Mercurial > repos > mvdbeek > bam_readtagger

annotate update_mapq.xml @ 16:ffd8bf1b9ebc draft

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author mvdbeek
date Fri, 31 Mar 2017 16:28:20 -0400
parents bf3eb0468af7
children 97c1b92dbd28
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mvdbeek
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1 <tool id="update_mapq" name="Update MAPQ score" version="0.3.12">
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2 <description>of supplementary alignments</description>
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3 <requirements>
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mvdbeek
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4 <requirement type="package" version="0.3.12">readtagger</requirement>
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5 </requirements>
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6 <version_command>update_mapq --version</version_command>
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7 <command detect_errors="aggressive"><![CDATA[
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8 update_mapq --source_path '$source_path' --remapped_path '$remapped_path' --output_path '$output_path'
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9 ]]></command>
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10 <inputs>
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11 <param argument="--source_path" label="Update supplementary MAPQ scores in this BAM file" type="data" format="bam"/>
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12 <param argument="--remapped_path" label="Extract MAPQ scores for secondary alignments from this BAM file." type="data" format="bam"/>
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13 </inputs>
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14 <outputs>
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15 <data name="output_path" format="bam"/>
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16 </outputs>
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17 <tests>
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18 <test>
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19 <param name="source_path" value="supplementary.bam" ftype="bam"/>
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20 <param name="remapped_path" value="remapped_supplementary.bam" ftype="bam"/>
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21 <output name="output_path" file="supplementary_new_mapq.bam" ftype="bam"/>
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22 </test>
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23 </tests>
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24 <help><![CDATA[
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25 .. code-block::
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27 Usage: update_mapq [OPTIONS]
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29 Update supplementary read MAPQ score after remapping.
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31 Options:
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32 --source_path PATH Alignment file where supplementary reads should be
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33 updated with new MAPQ scores [required]
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34 --remapped_path PATH Alignment file that contains reads that have been
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35 remapped and contain an updated MAPQ score [required]
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36 --output_path PATH Write all alignments in original_path to this
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37 location. Supplementary reads will take the MAPQ score
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38 as determined by remapping to the alignment file at
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39 `remapped_path` [required]
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40 --version Show the version and exit.
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41 --help Show this message and exit.
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44 ]]></help>
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45 </tool>