Mercurial > repos > mvdbeek > bam_readtagger
view filter_insertions.xml @ 46:4ebfef7b3488 draft
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 2699bbcad6c8598d60b597f3fb52ec0725ded134
author | mvdbeek |
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date | Tue, 15 Jan 2019 14:03:29 -0500 |
parents | d475729e90ea |
children | a4e30210fc3d |
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<tool id="confirm_insertions" name="Confirm or discard insertions" version="0.4.15"> <description>based on softclips in control files</description> <requirements> <requirement type="package" version="0.4.15">readtagger</requirement> </requirements> <version_command>confirm_insertions --version</version_command> <command detect_errors="aggressive"><![CDATA[ ln -fs $putative_insertions putative_insertions.gff && ln -fs $all_insertions all_insertions.gff && #for i, p in enumerate($all_controls) ln -fs '$p' all_controls_${i}.gff && #end for confirm_insertions --putative_insertions_path putative_insertions.gff --all_treatments_path all_insertions.gff #for i, p in enumerate($all_controls) --all_controls_paths all_controls_${i}.gff #end for --output_path '$output' $output_discard ]]></command> <inputs> <param name="putative_insertions" label="Path to filtered putative insertinos" argument="--putative_insertions_path" type="data" format="gff3"/> <param name="all_insertions" label="Path to all unfiltered insertions" argument="--all_treatments_path" type="data" format="gff3"/> <param name="all_controls" label="Path to all unfiltered insertions from one or more control samples" argument="--all_controls_path" multiple="True" type="data" format="gff3"/> <param name="output_discard" label="Output discarded records? Discarded records will be marked as failed." truevalue="--output_discarded_records" falsevalue="--no_output_discarded_records" checked="True" type="boolean"/> </inputs> <outputs> <data name="output" format="gff3"/> </outputs> <tests> <test> <param name="putative_insertions" value="putative_insertions.gff" ftype="gff3"/> <param name="all_insertions" value="all_treatment_insertions.gff" ftype="gff3"/> <param name="all_controls" value="all_control_insertions.gff" ftype="gff3"/> <output name="output" file="confirmed_insertions.gff" ftype="gff3"/> </test> </tests> <help><![CDATA[ .. code-block:: Usage: confirm_insertions [OPTIONS] Confirm insertions by checking that control file does not contain the same clipping pattern. Options: -p, --putative_insertions_path PATH Path to file containing putative somatic insertions [required] -t, --all_treatments_path PATH Path to file containing all treatment insertions [required] -c, --all_controls_path PATH Path to file containing all control insertions [required] -o, --output_path TEXT Write annotated output to this Path. --output_discarded_records / --no_output_discarded_records Discard an alternative flag if the current read is in a proper pair. --version Show the version and exit. --help Show this message and exit. ]]></help> </tool>