diff stacks_sstacks.xml @ 12:96de7538bf0c draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 74ee33c6e30744a6da8deb7116d431d80ee80edb

--- a/stacks_sstacks.xml	Tue Mar 22 23:15:15 2022 +0000
+++ b/stacks_sstacks.xml	Fri Apr 07 22:05:37 2023 +0000
@@ -1,9 +1,9 @@
-<tool id="stacks_sstacks" name="Stacks: sstacks" version="@WRAPPER_VERSION@.0">
+<tool id="stacks_sstacks" name="Stacks: sstacks" version="@WRAPPER_VERSION@.1">
     <description>match stacks to a catalog</description>
-    <expand macro="bio_tools"/>
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
     <expand macro="requirements"/>
     <expand macro="stdio"/>
     <command><![CDATA[
@@ -35,7 +35,12 @@
                 #set $filename = $filename + ".tsv"
             #end if
             #if not re.search('catalog\.[a-z]+(\.tsv)?$', $filename)
-                ln -s '${input_file}' 'stacks_inputs/$filename' &&
+                ## When using a popmap, stacks write to the input dir (see also below)
+                #if $popmap
+                    cp '${input_file}' 'stacks_inputs/$filename' &&
+                #else
+                    ln -s '${input_file}' 'stacks_inputs/$filename' &&
+                #end if
 
                 #if $filename.endswith('.tags.tsv')
                     #set samples += " -s 'stacks_inputs/"+$filename[:-9] + "'"
@@ -82,11 +87,11 @@
 
         <param name="popmap" type="data" format="tabular,txt" label="Population map" help="If set, matching will be done only for samples listed in this file" optional="true" argument="-M" />
 
-        <param name="g" argument="-g" type="boolean" checked="false" truevalue="-g" falsevalue="" label="Base catalog matching on genomic location, not sequence identity" />
+        <param argument="-g" type="boolean" checked="false" truevalue="-g" falsevalue="" label="Base catalog matching on genomic location, not sequence identity" />
 
         <param name="check_haplo" argument="-x" type="boolean" checked="false" truevalue="-x" falsevalue="" label="Don't verify haplotype of matching locus" />
 
-        <param name="gapped" argument="--gapped" type="boolean" checked="false" truevalue="--gapped" falsevalue="" label="Perform gapped alignments between stacks" />
+        <param argument="--gapped" type="boolean" checked="false" truevalue="--gapped" falsevalue="" label="Perform gapped alignments between stacks" />
     </inputs>
 
     <outputs>