Mercurial > repos > mvdbeek > bam_readtagger

annotate add_matesequence.xml @ 29:2c62ca47c455 draft

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author mvdbeek
date Tue, 09 May 2017 12:54:10 -0400
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mvdbeek
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1 <tool id="add_matesequence" name="Add matesequence" version="0.3.23">
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2 <description>into tag field</description>
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3 <requirements>
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mvdbeek
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4 <requirement type="package" version="0.3.23">readtagger</requirement>
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5 </requirements>
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6 <version_command>add_matesequence --version</version_command>
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7 <command detect_errors="aggressive"><![CDATA[
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8 add_matesequence --target '$file_to_annotate' --source '$annotate_source' --output_path '$output'
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9 ]]></command>
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10 <inputs>
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11 <param name="file_to_annotate" argument="--file_to_annotate" label="Annotate reads in this file with their mate sequence" type="data" format="bam"/>
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12 <param name="annotate_source" argument="--annotate_source" label="Use this file to find the mate sequence (can be same file as file_to_annotate)" type="data" format="bam"/>
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13 <param name="mate_sequence_tag" type="text" value="MS"/>
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14 </inputs>
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15 <outputs>
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16 <data name="output" format="bam" label="Add matesequence on $on_string"/>
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17 </outputs>
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18 <tests>
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19 <test>
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20 <param name="file_to_annotate" value="dm6.bam" ftype="bam"/>
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21 <param name="annotate_source" value="dm6.bam" ftype="bam"/>
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22 <output name="output" file="dm6_mate_annotated.bam" ftype="bam" lines_diff="2"/>
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23 </test>
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24 </tests>
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25 <help><![CDATA[
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26 .. code-block::
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28 usage: add_matesequence [-h] -a FILE_TO_ANNOTATE -s ANNOTATE_SOURE -o
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29 OUTPUT_PATH [--version]
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31 Annotate reads with Mate Sequence in tag field
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33 optional arguments:
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34 -h, --help show this help message and exit
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35 -a FILE_TO_ANNOTATE, --file_to_annotate FILE_TO_ANNOTATE
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36 Annotate reads in this file with their mate sequence
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37 -s ANNOTATE_SOURE, --annotate_soure ANNOTATE_SOURE
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38 Use this file to find the mate sequence (can be same
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39 file as file_to_annotate)
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40 -o OUTPUT_PATH, --output_path OUTPUT_PATH
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41 Write resulting BAM file to this path
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42 --version show program's version number and exit
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44 ]]></help>
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45 </tool>