Mercurial > repos > iuc > bioext_bam2msa

annotate bam2msa.xml @ 2:0a4ad829d87a draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"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
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
12729213b4ae planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
iuc
parents:
diff changeset
1 <?xml version="1.0"?>
2
0a4ad829d87a "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
iuc
parents: 0
diff changeset
2 <tool id="bioext_bam2msa" name="Convert BAM" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
0a4ad829d87a "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
iuc
parents: 0
diff changeset
3 <description>to FASTA multiple sequence alignment</description>
0a4ad829d87a "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
iuc
parents: 0
diff changeset
4 <macros>
0a4ad829d87a "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
iuc
parents: 0
diff changeset
5 <import>macros.xml</import>
0a4ad829d87a "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
iuc
parents: 0
diff changeset
6 <token name="@VERSION_SUFFIX@">0</token>
0a4ad829d87a "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
iuc
parents: 0
diff changeset
7 </macros>
0a4ad829d87a "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
iuc
parents: 0
diff changeset
8 <expand macro="requirements"/>
0a4ad829d87a "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
iuc
parents: 0
diff changeset
9 <command detect_errors="exit_code"><![CDATA[
0a4ad829d87a "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
iuc
parents: 0
diff changeset
10 bam2msa
0a4ad829d87a "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
iuc
parents: 0
diff changeset
11 #if $region_start and $region_end:
0a4ad829d87a "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
iuc
parents: 0
diff changeset
12 -r $region_start:$region_end
0a4ad829d87a "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
iuc
parents: 0
diff changeset
13 #end if
0a4ad829d87a "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
iuc
parents: 0
diff changeset
14 '$input' '$output'
0a4ad829d87a "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
iuc
parents: 0
diff changeset
15 ]]></command>
0a4ad829d87a "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
iuc
parents: 0
diff changeset
16 <inputs>
0a4ad829d87a "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
iuc
parents: 0
diff changeset
17 <param name="input" type="data" format="bam,sam" label="Input BAM file"/>
0a4ad829d87a "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
iuc
parents: 0
diff changeset
18 <param name="region_start" type="integer" value="0" optional="True" label="Starting coordinate" help="Leave blank to extract all sequences"/>
0a4ad829d87a "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
iuc
parents: 0
diff changeset
19 <param name="region_end" type="integer" value="0" optional="True" label="End coordinate"/>
0a4ad829d87a "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
iuc
parents: 0
diff changeset
20 </inputs>
0a4ad829d87a "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
iuc
parents: 0
diff changeset
21 <outputs>
0a4ad829d87a "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
iuc
parents: 0
diff changeset
22 <data name="output" format="fasta"/>
0a4ad829d87a "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
iuc
parents: 0
diff changeset
23 </outputs>
0a4ad829d87a "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
iuc
parents: 0
diff changeset
24 <tests>
0a4ad829d87a "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
iuc
parents: 0
diff changeset
25 <test>
0a4ad829d87a "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
iuc
parents: 0
diff changeset
26 <param name="input" ftype="bam" value="bealign-out1.bam"/>
0a4ad829d87a "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
iuc
parents: 0
diff changeset
27 <output name="output" file="bam2msa-out1.fa"/>
0a4ad829d87a "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
iuc
parents: 0
diff changeset
28 </test>
0a4ad829d87a "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
iuc
parents: 0
diff changeset
29 <test>
0a4ad829d87a "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
iuc
parents: 0
diff changeset
30 <param name="input" ftype="bam" value="bealign-out2.bam"/>
0a4ad829d87a "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
iuc
parents: 0
diff changeset
31 <output name="output" file="bam2msa-out2.fa"/>
0a4ad829d87a "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
iuc
parents: 0
diff changeset
32 </test>
0a4ad829d87a "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
iuc
parents: 0
diff changeset
33 </tests>
0a4ad829d87a "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
iuc
parents: 0
diff changeset
34 <help>Extract MSA from a BAM file</help>
0a4ad829d87a "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
iuc
parents: 0
diff changeset
35 <expand macro="citations"/>
0
12729213b4ae planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
iuc
parents:
diff changeset
36 </tool>