Mercurial > repos > iuc > delly_classify

comparison macros.xml @ 3:0d0075ddff0a draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 57b50253f326baf18bfbf417d8c788b4f5ba66e6
author iuc
date Mon, 27 Jun 2022 18:15:33 +0000
parents 15a02df32c2b
children
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2:15a02df32c2b 3:0d0075ddff0a
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <macros> 2 <macros>
3 <token name="@TOOL_VERSION@">0.9.1</token> 3 <token name="@TOOL_VERSION@">0.9.1</token>
4 <token name="@VERSION_SUFFIX@">0</token> 4 <token name="@VERSION_SUFFIX@">1</token>
5 <xml name="requirements"> 5 <xml name="requirements">
6 <requirements> 6 <requirements>
7 <requirement type="package" version="@TOOL_VERSION@">delly</requirement> 7 <requirement type="package" version="@TOOL_VERSION@">delly</requirement>
8 <requirement type="package" version="1.12">bcftools</requirement> 8 <requirement type="package" version="1.12">bcftools</requirement>
9 </requirements> 9 </requirements>
21 <xref type="bio.tools">delly2</xref> 21 <xref type="bio.tools">delly2</xref>
22 </xrefs> 22 </xrefs>
23 </xml> 23 </xml>
24 <!-- command --> 24 <!-- command -->
25 25
26 <token name="@SINGLE_BAM@"><![CDATA[
27 ln -s '$input' 'input.bam' &&
28 ln -s '$input.metadata.bam_index' 'input.bam.bai' &&
29 ]]></token>
26 <token name="@BAM@"><![CDATA[ 30 <token name="@BAM@"><![CDATA[
27 #for $i, $current in enumerate($input) 31 #for $i, $current in enumerate($input)
28 ln -s '${current}' 'input_${i}.bam' && 32 ln -s '${current}' 'input_${i}.bam' &&
29 ln -s '${current.metadata.bam_index}' 'input_${i}.bam.bai' && 33 ln -s '${current.metadata.bam_index}' 'input_${i}.bam.bai' &&
30 #end for 34 #end for
35 ]]></token>
36 <!-- fasta needs to be linked, because .fai file is created -->
37 <token name="@FASTA@"><![CDATA[
38 ln -s '$generic.genome' genome.fa &&
31 ]]></token> 39 ]]></token>
32 <token name="@DUMP@"><![CDATA[ 40 <token name="@DUMP@"><![CDATA[
33 #if 'dump' in $oo.out 41 #if 'dump' in $oo.out
34 && test -f 'dump.tsv.gz' && bgzip -d 'dump.tsv.gz' || echo 'No dump file.' 42 && test -f 'dump.tsv.gz' && bgzip -d 'dump.tsv.gz' || echo 'No dump file.'
35 #end if 43 #end if