Mercurial > repos > mvdbeek > bam_readtagger
annotate add_matesequence.xml @ 37:73e3060d104f draft
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
| author | mvdbeek |
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| date | Mon, 20 Nov 2017 10:50:23 -0500 |
| parents | e19ff7992765 |
| children | 700df574a69c |
| rev | line source |
|---|---|
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37
73e3060d104f
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
parents:
36
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1 <tool id="add_matesequence" name="Add matesequence" version="0.4.1"> |
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e0b1919b6bd8
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c
mvdbeek
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2 <description>into tag field</description> |
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e0b1919b6bd8
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c
mvdbeek
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3 <requirements> |
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37
73e3060d104f
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 4b06a6c763730d6e20140c03156863d8d6aeace4-dirty
mvdbeek
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36
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4 <requirement type="package" version="0.4.1">readtagger</requirement> |
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e0b1919b6bd8
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c
mvdbeek
parents:
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5 </requirements> |
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e0b1919b6bd8
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c
mvdbeek
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6 <version_command>add_matesequence --version</version_command> |
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e0b1919b6bd8
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c
mvdbeek
parents:
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7 <command detect_errors="aggressive"><![CDATA[ |
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29
4be52149b343
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9b9334bf4c0364e3e06e64a9b3e532d0b10f93ba
mvdbeek
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8 add_matesequence --target '$file_to_annotate' --source '$annotate_source' --output_path '$output' |
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e0b1919b6bd8
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c
mvdbeek
parents:
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9 ]]></command> |
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e0b1919b6bd8
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c
mvdbeek
parents:
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10 <inputs> |
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e0b1919b6bd8
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c
mvdbeek
parents:
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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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e0b1919b6bd8
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c
mvdbeek
parents:
diff
changeset
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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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e0b1919b6bd8
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c
mvdbeek
parents:
diff
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13 <param name="mate_sequence_tag" type="text" value="MS"/> |
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e0b1919b6bd8
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c
mvdbeek
parents:
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14 </inputs> |
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e0b1919b6bd8
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c
mvdbeek
parents:
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15 <outputs> |
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e0b1919b6bd8
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c
mvdbeek
parents:
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16 <data name="output" format="bam" label="Add matesequence on $on_string"/> |
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e0b1919b6bd8
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c
mvdbeek
parents:
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17 </outputs> |
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e0b1919b6bd8
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c
mvdbeek
parents:
diff
changeset
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18 <tests> |
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e0b1919b6bd8
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c
mvdbeek
parents:
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19 <test> |
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e0b1919b6bd8
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c
mvdbeek
parents:
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20 <param name="file_to_annotate" value="dm6.bam" ftype="bam"/> |
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e0b1919b6bd8
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c
mvdbeek
parents:
diff
changeset
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21 <param name="annotate_source" value="dm6.bam" ftype="bam"/> |
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e0b1919b6bd8
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c
mvdbeek
parents:
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changeset
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22 <output name="output" file="dm6_mate_annotated.bam" ftype="bam" lines_diff="2"/> |
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e0b1919b6bd8
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c
mvdbeek
parents:
diff
changeset
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23 </test> |
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e0b1919b6bd8
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c
mvdbeek
parents:
diff
changeset
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24 </tests> |
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e0b1919b6bd8
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c
mvdbeek
parents:
diff
changeset
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25 <help><![CDATA[ |
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e0b1919b6bd8
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c
mvdbeek
parents:
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26 .. code-block:: |
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e0b1919b6bd8
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c
mvdbeek
parents:
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27 |
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e0b1919b6bd8
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c
mvdbeek
parents:
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changeset
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28 usage: add_matesequence [-h] -a FILE_TO_ANNOTATE -s ANNOTATE_SOURE -o |
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e0b1919b6bd8
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c
mvdbeek
parents:
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29 OUTPUT_PATH [--version] |
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e0b1919b6bd8
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c
mvdbeek
parents:
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30 |
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e0b1919b6bd8
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c
mvdbeek
parents:
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31 Annotate reads with Mate Sequence in tag field |
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e0b1919b6bd8
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c
mvdbeek
parents:
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32 |
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e0b1919b6bd8
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c
mvdbeek
parents:
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33 optional arguments: |
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e0b1919b6bd8
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c
mvdbeek
parents:
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34 -h, --help show this help message and exit |
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e0b1919b6bd8
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c
mvdbeek
parents:
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35 -a FILE_TO_ANNOTATE, --file_to_annotate FILE_TO_ANNOTATE |
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e0b1919b6bd8
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c
mvdbeek
parents:
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changeset
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36 Annotate reads in this file with their mate sequence |
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e0b1919b6bd8
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c
mvdbeek
parents:
diff
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37 -s ANNOTATE_SOURE, --annotate_soure ANNOTATE_SOURE |
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e0b1919b6bd8
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c
mvdbeek
parents:
diff
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38 Use this file to find the mate sequence (can be same |
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e0b1919b6bd8
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c
mvdbeek
parents:
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39 file as file_to_annotate) |
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e0b1919b6bd8
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c
mvdbeek
parents:
diff
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40 -o OUTPUT_PATH, --output_path OUTPUT_PATH |
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e0b1919b6bd8
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c
mvdbeek
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41 Write resulting BAM file to this path |
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e0b1919b6bd8
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c
mvdbeek
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42 --version show program's version number and exit |
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e0b1919b6bd8
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c
mvdbeek
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43 |
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e0b1919b6bd8
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c
mvdbeek
parents:
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44 ]]></help> |
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e0b1919b6bd8
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c
mvdbeek
parents:
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45 </tool> |