Mercurial > repos > iuc > coverm_genome

changeset 4:0ff4b0e5a3bc draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit bc3831e3648809bd3d46611b2a74bd26a17985e5
author iuc
date Fri, 18 Aug 2023 09:23:39 +0000
parents bb3f59096c8e
children 847f274a60da
files macros.xml
diffstat 1 files changed, 5 insertions(+), 8 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Wed Jul 26 07:35:03 2023 +0000
+++ b/macros.xml	Fri Aug 18 09:23:39 2023 +0000
@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">0.6.1</token>
-    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@VERSION_SUFFIX@">2</token>
     <token name="@PROFILE@">22.01</token>
     <xml name="requirements">
         <requirements>
@@ -118,9 +118,6 @@
             <option value="interleaved">Interleaved</option>
         </param>
     </xml>
-    <xml name="paired_reads">
-        <param name="paired_reads" type="data_collection" collection_type="list:paired" format="@INPUT_FORMATS@" label="Collection of paired-end FASTA/Q files(s) for mapping" help="One or more pairs of forward and reverse possibly gzipped FASTA/Q files for mapping in order." />
-    </xml>
     <xml name="individual_assembly_reads">
         <conditional name="read_type">
             <expand macro="read_type"/>
@@ -132,7 +129,7 @@
                 <param argument="-2" name="read2" type="data" format="@INPUT_FORMATS@" label="Reverse FASTA/Q file for mapping" />
             </when>
             <when value="paired_collection">
-                <expand macro="paired_reads"/>
+                <param name="paired_reads" type="data_collection" collection_type="paired" format="@INPUT_FORMATS@" label="Collection of paired-end FASTA/Q files(s) for mapping" help="One or more pairs of forward and reverse possibly gzipped FASTA/Q files for mapping in order." />
             </when>
             <when value="interleaved">
                 <param argument="--interleaved" type="data" format="@INPUT_FORMATS@" label="Interleaved FASTA/Q files for mapping" />
@@ -168,7 +165,7 @@
 ln -s '$reads.paired_reads.forward' '$fn' &&
             #set $fn = "rv/" + $id
             #silent $rv_fp.append( $fn )
-ln -s '$mreads.paired_reads.reverse' '${fn}' &&
+ln -s '$reads.paired_reads.reverse' '$fn' &&
         #else if $reads.type == 'interleaved'
             #set $fn = "interl/" + re.sub('[^\s\w\-\\.]', '_', str($reads.interleaved.element_identifier))
             #silent $interl_fp.append( $fn )
@@ -206,7 +203,7 @@
                 <param argument="-2" name="read2" type="data" format="@INPUT_FORMATS@" multiple="true" label="Reverse FASTA/Q file(s) for mapping" />
             </when>
             <when value="paired_collection">
-                <expand macro="paired_reads"/>
+                <param name="paired_reads" type="data_collection" collection_type="list:paired" format="@INPUT_FORMATS@" label="Collection of paired-end FASTA/Q files(s) for mapping" help="One or more pairs of forward and reverse possibly gzipped FASTA/Q files for mapping in order." />
             </when>
             <when value="interleaved">
                 <param argument="--interleaved" type="data" format="@INPUT_FORMATS@" multiple="true" label="Interleaved FASTA/Q files(s) for mapping" />
@@ -341,4 +338,4 @@
             <yield />
         </citations>
     </xml>
-</macros>
\ No newline at end of file
+</macros>