Mercurial > repos > mvdbeek > bam_readtagger

annotate write_supplementary_fastq.xml @ 56:b50e114fece9 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 c3a7b2f6aa429ea2881ee8d111ace3cce95bb9e7
author mvdbeek
date Sun, 28 Jul 2019 15:59:14 -0400
parents 7191da0bc7be
children 38ae00c376ef
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
56
b50e114fece9 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit c3a7b2f6aa429ea2881ee8d111ace3cce95bb9e7
mvdbeek
parents: 54
diff changeset
1 <tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.5.3">
9
53b71263e2a2 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff changeset
2 <description>from SAM/BAM alignment files as FASTQ</description>
53b71263e2a2 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff changeset
3 <requirements>
56
b50e114fece9 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit c3a7b2f6aa429ea2881ee8d111ace3cce95bb9e7
mvdbeek
parents: 54
diff changeset
4 <requirement type="package" version="0.5.3">readtagger</requirement>
9
53b71263e2a2 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff changeset
5 </requirements>
53b71263e2a2 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff changeset
6 <version_command>write_supplementary_fastq --version</version_command>
53b71263e2a2 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff changeset
7 <command detect_errors="aggressive"><![CDATA[
53b71263e2a2 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff changeset
8 write_supplementary_fastq --input_path '$input' --output_path '$output'
53b71263e2a2 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff changeset
9 ]]></command>
53b71263e2a2 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff changeset
10 <inputs>
53b71263e2a2 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff changeset
11 <param name="input" argument="--input_path" type="data" format="bam"/>
53b71263e2a2 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff changeset
12 </inputs>
53b71263e2a2 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff changeset
13 <outputs>
53b71263e2a2 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff changeset
14 <data name="output" format="fastqsanger"/>
53b71263e2a2 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff changeset
15 </outputs>
53b71263e2a2 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff changeset
16 <tests>
53b71263e2a2 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff changeset
17 <test>
53b71263e2a2 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff changeset
18 <param name="input" value="supplementary.bam" ftype="bam"/>
53b71263e2a2 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff changeset
19 <output name="output" file="supplementary.fastq" ftype="fastqsanger"/>
53b71263e2a2 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff changeset
20 </test>
53b71263e2a2 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff changeset
21 </tests>
53b71263e2a2 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff changeset
22 <help><![CDATA[
53b71263e2a2 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff changeset
23 .. code-block::
53b71263e2a2 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff changeset
24
53b71263e2a2 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff changeset
25 Usage: write_supplementary_fastq [OPTIONS]
53b71263e2a2 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff changeset
26
53b71263e2a2 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff changeset
27 Write all supplementary alignments in `input_path` to an output fastq file
53b71263e2a2 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff changeset
28 at `output_path`.
53b71263e2a2 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff changeset
29
53b71263e2a2 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff changeset
30 Options:
53b71263e2a2 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff changeset
31 --input_path PATH Collect supplementary reads in this alignment file.
53b71263e2a2 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff changeset
32 --output_path PATH Write supplementary reads to this FASTQ file.
53b71263e2a2 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff changeset
33 --help Show this message and exit.
53b71263e2a2 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff changeset
34
53b71263e2a2 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff changeset
35
53b71263e2a2 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff changeset
36 ]]></help>
53b71263e2a2 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff changeset
37 </tool>