Mercurial > repos > iuc > bioext_bam2msa
comparison bam2msa.xml @ 2:0a4ad829d87a draft
"planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
| author | iuc |
|---|---|
| date | Fri, 09 Jul 2021 15:18:46 +0000 |
| parents | 12729213b4ae |
| children | b226e0c805a5 |
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| 1:f5792425ea50 | 2:0a4ad829d87a |
|---|---|
| 1 <?xml version="1.0"?> | 1 <?xml version="1.0"?> |
| 2 <tool id="bioext_bam2msa" name="Convert BAM" version="@VERSION@.0"> | 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 </macros> | 6 <token name="@VERSION_SUFFIX@">0</token> |
| 7 <expand macro="requirements"/> | 7 </macros> |
| 8 <command detect_errors="exit_code"><![CDATA[ | 8 <expand macro="requirements"/> |
| 9 bam2msa | 9 <command detect_errors="exit_code"><![CDATA[ |
| 10 #if $region_start and $region_end: | 10 bam2msa |
| 11 -r $region_start:$region_end | 11 #if $region_start and $region_end: |
| 12 #end if | 12 -r $region_start:$region_end |
| 13 '$input' '$output' | 13 #end if |
| 14 ]]></command> | 14 '$input' '$output' |
| 15 <inputs> | 15 ]]></command> |
| 16 <param name="input" type="data" format="bam,sam" label="Input BAM file"/> | 16 <inputs> |
| 17 <param name="region_start" type="integer" value="0" optional="True" label="Starting coordinate" help="Leave blank to extract all sequences"/> | 17 <param name="input" type="data" format="bam,sam" label="Input BAM file"/> |
| 18 <param name="region_end" type="integer" value="0" optional="True" label="End coordinate"/> | 18 <param name="region_start" type="integer" value="0" optional="True" label="Starting coordinate" help="Leave blank to extract all sequences"/> |
| 19 </inputs> | 19 <param name="region_end" type="integer" value="0" optional="True" label="End coordinate"/> |
| 20 <outputs> | 20 </inputs> |
| 21 <data name="output" format="fasta"/> | 21 <outputs> |
| 22 </outputs> | 22 <data name="output" format="fasta"/> |
| 23 <tests> | 23 </outputs> |
| 24 <test> | 24 <tests> |
| 25 <param name="input" ftype="bam" value="bealign-out1.bam"/> | 25 <test> |
| 26 <output name="output" file="bam2msa-out1.fa"/> | 26 <param name="input" ftype="bam" value="bealign-out1.bam"/> |
| 27 </test> | 27 <output name="output" file="bam2msa-out1.fa"/> |
| 28 <test> | 28 </test> |
| 29 <param name="input" ftype="bam" value="bealign-out2.bam"/> | 29 <test> |
| 30 <output name="output" file="bam2msa-out2.fa"/> | 30 <param name="input" ftype="bam" value="bealign-out2.bam"/> |
| 31 </test> | 31 <output name="output" file="bam2msa-out2.fa"/> |
| 32 </tests> | 32 </test> |
| 33 <help>Extract MSA from a BAM file</help> | 33 </tests> |
| 34 <expand macro="citations"/> | 34 <help>Extract MSA from a BAM file</help> |
| 35 <expand macro="citations"/> | |
| 35 </tool> | 36 </tool> |