Mercurial > repos > mvdbeek > bam_readtagger

annotate write_supplementary_fastq.xml @ 78:6178c24ddd5a draft

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"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit a1ef57aa402ca6a3cfc75a9652a02372b8b2c013"
author mvdbeek
date Tue, 07 Apr 2020 08:57:47 -0400
parents 8c3d8d38674a
children c42dd2551c9c
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6178c24ddd5a "planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit a1ef57aa402ca6a3cfc75a9652a02372b8b2c013"
mvdbeek
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1 <tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.5.24">
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2 <description>from SAM/BAM alignment files as FASTQ</description>
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3 <requirements>
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mvdbeek
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4 <requirement type="package" version="0.5.24">readtagger</requirement>
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5 </requirements>
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6 <version_command>write_supplementary_fastq --version</version_command>
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7 <command detect_errors="aggressive"><![CDATA[
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8 write_supplementary_fastq --input_path '$input' --output_path '$output'
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9 ]]></command>
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10 <inputs>
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11 <param name="input" argument="--input_path" type="data" format="bam"/>
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12 </inputs>
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13 <outputs>
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14 <data name="output" format="fastqsanger"/>
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15 </outputs>
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16 <tests>
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17 <test>
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18 <param name="input" value="supplementary.bam" ftype="bam"/>
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19 <output name="output" file="supplementary.fastq" ftype="fastqsanger"/>
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20 </test>
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21 </tests>
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22 <help><![CDATA[
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23 .. code-block::
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25 Usage: write_supplementary_fastq [OPTIONS]
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27 Write all supplementary alignments in `input_path` to an output fastq file
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28 at `output_path`.
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30 Options:
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31 --input_path PATH Collect supplementary reads in this alignment file.
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32 --output_path PATH Write supplementary reads to this FASTQ file.
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33 --help Show this message and exit.
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36 ]]></help>
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37 </tool>