Mercurial > repos > mvdbeek > bam_readtagger

annotate extract_variants.xml @ 73:676b7ff2d899 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit cfb6ee6e3587f19540eb97d9b761623728aa6ee8"
author mvdbeek
date Sat, 11 Jan 2020 16:20:59 -0500
parents 8ef26717ba8b
children 6c15dd4415ea
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
73
676b7ff2d899 "planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit cfb6ee6e3587f19540eb97d9b761623728aa6ee8"
mvdbeek
parents: 72
diff changeset
1 <tool id="extract_variants" name="Extract variant fragments" version="0.5.20">
54
7191da0bc7be planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0c8bad7554890f0f0e2c53d11e64e41fc835d920
mvdbeek
parents:
diff changeset
2 <description>from long reads</description>
7191da0bc7be planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0c8bad7554890f0f0e2c53d11e64e41fc835d920
mvdbeek
parents:
diff changeset
3 <requirements>
73
676b7ff2d899 "planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit cfb6ee6e3587f19540eb97d9b761623728aa6ee8"
mvdbeek
parents: 72
diff changeset
4 <requirement type="package" version="0.5.20">readtagger</requirement>
54
7191da0bc7be planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0c8bad7554890f0f0e2c53d11e64e41fc835d920
mvdbeek
parents:
diff changeset
5 </requirements>
7191da0bc7be planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0c8bad7554890f0f0e2c53d11e64e41fc835d920
mvdbeek
parents:
diff changeset
6 <version_command>extract_variants --version</version_command>
7191da0bc7be planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0c8bad7554890f0f0e2c53d11e64e41fc835d920
mvdbeek
parents:
diff changeset
7 <command detect_errors="aggressive"><![CDATA[
7191da0bc7be planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0c8bad7554890f0f0e2c53d11e64e41fc835d920
mvdbeek
parents:
diff changeset
8 ln -fs '$insert_reference.fields.path' reference.fa &&
70
f383ca1c5033 "planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 1bc80492c93251d0cbe39d120872869e08d8d435"
mvdbeek
parents: 69
diff changeset
9 extract_variants '$input' '$output_alignment' reference.fa &&
f383ca1c5033 "planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 1bc80492c93251d0cbe39d120872869e08d8d435"
mvdbeek
parents: 69
diff changeset
10 summarize_fragments '$output_alignment' '$output_tabular'
54
7191da0bc7be planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0c8bad7554890f0f0e2c53d11e64e41fc835d920
mvdbeek
parents:
diff changeset
11 ]]></command>
7191da0bc7be planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0c8bad7554890f0f0e2c53d11e64e41fc835d920
mvdbeek
parents:
diff changeset
12 <inputs>
7191da0bc7be planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0c8bad7554890f0f0e2c53d11e64e41fc835d920
mvdbeek
parents:
diff changeset
13 <param name="input" label="Select alignment for which to extract variants" type="data" format="bam,cram"/>
7191da0bc7be planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0c8bad7554890f0f0e2c53d11e64e41fc835d920
mvdbeek
parents:
diff changeset
14 <param name="insert_reference" label="Select a reference. If a variant aligns against this reference it will be retained" type="select">
7191da0bc7be planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0c8bad7554890f0f0e2c53d11e64e41fc835d920
mvdbeek
parents:
diff changeset
15 <options from_data_table="all_fasta"/>
7191da0bc7be planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0c8bad7554890f0f0e2c53d11e64e41fc835d920
mvdbeek
parents:
diff changeset
16 </param>
7191da0bc7be planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0c8bad7554890f0f0e2c53d11e64e41fc835d920
mvdbeek
parents:
diff changeset
17 </inputs>
7191da0bc7be planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0c8bad7554890f0f0e2c53d11e64e41fc835d920
mvdbeek
parents:
diff changeset
18 <outputs>
70
f383ca1c5033 "planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 1bc80492c93251d0cbe39d120872869e08d8d435"
mvdbeek
parents: 69
diff changeset
