Mercurial > repos > mvdbeek > bam_readtagger
comparison extract_variants.xml @ 50:95ada1410aed draft
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 0c8bad7554890f0f0e2c53d11e64e41fc835d920
| author | mvdbeek |
|---|---|
| date | Sun, 28 Jul 2019 12:58:39 -0400 |
| parents | |
| children | 962b7fa09d01 |
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| 49:534d6b4aebb0 | 50:95ada1410aed |
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| 1 <tool id="extract_variants" name="Extract variant fragments" version="0.5.1"> | |
| 2 <description>from long reads</description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="0.5.1">readtagger</requirement> | |
| 5 </requirements> | |
| 6 <version_command>extract_variants --version</version_command> | |
| 7 <command detect_errors="aggressive"><![CDATA[ | |
| 8 ln -fs '$insert_reference.fields.path' reference.fa && | |
| 9 extract_variants '$input' '$output' reference.fa | |
| 10 ]]></command> | |
| 11 <inputs> | |
| 12 <param name="input" label="Select alignment for which to extract variants" type="data" format="bam,cram"/> | |
| 13 <param name="insert_reference" label="Select a reference. If a variant aligns against this reference it will be retained" type="select"> | |
| 14 <options from_data_table="all_fasta"/> | |
| 15 </param> | |
| 16 </inputs> | |
| 17 <outputs> | |
| 18 <data name="output" format_source="input"/> | |
| 19 </outputs> | |
| 20 <tests> | |
| 21 <test> | |
| 22 <param name="input" value="long_insertion.bam" ftype="bam"/> | |
| 23 <param name="insert_reference" value="transposon"/> | |
| 24 <output name="output" file="long_insert_tagged.bam" ftype="bam"/> | |
| 25 </test> | |
| 26 </tests> | |
| 27 <help><![CDATA[ | |
| 28 | |
| 29 Extract variants will find soft-clipped alignments and alignments with insertions, | |
| 30 and, if the inserted sequence aligns with the selected reference, write out | |
| 31 a the alignment, but clip the aligned portion of the read to a single N | |
| 32 and will add 2 tags, AR and AD to the alignment. | |
| 33 The AR tag will list the contig, the AD tag contains detailed | |
| 34 information on how the insert/clipped sequence aligned against the selected | |
| 35 reference. | |
| 36 ]]></help> | |
| 37 </tool> |