Mercurial > repos > mvdbeek > bam_readtagger

annotate findcluster.xml @ 8:bf8ffb337cbe draft

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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 1d14dc7cdb21c782dee08a1d5be1bd956d1a6dc8-dirty
author mvdbeek
date Sun, 05 Mar 2017 13:29:42 -0500
parents d2009cdcdeba
children 53b71263e2a2
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bf8ffb337cbe planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 1d14dc7cdb21c782dee08a1d5be1bd956d1a6dc8-dirty
mvdbeek
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1 <tool id="findcluster" name="Find clusters of reads" version="0.3.4">
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mvdbeek
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2 <description>in bam files</description>
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3 <requirements>
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mvdbeek
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4 <requirement type="package" version="0.3.4">readtagger</requirement>
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5 </requirements>
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6 <version_command>findcluster --version</version_command>
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7 <command detect_errors="aggressive"><![CDATA[
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8 findcluster
7625c594bc37 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29-dirty
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9 --input_path '$input'
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10 --output_bam '$output_bam'
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11 --output_gff '$output_gff'
7625c594bc37 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29-dirty
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12 --sample_name '$input.element_identifier'
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bf8ffb337cbe planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 1d14dc7cdb21c782dee08a1d5be1bd956d1a6dc8-dirty
mvdbeek
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13 --threads "\${GALAXY_SLOTS:-2}"
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14 ]]></command>
7625c594bc37 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29-dirty
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15 <inputs>
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16 <param name="input" argument="--input_path" type="data" format="bam"/>
7625c594bc37 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29-dirty
mvdbeek
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17 </inputs>
7625c594bc37 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29-dirty
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18 <outputs>
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mvdbeek
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19 <data name="output_bam" format="bam" label="findcluster BAM on $on_string"/>
7625c594bc37 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29-dirty
mvdbeek
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20 <data name="output_gff" format="gff3" label="findcluster GFF on $on_string"/>
7625c594bc37 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29-dirty
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21 </outputs>
7625c594bc37 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29-dirty
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22 <tests>
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23 <test>
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24 <param name="input" value="extended_and_annotated_roi.bam" ftype="bam"/>
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25 <output name="output_bam" file="three_cluster_out.bam" ftype="bam" lines_diff="2"/>
7625c594bc37 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29-dirty
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26 <output name="output_gff" file="three_cluster_out.gff" ftype="gff3" lines_diff="0"/>
7625c594bc37 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29-dirty
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27 </test>
7625c594bc37 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29-dirty
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28 </tests>
7625c594bc37 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29-dirty
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29 <help><![CDATA[
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30 .. code-block::
7625c594bc37 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29-dirty
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32 Find clusters of reads that support a TE insertion.
7625c594bc37 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29-dirty
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34 optional arguments:
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35 -h, --help show this help message and exit
7625c594bc37 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29-dirty
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36 --input_path INPUT_PATH
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37 Find cluster in this BAM file. (default: None)
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mvdbeek
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38 --output_bam OUTPUT_BAM
7625c594bc37 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29-dirty
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39 Write out BAM file with cluster information to this
7625c594bc37 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29-dirty
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40 path. Reads will have an additional "CD" tag to
7625c594bc37 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29-dirty
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41 indicate the cluster number (default: None)
7625c594bc37 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29-dirty
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42 --output_gff OUTPUT_GFF
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43 Write out GFF file with cluster information to this
7625c594bc37 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29-dirty
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44 path. (default: None)
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45 --version show program's version number and exit
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46
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47 ]]></help>
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48 </tool>