Mercurial > repos > mvdbeek > bam_readtagger
annotate write_supplementary_fastq.xml @ 61:210427d5c65a draft
"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9f56650c365197dbf3bc1f32a0f4edffd92d488d"
author | mvdbeek |
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date | Sat, 31 Aug 2019 07:19:00 -0400 |
parents | 01acf62d5012 |
children | 16eba798cbc6 |
rev | line source |
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61
210427d5c65a
"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9f56650c365197dbf3bc1f32a0f4edffd92d488d"
mvdbeek
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1 <tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.5.8"> |
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53b71263e2a2
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
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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
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3 <requirements> |
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210427d5c65a
"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9f56650c365197dbf3bc1f32a0f4edffd92d488d"
mvdbeek
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4 <requirement type="package" version="0.5.8">readtagger</requirement> |
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53b71263e2a2
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
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5 </requirements> |
53b71263e2a2
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
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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
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7 <command detect_errors="aggressive"><![CDATA[ |
53b71263e2a2
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
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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
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9 ]]></command> |
53b71263e2a2
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
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10 <inputs> |
53b71263e2a2
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
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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
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12 </inputs> |
53b71263e2a2
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
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13 <outputs> |
53b71263e2a2
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
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14 <data name="output" format="fastqsanger"/> |
53b71263e2a2
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
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15 </outputs> |
53b71263e2a2
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
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16 <tests> |
53b71263e2a2
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
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17 <test> |
53b71263e2a2
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
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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:
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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
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20 </test> |
53b71263e2a2
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
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21 </tests> |
53b71263e2a2
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
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22 <help><![CDATA[ |
53b71263e2a2
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
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23 .. code-block:: |
53b71263e2a2
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
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24 |
53b71263e2a2
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
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25 Usage: write_supplementary_fastq [OPTIONS] |
53b71263e2a2
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
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26 |
53b71263e2a2
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
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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
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28 at `output_path`. |
53b71263e2a2
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
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29 |
53b71263e2a2
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
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30 Options: |
53b71263e2a2
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
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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:
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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
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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
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34 |
53b71263e2a2
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
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35 |
53b71263e2a2
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
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36 ]]></help> |
53b71263e2a2
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
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37 </tool> |