Mercurial > repos > iuc > bioext_bam2msa

annotate bam2msa.xml @ 7:359e043a285c 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 a75f8fb61d83b938eb6f291ad54fa1cb87d8a562"
author iuc
date Mon, 08 Nov 2021 11:40:50 +0000
parents a68cb16fa1a0
children 27673f5b5343
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[
4
a68cb16fa1a0 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit 0c2133318563cdb508cb5561e95c9066bc17345f"
iuc
parents: 3
diff changeset
10 ## avoid bam2msa to create .bai in inputdir
a68cb16fa1a0 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit 0c2133318563cdb508cb5561e95c9066bc17345f"
iuc
parents: 3
diff changeset
11 ln -s '$input' input_bam &&
a68cb16fa1a0 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit 0c2133318563cdb508cb5561e95c9066bc17345f"
iuc
parents: 3
diff changeset
12 ln -s '$input.metadata.bam_index' input_bam.bai &&
2
0a4ad829d87a "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
iuc
parents: 0
diff changeset
13 bam2msa
0a4ad829d87a "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
iuc
parents: 0
diff changeset
14 #if $region_start and $region_end:
0a4ad829d87a "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
iuc
parents: 0
diff changeset
15 -r $region_start:$region_end
0a4ad829d87a "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
iuc
parents: 0
diff changeset
16 #end if
4
a68cb16fa1a0 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit 0c2133318563cdb508cb5561e95c9066bc17345f"
iuc
parents: 3
diff changeset
17 'input_bam' '$output'
2
0a4ad829d87a "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
iuc
parents: 0
diff changeset
18 ]]></command>
0a4ad829d87a "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
iuc
parents: 0
diff changeset
19 <inputs>
0a4ad829d87a "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
iuc
parents: 0
diff changeset
20 <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
21 <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
22 <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
23 </inputs>
0a4ad829d87a "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
iuc
parents: 0
diff changeset
24 <outputs>
0a4ad829d87a "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
iuc
parents: 0
diff changeset
25 <data name="output" format="fasta"/>
0a4ad829d87a "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
iuc
parents: 0
diff changeset
26 </outputs>
0a4ad829d87a "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
iuc
parents: 0
diff changeset
27 <tests>
0a4ad829d87a "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
iuc
parents: 0
diff changeset
28 <test>
3
b226e0c805a5 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents: 2
diff changeset
29 <param name="input" ftype="bam" value="bam2msa-in1.bam"/>
2
0a4ad829d87a "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
iuc
parents: 0
diff changeset
30 <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
31 </test>
0a4ad829d87a "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
iuc
parents: 0
diff changeset
32 <test>
3
b226e0c805a5 "planemo upload for repository https://github.com/davebx/bioext-gx/ commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents: 2
diff changeset
33 <param name="input" ftype="bam" value="bam2msa-in2.bam"/>
2
0a4ad829d87a "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
iuc
parents: 0
diff changeset
34 <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
35 </test>
0a4ad829d87a "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
iuc
parents: 0
diff changeset
36 </tests>
0a4ad829d87a "planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
iuc
parents: 0
diff changeset
37 <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
38 <expand macro="citations"/>
0
12729213b4ae planemo upload for repository https://github.com/davebx/bioext-gx/ commit e85b8f45da435793513a47e4586b90ddec63fa86
iuc
parents:
diff changeset
39 </tool>