Mercurial > repos > iuc > bioext_bam2msa

comparison bam2msa.xml @ 2:31e5a2d73131 draft

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"planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
author iuc
date Fri, 09 Jul 2021 15:17:20 +0000
parents cf735919c2de
children 3afd5c92b4a1
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1:568ffb568f3f 2:31e5a2d73131
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>