Mercurial > repos > iuc > delly_lr
comparison macros.xml @ 4:7bd397ff21a2 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 57b50253f326baf18bfbf417d8c788b4f5ba66e6
author | iuc |
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date | Mon, 27 Jun 2022 18:17:41 +0000 |
parents | d30785dbe6b7 |
children |
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3:d30785dbe6b7 | 4:7bd397ff21a2 |
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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 |