Mercurial > repos > mvdbeek > bam_readtagger

annotate findcluster.xml @ 7:daab5b2bfd11 draft

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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6bb8de56027e615ab2a5fed1796c610cdeb2aa77
author mvdbeek
date Thu, 02 Mar 2017 12:00:44 -0500
parents 7434aa9a8638
children 24c84a4dcd57
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7
daab5b2bfd11 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6bb8de56027e615ab2a5fed1796c610cdeb2aa77
mvdbeek
parents: 6
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1 <tool id="findcluster" name="Find clusters of reads" version="0.3.2">
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mvdbeek
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2 <description>in bam files</description>
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mvdbeek
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3 <requirements>
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mvdbeek
parents: 6
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4 <requirement type="package" version="0.3.2">readtagger</requirement>
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5 </requirements>
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mvdbeek
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6 <version_command>findcluster --version</version_command>
f002e5797570 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29
mvdbeek
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7 <command detect_errors="aggressive"><![CDATA[
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8 findcluster
f002e5797570 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29
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9 --input_path '$input'
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mvdbeek
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10 --output_bam '$output_bam'
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11 --output_gff '$output_gff'
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12 --sample_name '$input.element_identifier'
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13 ]]></command>
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mvdbeek
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14 <inputs>
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15 <param name="input" argument="--input_path" type="data" format="bam"/>
f002e5797570 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29
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16 </inputs>
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17 <outputs>
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18 <data name="output_bam" format="bam" label="findcluster BAM on $on_string"/>
f002e5797570 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29
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19 <data name="output_gff" format="gff3" label="findcluster GFF on $on_string"/>
f002e5797570 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29
mvdbeek
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20 </outputs>
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21 <tests>
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22 <test>
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23 <param name="input" value="extended_and_annotated_roi.bam" ftype="bam"/>
f002e5797570 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29
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24 <output name="output_bam" file="three_cluster_out.bam" ftype="bam" lines_diff="2"/>
f002e5797570 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29
mvdbeek
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25 <output name="output_gff" file="three_cluster_out.gff" ftype="gff3" lines_diff="0"/>
f002e5797570 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29
mvdbeek
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26 </test>
f002e5797570 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29
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27 </tests>
f002e5797570 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29
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28 <help><![CDATA[
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29 .. code-block::
f002e5797570 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29
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30
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31 Find clusters of reads that support a TE insertion.
f002e5797570 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29
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32
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33 optional arguments:
f002e5797570 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29
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34 -h, --help show this help message and exit
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35 --input_path INPUT_PATH
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36 Find cluster in this BAM file. (default: None)
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37 --output_bam OUTPUT_BAM
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38 Write out BAM file with cluster information to this
f002e5797570 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29
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39 path. Reads will have an additional "CD" tag to
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40 indicate the cluster number (default: None)
f002e5797570 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29
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41 --output_gff OUTPUT_GFF
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42 Write out GFF file with cluster information to this
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43 path. (default: None)
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44 --version show program's version number and exit
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45
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46 ]]></help>
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47 </tool>