Mercurial > repos > mvdbeek > bam_readtagger
annotate extract_variants.xml @ 61:210427d5c65a draft
"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9f56650c365197dbf3bc1f32a0f4edffd92d488d"
author | mvdbeek |
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date | Sat, 31 Aug 2019 07:19:00 -0400 |
parents | 01acf62d5012 |
children | 16eba798cbc6 |
rev | line source |
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61
210427d5c65a
"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9f56650c365197dbf3bc1f32a0f4edffd92d488d"
mvdbeek
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1 <tool id="extract_variants" name="Extract variant fragments" version="0.5.8"> |
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7191da0bc7be
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0c8bad7554890f0f0e2c53d11e64e41fc835d920
mvdbeek
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2 <description>from long reads</description> |
7191da0bc7be
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0c8bad7554890f0f0e2c53d11e64e41fc835d920
mvdbeek
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3 <requirements> |
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210427d5c65a
"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9f56650c365197dbf3bc1f32a0f4edffd92d488d"
mvdbeek
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4 <requirement type="package" version="0.5.8">readtagger</requirement> |
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7191da0bc7be
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0c8bad7554890f0f0e2c53d11e64e41fc835d920
mvdbeek
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5 </requirements> |
7191da0bc7be
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0c8bad7554890f0f0e2c53d11e64e41fc835d920
mvdbeek
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6 <version_command>extract_variants --version</version_command> |
7191da0bc7be
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0c8bad7554890f0f0e2c53d11e64e41fc835d920
mvdbeek
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7 <command detect_errors="aggressive"><![CDATA[ |
7191da0bc7be
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0c8bad7554890f0f0e2c53d11e64e41fc835d920
mvdbeek
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8 ln -fs '$insert_reference.fields.path' reference.fa && |
7191da0bc7be
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0c8bad7554890f0f0e2c53d11e64e41fc835d920
mvdbeek
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9 extract_variants '$input' '$output' reference.fa |
7191da0bc7be
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0c8bad7554890f0f0e2c53d11e64e41fc835d920
mvdbeek
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10 ]]></command> |
7191da0bc7be
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0c8bad7554890f0f0e2c53d11e64e41fc835d920
mvdbeek
parents:
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11 <inputs> |
7191da0bc7be
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0c8bad7554890f0f0e2c53d11e64e41fc835d920
mvdbeek
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12 <param name="input" label="Select alignment for which to extract variants" type="data" format="bam,cram"/> |
7191da0bc7be
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0c8bad7554890f0f0e2c53d11e64e41fc835d920
mvdbeek
parents:
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13 <param name="insert_reference" label="Select a reference. If a variant aligns against this reference it will be retained" type="select"> |
7191da0bc7be
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0c8bad7554890f0f0e2c53d11e64e41fc835d920
mvdbeek
parents:
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14 <options from_data_table="all_fasta"/> |
7191da0bc7be
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0c8bad7554890f0f0e2c53d11e64e41fc835d920
mvdbeek
parents:
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15 </param> |
7191da0bc7be
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0c8bad7554890f0f0e2c53d11e64e41fc835d920
mvdbeek
parents:
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16 </inputs> |
7191da0bc7be
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0c8bad7554890f0f0e2c53d11e64e41fc835d920
mvdbeek
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17 <outputs> |
7191da0bc7be
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0c8bad7554890f0f0e2c53d11e64e41fc835d920
mvdbeek
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18 <data name="output" format_source="input"/> |
7191da0bc7be
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0c8bad7554890f0f0e2c53d11e64e41fc835d920
mvdbeek
parents:
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19 </outputs> |
7191da0bc7be
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0c8bad7554890f0f0e2c53d11e64e41fc835d920
mvdbeek
parents:
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20 <tests> |
7191da0bc7be
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0c8bad7554890f0f0e2c53d11e64e41fc835d920
mvdbeek
parents:
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21 <test> |
7191da0bc7be
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0c8bad7554890f0f0e2c53d11e64e41fc835d920
mvdbeek
parents:
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22 <param name="input" value="long_insertion.bam" ftype="bam"/> |
7191da0bc7be
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0c8bad7554890f0f0e2c53d11e64e41fc835d920
mvdbeek
parents:
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23 <param name="insert_reference" value="transposon"/> |
7191da0bc7be
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0c8bad7554890f0f0e2c53d11e64e41fc835d920
mvdbeek
parents:
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24 <output name="output" file="long_insert_tagged.bam" ftype="bam"/> |
7191da0bc7be
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0c8bad7554890f0f0e2c53d11e64e41fc835d920
mvdbeek
parents:
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25 </test> |
7191da0bc7be
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0c8bad7554890f0f0e2c53d11e64e41fc835d920
mvdbeek
parents:
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changeset
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26 </tests> |
7191da0bc7be
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0c8bad7554890f0f0e2c53d11e64e41fc835d920
mvdbeek
parents:
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27 <help><![CDATA[ |
7191da0bc7be
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0c8bad7554890f0f0e2c53d11e64e41fc835d920
mvdbeek
parents:
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28 |
7191da0bc7be
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0c8bad7554890f0f0e2c53d11e64e41fc835d920
mvdbeek
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29 Extract variants will find soft-clipped alignments and alignments with insertions, |
7191da0bc7be
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0c8bad7554890f0f0e2c53d11e64e41fc835d920
mvdbeek
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30 and, if the inserted sequence aligns with the selected reference, write out |
7191da0bc7be
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0c8bad7554890f0f0e2c53d11e64e41fc835d920
mvdbeek
parents:
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31 a the alignment, but clip the aligned portion of the read to a single N |
7191da0bc7be
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0c8bad7554890f0f0e2c53d11e64e41fc835d920
mvdbeek
parents:
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32 and will add 2 tags, AR and AD to the alignment. |
7191da0bc7be
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0c8bad7554890f0f0e2c53d11e64e41fc835d920
mvdbeek
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33 The AR tag will list the contig, the AD tag contains detailed |
7191da0bc7be
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0c8bad7554890f0f0e2c53d11e64e41fc835d920
mvdbeek
parents:
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34 information on how the insert/clipped sequence aligned against the selected |
7191da0bc7be
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0c8bad7554890f0f0e2c53d11e64e41fc835d920
mvdbeek
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35 reference. |
7191da0bc7be
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0c8bad7554890f0f0e2c53d11e64e41fc835d920
mvdbeek
parents:
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36 ]]></help> |
7191da0bc7be
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0c8bad7554890f0f0e2c53d11e64e41fc835d920
mvdbeek
parents:
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37 </tool> |