Mercurial > repos > devteam > samtools_mpileup

comparison samtools_mpileup.xml @ 10:8da515fbc1bf draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_mpileup commit a18f79e7cfe15fd6e1a5f70533616c379e4e7c6a"
author iuc
date Tue, 21 Sep 2021 09:33:51 +0000
parents fa7ad9b89f4a
children 111f83918fe6
comparison
equal deleted inserted replaced
9:fa7ad9b89f4a 10:8da515fbc1bf
10 10
11 #set $input_bams = $reference_source.input_bam 11 #set $input_bams = $reference_source.input_bam
12 @PREPARE_IDX_MULTIPLE@ 12 @PREPARE_IDX_MULTIPLE@
13 13
14 #if $reference_source.reference_source_selector == "history": 14 #if $reference_source.reference_source_selector == "history":
15 ln -s '${reference_source.ref_file}' && 15 #set ref_fa = 'ref.fa'
16 samtools faidx `basename '${reference_source.ref_file}'` && 16 ln -s '${reference_source.ref_file}' 'ref.fa' &&
17 samtools faidx ref.fa &&
18 #else:
19 #set ref_fa = str( $reference_source.ref_file.fields.path )
17 #end if 20 #end if
18 21
19 samtools mpileup 22 samtools mpileup
20 #if $reference_source.reference_source_selector != "history": 23 -f '$ref_fa'
21 -f '${reference_source.ref_file.fields.path}'
22 #else:
23 -f '${reference_source.ref_file}'
24 #end if
25 #for $i in range(len( $input_bams )): 24 #for $i in range(len( $input_bams )):
26 '${i}' 25 '${i}'
27 #end for 26 #end for
28 27
29 #if str( $advanced_options.advanced_options_selector ) == "advanced": 28 #if str( $advanced_options.advanced_options_selector ) == "advanced":