Mercurial > repos > mvdbeek > bam_readtagger

annotate extract_variants.xml @ 62:16eba798cbc6 draft

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"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 20d187a08a5c511cb38e7e60aeadfc2962dc03d3"
author mvdbeek
date Sat, 31 Aug 2019 09:48:36 -0400
parents 210427d5c65a
children e675e6d349bd
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62
16eba798cbc6 "planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 20d187a08a5c511cb38e7e60aeadfc2962dc03d3"
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1 <tool id="extract_variants" name="Extract variant fragments" version="0.5.9">
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2 <description>from long reads</description>
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3 <requirements>
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16eba798cbc6 "planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 20d187a08a5c511cb38e7e60aeadfc2962dc03d3"
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4 <requirement type="package" version="0.5.9">readtagger</requirement>
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5 </requirements>
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6 <version_command>extract_variants --version</version_command>
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7 <command detect_errors="aggressive"><![CDATA[
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8 ln -fs '$insert_reference.fields.path' reference.fa &&
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9 extract_variants '$input' '$output' reference.fa
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10 ]]></command>
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11 <inputs>
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12 <param name="input" label="Select alignment for which to extract variants" type="data" format="bam,cram"/>
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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">
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14 <options from_data_table="all_fasta"/>
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15 </param>
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16 </inputs>
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17 <outputs>
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18 <data name="output" format_source="input"/>
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19 </outputs>
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20 <tests>
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21 <test>
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22 <param name="input" value="long_insertion.bam" ftype="bam"/>
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23 <param name="insert_reference" value="transposon"/>
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24 <output name="output" file="long_insert_tagged.bam" ftype="bam"/>
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25 </test>
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26 </tests>
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27 <help><![CDATA[
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28
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29 Extract variants will find soft-clipped alignments and alignments with insertions,
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30 and, if the inserted sequence aligns with the selected reference, write out
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31 a the alignment, but clip the aligned portion of the read to a single N
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32 and will add 2 tags, AR and AD to the alignment.
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33 The AR tag will list the contig, the AD tag contains detailed
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34 information on how the insert/clipped sequence aligned against the selected
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35 reference.
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36 ]]></help>
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37 </tool>