19 <data name="output_alignment" format_source="input" label="${tool.name} on ${on_string}: alignment"/>
f383ca1c5033 "planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 1bc80492c93251d0cbe39d120872869e08d8d435"
mvdbeek
parents: 69
diff changeset
20 <data name="output_tabular" format="tabular" label="${tool.name} on ${on_string}: summary"/>
54
7191da0bc7be planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0c8bad7554890f0f0e2c53d11e64e41fc835d920
mvdbeek
parents:
diff changeset
21 </outputs>
7191da0bc7be planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0c8bad7554890f0f0e2c53d11e64e41fc835d920
mvdbeek
parents:
diff changeset
22 <tests>
7191da0bc7be planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0c8bad7554890f0f0e2c53d11e64e41fc835d920
mvdbeek
parents:
diff changeset
23 <test>
7191da0bc7be planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0c8bad7554890f0f0e2c53d11e64e41fc835d920
mvdbeek
parents:
diff changeset
24 <param name="input" value="long_insertion.bam" ftype="bam"/>
7191da0bc7be planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0c8bad7554890f0f0e2c53d11e64e41fc835d920
mvdbeek
parents:
diff changeset
25 <param name="insert_reference" value="transposon"/>
70
f383ca1c5033 "planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 1bc80492c93251d0cbe39d120872869e08d8d435"
mvdbeek
parents: 69
diff changeset
26 <output name="output_alignment" file="long_insert_tagged.bam" ftype="bam"/>
f383ca1c5033 "planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 1bc80492c93251d0cbe39d120872869e08d8d435"
mvdbeek
parents: 69
diff changeset
27 <output name="output_tabular" file="long_insert_tagged.tab" ftype="tabular"/>
54
7191da0bc7be planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0c8bad7554890f0f0e2c53d11e64e41fc835d920
mvdbeek
parents:
diff changeset
28 </test>
7191da0bc7be planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0c8bad7554890f0f0e2c53d11e64e41fc835d920
mvdbeek
parents:
diff changeset
29 </tests>
7191da0bc7be planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0c8bad7554890f0f0e2c53d11e64e41fc835d920
mvdbeek
parents:
diff changeset
30 <help><![CDATA[
7191da0bc7be planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0c8bad7554890f0f0e2c53d11e64e41fc835d920
mvdbeek
parents:
diff changeset
31
7191da0bc7be planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0c8bad7554890f0f0e2c53d11e64e41fc835d920
mvdbeek
parents:
diff changeset
32 Extract variants will find soft-clipped alignments and alignments with insertions,
7191da0bc7be planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0c8bad7554890f0f0e2c53d11e64e41fc835d920
mvdbeek
parents:
diff changeset
33 and, if the inserted sequence aligns with the selected reference, write out
7191da0bc7be planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0c8bad7554890f0f0e2c53d11e64e41fc835d920
mvdbeek
parents:
diff changeset
34 a the alignment, but clip the aligned portion of the read to a single N
7191da0bc7be planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0c8bad7554890f0f0e2c53d11e64e41fc835d920
mvdbeek
parents:
diff changeset
35 and will add 2 tags, AR and AD to the alignment.
7191da0bc7be planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0c8bad7554890f0f0e2c53d11e64e41fc835d920
mvdbeek
parents:
diff changeset
36 The AR tag will list the contig, the AD tag contains detailed
7191da0bc7be planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0c8bad7554890f0f0e2c53d11e64e41fc835d920
mvdbeek
parents:
diff changeset
37 information on how the insert/clipped sequence aligned against the selected
7191da0bc7be planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0c8bad7554890f0f0e2c53d11e64e41fc835d920
mvdbeek
parents:
diff changeset
38 reference.
7191da0bc7be planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0c8bad7554890f0f0e2c53d11e64e41fc835d920
mvdbeek
parents:
diff changeset
39 ]]></help>
7191da0bc7be planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0c8bad7554890f0f0e2c53d11e64e41fc835d920
mvdbeek
parents:
diff changeset
40 </tool>