
-
     <inputs>
         <!-- Input data files -->
-        <param argument="-s" type="data" format="fasta" label="Starters" help="Set of input sequences" />
-        <param argument="-r" type="data" multiple="true" format="fasta,fastq" label="List of reads" />
+        <param argument="-s" type="data" format="fasta,fasta.gz" label="Starters" help="Set of input sequences" />
+        <param argument="-r" type="data" multiple="true" format="fasta,fasta.gz,fastq,fastq.gz" label="List of reads" />
         <param argument="-t" type="select" label="Select your output extension type">
             <option value="1">a strict sequence</option>
             <option value="2">a consensus sequence</option>
@@ -51,31 +51,28 @@
         <param argument="-x" type="integer" label="Max length of nodes" value="40" help="Set the maximal length of nodes"/>
         <param argument="-y" type="integer" label="Max depth of nodes" value="10000" help="Set the maximal depth of the graph"/>
     </inputs>
-
     <outputs>
         <data name="fasta" from_work_dir="res_k_*.fasta" format="fasta" label="Assembly with ${tool.name} on $on_string"/>
         <data name="coherent" from_work_dir="res_coherent_*.fasta" format="fasta" label="Coherent with ${tool.name} on $on_string" hidden="true"/>
         <data name="uncoherent" from_work_dir="res_uncoherent_*.fasta" format="fasta" label="Uncoherent with ${tool.name} on $on_string" hidden="true"/>
         <data name="extremities" from_work_dir="starter_extremities.fa" format="fasta" label="Starter extremities with ${tool.name} on $on_string" hidden="true"/>
     </outputs>
-
     <tests>
         <test>
-            <param name="s" value="mapsembler2/starter.fa" />
-            <param name="r" value="mapsembler2/reads1,mapsembler2/reads2" />
+            <param name="s" value="mapsembler2/starter.fa.gz" ftype="fasta.gz"/>
+            <param name="r" value="mapsembler2/reads1.gz,mapsembler2/reads2.gz" ftype="fasta.gz"/>
             <param name="t" value="2"/>
             <output name="fasta" file="mapsembler2/assembly.fa"/>
         </test>
         <test>
-            <param name="s" value="mapsembler2/starter.fa" />
-            <param name="r" value="mapsembler2/reads2,mapsembler2/reads1" />
+            <param name="s" value="mapsembler2/starter.fa.gz" ftype="fasta.gz"/>
+            <param name="r" value="mapsembler2/reads2.gz,mapsembler2/reads1.gz" ftype="fasta.gz"/>
             <param name="t" value="1"/>
             <output name="fasta" file="mapsembler2/assembly_2.fa"/>
             <output name="coherent" file="mapsembler2/coherent.fa"/>
             <output name="extremities" file="mapsembler2/starter_extremities.fa"/>
         </test>
     </tests>
-
     <help><![CDATA[
 
 **Description**