Mercurial > repos > mvdbeek > bam_readtagger

comparison extract_variants.xml @ 65:08a10eefc2ca 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 05:05:32 -0500
parents 31dc40ec7067
children 9ac536101591
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64:31dc40ec7067 65:08a10eefc2ca
1 <tool id="extract_variants" name="Extract variant fragments" version="0.5.16"> 1 <tool id="extract_variants" name="Extract variant fragments" version="0.5.17">
2 <description>from long reads</description> 2 <description>from long reads</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.5.16">readtagger</requirement> 4 <requirement type="package" version="0.5.17">readtagger</requirement>
5 </requirements> 5 </requirements>
6 <version_command>extract_variants --version</version_command> 6 <version_command>extract_variants --version</version_command>
7 <command detect_errors="aggressive"><![CDATA[ 7 <command detect_errors="aggressive"><![CDATA[
8 ln -fs '$insert_reference.fields.path' reference.fa && 8 ln -fs '$insert_reference.fields.path' reference.fa &&
9 extract_variants '$input' '$output' reference.fa 9 extract_variants '$input' '$output_alignment' reference.fa &&
10 summarize_fragments '$output_alignment' '$output_tabular'
10 ]]></command> 11 ]]></command>
11 <inputs> 12 <inputs>
12 <param name="input" label="Select alignment for which to extract variants" type="data" format="bam,cram"/> 13 <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 <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 <options from_data_table="all_fasta"/>
15 </param> 16 </param>
16 </inputs> 17 </inputs>
17 <outputs> 18 <outputs>
18 <data name="output" format_source="input"/> 19 <data name="output_alignment" format_source="input" label="${tool.name} on ${on_string}: alignment"/>
20 <data name="output_tabular" format="tabular" label="${tool.name} on ${on_string}: summary"/>
19 </outputs> 21 </outputs>
20 <tests> 22 <tests>
21 <test> 23 <test>
22 <param name="input" value="long_insertion.bam" ftype="bam"/> 24 <param name="input" value="long_insertion.bam" ftype="bam"/>
23 <param name="insert_reference" value="transposon"/> 25 <param name="insert_reference" value="transposon"/>
24 <output name="output" file="long_insert_tagged.bam" ftype="bam"/> 26 <output name="output_alignment" file="long_insert_tagged.bam" ftype="bam"/>
27 <output name="output_tabular" file="long_insert_tagged.tab" ftype="tabular"/>
25 </test> 28 </test>
26 </tests> 29 </tests>
27 <help><![CDATA[ 30 <help><![CDATA[
28 31
29 Extract variants will find soft-clipped alignments and alignments with insertions, 32 Extract variants will find soft-clipped alignments and alignments with insertions,