Mercurial > repos > mvdbeek > bam_readtagger

diff filter_insertions.xml @ 39:432bb619c079 draft

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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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line diff
--- 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"/>