Mercurial > repos > mvdbeek > bam_readtagger
view extract_variants.xml @ 70:f383ca1c5033 draft
"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 |
line wrap: on
line source
<tool id="extract_variants" name="Extract variant fragments" version="0.5.17"> <description>from long reads</description> <requirements> <requirement type="package" version="0.5.17">readtagger</requirement> </requirements> <version_command>extract_variants --version</version_command> <command detect_errors="aggressive"><![CDATA[ ln -fs '$insert_reference.fields.path' reference.fa && extract_variants '$input' '$output_alignment' reference.fa && summarize_fragments '$output_alignment' '$output_tabular' ]]></command> <inputs> <param name="input" label="Select alignment for which to extract variants" type="data" format="bam,cram"/> <param name="insert_reference" label="Select a reference. If a variant aligns against this reference it will be retained" type="select"> <options from_data_table="all_fasta"/> </param> </inputs> <outputs> <data name="output_alignment" format_source="input" label="${tool.name} on ${on_string}: alignment"/> <data name="output_tabular" format="tabular" label="${tool.name} on ${on_string}: summary"/> </outputs> <tests> <test> <param name="input" value="long_insertion.bam" ftype="bam"/> <param name="insert_reference" value="transposon"/> <output name="output_alignment" file="long_insert_tagged.bam" ftype="bam"/> <output name="output_tabular" file="long_insert_tagged.tab" ftype="tabular"/> </test> </tests> <help><![CDATA[ Extract variants will find soft-clipped alignments and alignments with insertions, and, if the inserted sequence aligns with the selected reference, write out a the alignment, but clip the aligned portion of the read to a single N and will add 2 tags, AR and AD to the alignment. The AR tag will list the contig, the AD tag contains detailed information on how the insert/clipped sequence aligned against the selected reference. ]]></help> </tool>