Mercurial > repos > mvdbeek > bam_readtagger
annotate update_mapq.xml @ 41:4fdf606153df draft
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 89e57ebe9ad1eb4ba44167f83935869fb54b8396-dirty
author | mvdbeek |
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date | Thu, 24 May 2018 11:05:38 -0400 |
parents | 4b1ebfcd0f46 |
children | 6f9b1b81b593 |
rev | line source |
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41
4fdf606153df
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 89e57ebe9ad1eb4ba44167f83935869fb54b8396-dirty
mvdbeek
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1 <tool id="update_mapq" name="Update MAPQ score" version="0.4.11"> |
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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
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2 <description>of supplementary alignments</description> |
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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
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3 <requirements> |
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4fdf606153df
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 89e57ebe9ad1eb4ba44167f83935869fb54b8396-dirty
mvdbeek
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4 <requirement type="package" version="0.4.11">readtagger</requirement> |
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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
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5 </requirements> |
53b71263e2a2
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
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6 <version_command>update_mapq --version</version_command> |
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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
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7 <command detect_errors="aggressive"><![CDATA[ |
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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
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8 update_mapq --source_path '$source_path' --remapped_path '$remapped_path' --output_path '$output_path' |
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
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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 argument="--source_path" label="Update supplementary MAPQ scores in this BAM file" type="data" format="bam"/> |
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124f7f8ee080
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 13fe863ca4079d83d897fdf7e394a7474eea6117-dirty
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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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53b71263e2a2
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
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13 </inputs> |
53b71263e2a2
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
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14 <outputs> |
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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
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15 <data name="output_path" format="bam"/> |
53b71263e2a2
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
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16 </outputs> |
53b71263e2a2
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
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17 <tests> |
53b71263e2a2
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
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18 <test> |
53b71263e2a2
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
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19 <param name="source_path" value="supplementary.bam" ftype="bam"/> |
53b71263e2a2
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
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20 <param name="remapped_path" value="remapped_supplementary.bam" ftype="bam"/> |
53b71263e2a2
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
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21 <output name="output_path" file="supplementary_new_mapq.bam" ftype="bam"/> |
53b71263e2a2
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
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22 </test> |
53b71263e2a2
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
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23 </tests> |
53b71263e2a2
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
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24 <help><![CDATA[ |
53b71263e2a2
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
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25 .. code-block:: |
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 Usage: update_mapq [OPTIONS] |
53b71263e2a2
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
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28 |
53b71263e2a2
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
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29 Update supplementary read MAPQ score after remapping. |
53b71263e2a2
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
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30 |
53b71263e2a2
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
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31 Options: |
53b71263e2a2
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
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32 --source_path PATH Alignment file where supplementary reads should be |
53b71263e2a2
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
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33 updated with new MAPQ scores [required] |
53b71263e2a2
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
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34 --remapped_path PATH Alignment file that contains reads that have been |
53b71263e2a2
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
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35 remapped and contain an updated MAPQ score [required] |
53b71263e2a2
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
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36 --output_path PATH Write all alignments in original_path to this |
53b71263e2a2
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
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37 location. Supplementary reads will take the MAPQ score |
53b71263e2a2
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
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38 as determined by remapping to the alignment file at |
53b71263e2a2
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
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39 `remapped_path` [required] |
53b71263e2a2
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
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40 --version Show the version and exit. |
53b71263e2a2
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
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41 --help Show this message and exit. |
53b71263e2a2
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
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42 |
53b71263e2a2
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
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43 |
53b71263e2a2
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
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44 ]]></help> |
53b71263e2a2
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
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45 </tool> |