Mercurial > repos > mvdbeek > bam_readtagger

annotate extract_variants.xml @ 70:f383ca1c5033 draft

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"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 1bc80492c93251d0cbe39d120872869e08d8d435"
author mvdbeek
date Tue, 05 Nov 2019 05:06:18 -0500
parents 97411db5f752
children b090e190c813
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70
f383ca1c5033 "planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 1bc80492c93251d0cbe39d120872869e08d8d435"
mvdbeek
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1 <tool id="extract_variants" name="Extract variant fragments" version="0.5.17">
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2 <description>from long reads</description>
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3 <requirements>
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4 <requirement type="package" version="0.5.17">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' '$output_alignment' reference.fa &&
f383ca1c5033 "planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 1bc80492c93251d0cbe39d120872869e08d8d435"
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10 summarize_fragments '$output_alignment' '$output_tabular'
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11 ]]></command>
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12 <inputs>
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13 <param name="input" label="Select alignment for which to extract variants" type="data" format="bam,cram"/>
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14 <param name="insert_reference" label="Select a reference. If a variant aligns against this reference it will be retained" type="select">
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15 <options from_data_table="all_fasta"/>
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16 </param>
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17 </inputs>
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18 <outputs>
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19 <data name="output_alignment" format_source="input" label="${tool.name} on ${on_string}: alignment"/>
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20 <data name="output_tabular" format="tabular" label="${tool.name} on ${on_string}: summary"/>
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21 </outputs>
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22 <tests>
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23 <test>
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24 <param name="input" value="long_insertion.bam" ftype="bam"/>
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25 <param name="insert_reference" value="transposon"/>
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26 <output name="output_alignment" file="long_insert_tagged.bam" ftype="bam"/>
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27 <output name="output_tabular" file="long_insert_tagged.tab" ftype="tabular"/>
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28 </test>
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29 </tests>
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30 <help><![CDATA[
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32 Extract variants will find soft-clipped alignments and alignments with insertions,
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33 and, if the inserted sequence aligns with the selected reference, write out
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34 a the alignment, but clip the aligned portion of the read to a single N
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35 and will add 2 tags, AR and AD to the alignment.
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36 The AR tag will list the contig, the AD tag contains detailed
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37 information on how the insert/clipped sequence aligned against the selected
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38 reference.
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39 ]]></help>
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40 </tool>