Mercurial > repos > iuc > samtools_cram_to_bam

comparison samtools_cram_to_bam.xml @ 3:858ada516d8f draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 9aed35e37c5bc8ee17a02930c1f2edceb8b0d97b"
author iuc
date Sat, 31 Jul 2021 07:26:19 +0000
parents a744bb7196a2
children 1551b0dd2d16
comparison
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2:a744bb7196a2 3:858ada516d8f
1 <tool id="samtools_cram_to_bam" name="samtools CRAM to BAM" version="@TOOL_VERSION@"> 1 <tool id="samtools_cram_to_bam" name="samtools CRAM to BAM" version="@TOOL_VERSION@+galaxy1">
2 <description>convert CRAM alignments to BAM format</description> 2 <description>convert CRAM alignments to BAM format</description>
3 3
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements"/> 7 <expand macro="requirements"/>
8 <expand macro="stdio"/> 8 <expand macro="stdio"/>
9 <expand macro="version_command"/> 9 <expand macro="version_command"/>
10 10
11 <command><![CDATA[ 11 <command><![CDATA[
12 #set input_cram = "input.cram"
13 ln -s '${input_alignment}' '${input_cram}' &&
12 #if str( $input_alignment.metadata.cram_index ) != "None": 14 #if str( $input_alignment.metadata.cram_index ) != "None":
13 ln -f -s '${input_alignment.metadata.cram_index}' '${input_alignment}.crai' && 15 ln -f -s '${input_alignment.metadata.cram_index}' '${input_cram}.crai' &&
14 #end if 16 #end if
15 17
16 #if $reference_source.reference_source_selector == 'history': 18 #if $reference_source.reference_source_selector == 'history':
17 #set ref_fa = 'ref.fa' 19 #set ref_fa = 'ref.fa'
18 ln -s '${reference_source.input_reference}' ref.fa && 20 ln -s '${reference_source.input_reference}' ref.fa &&
26 #end if 28 #end if
27 -@ \${GALAXY_SLOTS:-2} 29 -@ \${GALAXY_SLOTS:-2}
28 -b 30 -b
29 -T '$ref_fa' 31 -T '$ref_fa'
30 -o '$output_alignment' 32 -o '$output_alignment'
31 '$input_alignment' 33 '$input_cram'
32 #if $parameter_regions.target_region == "region" 34 #if $parameter_regions.target_region == "region"
33 '${parameter_regions.region_string}' 35 '${parameter_regions.region_string}'
34 #end if 36 #end if
35 ]]></command> 37 ]]></command>
36 38