Mercurial > repos > mvdbeek > bam_readtagger
diff filter_insertions.xml @ 38:f6311a04a6c9 draft
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6ac744bd9d610990d1d54a2c36ddfca671b15205-dirty
author | mvdbeek |
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date | Thu, 15 Mar 2018 05:13:22 -0400 |
parents | |
children | 432bb619c079 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/filter_insertions.xml Thu Mar 15 05:13:22 2018 -0400 @@ -0,0 +1,56 @@ +<tool id="confirm_insertions" name="Confirm or discard insertions" version="0.4.9"> + <description>based on softclips in control files</description> + <requirements> + <requirement type="package" version="0.4.9">readtagger</requirement> + </requirements> + <version_command>confirm_insertions --version</version_command> + <command detect_errors="aggressive"><![CDATA[ + confirm_insertions + --putative_insertions_path '$putative_insertions' + --all_treatments_path '$all_insertions' + --all_controls_path '$all_controls' + --output_path '$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 control sample" argument="--all_controls_path" type="data" format="gff3"/> + <param name="output_discard" label="Output discarded records? Thye 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>