Mercurial > repos > iuc > bioext_bam2msa
comparison bam2msa.xml @ 8:27673f5b5343 draft
planemo upload for repository https://github.com/davebx/bioext-gx/ commit 473fd4bfc9bc6dc149978013545525529978b988
| author | iuc |
|---|---|
| date | Sun, 25 Feb 2024 19:30:19 +0000 |
| parents | a68cb16fa1a0 |
| children |
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| 7:359e043a285c | 8:27673f5b5343 |
|---|---|
| 1 <?xml version="1.0"?> | 1 <?xml version="1.0"?> |
| 2 <tool id="bioext_bam2msa" name="Convert BAM" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> | 2 <tool id="bioext_bam2msa" name="Convert BAM" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> |
| 3 <description>to FASTA multiple sequence alignment</description> | 3 <description>to FASTA multiple sequence alignment</description> |
| 4 <macros> | 4 <macros> |
| 5 <import>macros.xml</import> | 5 <import>macros.xml</import> |
| 6 <token name="@VERSION_SUFFIX@">0</token> | |
| 7 </macros> | 6 </macros> |
| 8 <expand macro="requirements"/> | 7 <expand macro="requirements"/> |
| 9 <command detect_errors="exit_code"><![CDATA[ | 8 <command detect_errors="exit_code"><![CDATA[ |
| 10 ## avoid bam2msa to create .bai in inputdir | 9 ## avoid bam2msa to create .bai in inputdir |
| 11 ln -s '$input' input_bam && | 10 ln -sf '$input' input_bam && |
| 12 ln -s '$input.metadata.bam_index' input_bam.bai && | 11 ln -sf '$input.metadata.bam_index' input_bam.bai && |
| 13 bam2msa | 12 bam2msa |
| 14 #if $region_start and $region_end: | 13 #if $region_start and $region_end: |
| 15 -r $region_start:$region_end | 14 -r $region_start:$region_end |
| 16 #end if | 15 #end if |
| 17 'input_bam' '$output' | 16 'input_bam' |
| 17 '$output' | |
| 18 ]]></command> | 18 ]]></command> |
| 19 <inputs> | 19 <inputs> |
| 20 <param name="input" type="data" format="bam,sam" label="Input BAM file"/> | 20 <param name="input" type="data" format="bam,sam" label="Input BAM file"/> |
| 21 <param name="region_start" type="integer" value="0" optional="True" label="Starting coordinate" help="Leave blank to extract all sequences"/> | 21 <param name="region_start" type="integer" value="0" optional="True" label="Starting coordinate" help="Leave blank to extract all sequences"/> |
| 22 <param name="region_end" type="integer" value="0" optional="True" label="End coordinate"/> | 22 <param name="region_end" type="integer" value="0" optional="True" label="End coordinate"/> |