Mercurial > repos > rdvelazquez > bioext_bam2msa
changeset 1:c7c46222ee0c draft
planemo upload for repository https://github.com/davebx/bioext-gx/ commit b'e1040dcb57f809b5ac44c211a21bfd10ba0be417\n'-dirty
| author | rdvelazquez |
|---|---|
| date | Thu, 19 Apr 2018 12:11:32 -0400 |
| parents | 72b7678b5b09 |
| children | 80fc71979f19 |
| files | bam2msa.xml test-data/bealign-out3.bam |
| diffstat | 2 files changed, 28 insertions(+), 30 deletions(-) [+] |
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--- a/bam2msa.xml Wed Mar 14 14:46:48 2018 -0400 +++ b/bam2msa.xml Thu Apr 19 12:11:32 2018 -0400 @@ -1,37 +1,35 @@ <?xml version="1.0"?> <tool id="bioext_bam2msa" name="Convert BAM" version="@VERSION@.0"> - <description>to FASTA multiple sequence alignment</description> - <macros> - <import>macros.xml</import> - </macros> - <expand macro="requirements" /> - <command detect_errors="exit_code"> - <![CDATA[ + <description>to FASTA multiple sequence alignment</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <command detect_errors="exit_code"><![CDATA[ bam2msa #if $region_start and $region_end: -r $region_start:$region_end #end if - $input $output - ]]> - </command> - <inputs> - <param name="input" type="data" format="bam,sam" label="Input BAM file" /> - <param name="region_start" type="integer" value="0" optional="True" label="Starting coordinate" help="Leave blank to extract all sequences" /> - <param name="region_end" type="integer" value="0" optional="True" label="End coordinate" /> - </inputs> - <outputs> - <data name="output" format="fasta" /> - </outputs> - <tests> - <test> - <param name="input" ftype="bam" value="bealign-out1.bam" /> - <output name="output" file="bam2msa-out1.fa" /> - </test> - <test> - <param name="input" ftype="bam" value="bealign-out2.bam" /> - <output name="output" file="bam2msa-out2.fa" /> - </test> - </tests> - <help>Extract MSA from a BAM file</help> - <expand macro="citations" /> + '$input' '$output' + ]]></command> + <inputs> + <param name="input" type="data" format="bam,sam" label="Input BAM file"/> + <param name="region_start" type="integer" value="0" optional="True" label="Starting coordinate" help="Leave blank to extract all sequences"/> + <param name="region_end" type="integer" value="0" optional="True" label="End coordinate"/> + </inputs> + <outputs> + <data name="output" format="fasta"/> + </outputs> + <tests> + <test> + <param name="input" ftype="bam" value="bealign-out1.bam"/> + <output name="output" file="bam2msa-out1.fa"/> + </test> + <test> + <param name="input" ftype="bam" value="bealign-out2.bam"/> + <output name="output" file="bam2msa-out2.fa"/> + </test> + </tests> + <help>Extract MSA from a BAM file</help> + <expand macro="citations"/> </tool>