Mercurial > repos > mvdbeek > bam_readtagger

diff filter_insertions.xml @ 41:4fdf606153df draft

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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 89e57ebe9ad1eb4ba44167f83935869fb54b8396-dirty
author mvdbeek
date Thu, 24 May 2018 11:05:38 -0400
parents 4b1ebfcd0f46
children 5b8781514bc1
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--- a/filter_insertions.xml	Sun Apr 01 03:53:15 2018 -0400
+++ b/filter_insertions.xml	Thu May 24 11:05:38 2018 -0400
@@ -1,7 +1,7 @@
-<tool id="confirm_insertions" name="Confirm or discard insertions" version="0.4.10">
+<tool id="confirm_insertions" name="Confirm or discard insertions" version="0.4.11">
     <description>based on softclips in control files</description>
     <requirements>
-        <requirement type="package" version="0.4.10">readtagger</requirement>
+        <requirement type="package" version="0.4.11">readtagger</requirement>
     </requirements>
     <version_command>confirm_insertions --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
@@ -11,14 +11,16 @@
         confirm_insertions
         --putative_insertions_path putative_insertions.gff
         --all_treatments_path all_insertions.gff
-        --all_controls_path all_controls_path.gff
+        #for p in $all_controls
+            --all_controls_paths '$p'
+        #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 control sample" argument="--all_controls_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>