Mercurial > repos > mvdbeek > bam_readtagger
diff filter_insertions.xml @ 39:432bb619c079 draft
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 5adc383da0811cbfc6f82c6bad594efbe6c7b682-dirty
author | mvdbeek |
---|---|
date | Thu, 15 Mar 2018 07:20:58 -0400 |
parents | f6311a04a6c9 |
children | 4b1ebfcd0f46 |
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--- a/filter_insertions.xml Thu Mar 15 05:13:22 2018 -0400 +++ b/filter_insertions.xml Thu Mar 15 07:20:58 2018 -0400 @@ -5,10 +5,13 @@ </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 && + ln -fs $all_controls all_controls_path.gff && confirm_insertions - --putative_insertions_path '$putative_insertions' - --all_treatments_path '$all_insertions' - --all_controls_path '$all_controls' + --putative_insertions_path putative_insertions.gff + --all_treatments_path all_insertions.gff + --all_controls_path all_controls_path.gff --output_path '$output' $output_discard ]]></command> @@ -16,7 +19,7 @@ <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"/> + <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"/>