Mercurial > repos > artbio > artbio_mutect2

comparison artbio_mutect2.xml @ 1:2b6ee93fd144 draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit 5f88428431700b059b950043d24c46ab92e580de"
author artbio
date Sat, 09 May 2020 15:08:07 -0400
parents 504de035ac0f
children 5d9c84514103
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0:504de035ac0f 1:2b6ee93fd144
17 17
18 #if str($reference_source.reference_source_selector) == 'history' 18 #if str($reference_source.reference_source_selector) == 'history'
19 ln -s '$reference_source.reference_sequence' reference.fa && 19 ln -s '$reference_source.reference_sequence' reference.fa &&
20 samtools faidx reference.fa && 20 samtools faidx reference.fa &&
21 gatk CreateSequenceDictionary --REFERENCE="reference.fa" --OUTPUT="reference.dict" && 21 gatk CreateSequenceDictionary --REFERENCE="reference.fa" --OUTPUT="reference.dict" &&
22 #else if str($reference_source.reference_source_selector) == 'history' 22 #else if str($reference_source.reference_source_selector) == 'cached'
23 ln -s '$reference_source.reference_sequence.fields.path' reference.fa && 23 ln -s '$reference_source.reference_sequence.fields.path' reference.fa &&
24 samtools faidx reference.fa && 24 samtools faidx reference.fa &&
25 gatk CreateSequenceDictionary --REFERENCE="reference.fa" --OUTPUT="reference.dict" && 25 gatk CreateSequenceDictionary --REFERENCE="reference.fa" --OUTPUT="reference.dict" &&
26 #else 26 #else
27 #set ref_flag='' 27 #set ref_flag=''