Mercurial > repos > devteam > samtools_calmd
comparison samtools_calmd.xml @ 7:d97988f07983 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit a972815cbd43dea553b3c0e4ad548f35d0023228-dirty
| author | iuc |
|---|---|
| date | Sun, 28 Jul 2019 14:46:45 -0400 |
| parents | 3b6f46492fd8 |
| children | d29b421f5aaf |
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| 6:3b6f46492fd8 | 7:d97988f07983 |
|---|---|
| 5 </macros> | 5 </macros> |
| 6 <expand macro="requirements"/> | 6 <expand macro="requirements"/> |
| 7 <expand macro="stdio"/> | 7 <expand macro="stdio"/> |
| 8 <expand macro="version_command"/> | 8 <expand macro="version_command"/> |
| 9 <command><![CDATA[ | 9 <command><![CDATA[ |
| 10 #if str( $reference_source.reference_source_selector ) == "history": | 10 @ADDTHREADS@ |
| 11 #set ref_fa = 'ref.fa' | 11 #if str( $reference_source.reference_source_selector ) == "history": |
| 12 ln -s '${reference_source.ref_fasta}' ref.fa && | 12 #set ref_fa = 'ref.fa' |
| 13 samtools faidx ref.fa && | 13 ln -s '${reference_source.ref_fasta}' ref.fa && |
| 14 #else: | 14 samtools faidx ref.fa && |
| 15 #set ref_fa = str( $reference_source.ref_fasta.fields.path ) | 15 #else: |
| 16 #end if | 16 #set ref_fa = str( $reference_source.ref_fasta.fields.path ) |
| 17 #end if | |
| 17 | 18 |
| 18 samtools calmd | 19 samtools calmd |
| 19 $baq_settings.use_baq $baq_settings.modify_quality $baq_settings.extended_baq | 20 $baq_settings.use_baq $baq_settings.modify_quality $baq_settings.extended_baq |
| 20 #if str($option_set.option_sets) == 'advanced': | 21 #if str($option_set.option_sets) == 'advanced': |
| 21 $option_set.change_identical -C $option_set.adjust_mq | 22 $option_set.change_identical -C $option_set.adjust_mq |
| 22 #end if | 23 #end if |
| 23 -b | 24 -b |
| 24 '$input_bam' | 25 -@ \$addthreads |
| 25 '$ref_fa' | 26 '$input_bam' |
| 26 > '$calmd_output' | 27 '$ref_fa' |
| 28 > '$calmd_output' | |
| 27 ]]></command> | 29 ]]></command> |
| 28 <inputs> | 30 <inputs> |
| 29 <param name="input_bam" type="data" format="bam" label="BAM file to recalculate" /> | 31 <param name="input_bam" type="data" format="bam" label="BAM file to recalculate" /> |
| 30 <conditional name="reference_source"> | 32 <conditional name="reference_source"> |
| 31 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome"> | 33 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome"> |