Mercurial > repos > mvdbeek > bam_readtagger
comparison write_supplementary_fastq.xml @ 9:53b71263e2a2 draft
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
author | mvdbeek |
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date | Wed, 08 Mar 2017 05:14:25 -0500 |
parents | |
children | c179d081b6ba |
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8:bf8ffb337cbe | 9:53b71263e2a2 |
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1 <tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.3.5"> | |
2 <description>from SAM/BAM alignment files as FASTQ</description> | |
3 <requirements> | |
4 <requirement type="package" version="0.3.5">readtagger</requirement> | |
5 </requirements> | |
6 <version_command>write_supplementary_fastq --version</version_command> | |
7 <command detect_errors="aggressive"><![CDATA[ | |
8 write_supplementary_fastq --input_path '$input' --output_path '$output' | |
9 ]]></command> | |
10 <inputs> | |
11 <param name="input" argument="--input_path" type="data" format="bam"/> | |
12 </inputs> | |
13 <outputs> | |
14 <data name="output" format="fastqsanger"/> | |
15 </outputs> | |
16 <tests> | |
17 <test> | |
18 <param name="input" value="supplementary.bam" ftype="bam"/> | |
19 <output name="output" file="supplementary.fastq" ftype="fastqsanger"/> | |
20 </test> | |
21 </tests> | |
22 <help><![CDATA[ | |
23 .. code-block:: | |
24 | |
25 Usage: write_supplementary_fastq [OPTIONS] | |
26 | |
27 Write all supplementary alignments in `input_path` to an output fastq file | |
28 at `output_path`. | |
29 | |
30 Options: | |
31 --input_path PATH Collect supplementary reads in this alignment file. | |
32 --output_path PATH Write supplementary reads to this FASTQ file. | |
33 --help Show this message and exit. | |
34 | |
35 | |
36 ]]></help> | |
37 </tool> |