Mercurial > repos > jackcurragh > trips_viz_bam_to_sqlite

diff trips_bam_to_sqlite/trips_bam_to_sqlite.xml @ 2:c8d8675697c6 draft

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author jackcurragh
date Wed, 20 Apr 2022 15:18:00 +0000
parents 3ac12b611d7f
children
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--- a/trips_bam_to_sqlite/trips_bam_to_sqlite.xml	Sun Apr 17 08:44:20 2022 +0000
+++ b/trips_bam_to_sqlite/trips_bam_to_sqlite.xml	Wed Apr 20 15:18:00 2022 +0000
@@ -2,11 +2,11 @@
     <description>Convert BAM file to SQLITE for TRIPS-Viz</description>
     <requirements>
         <requirement type="package" version="0.19.0">pysam</requirement>
-        <requirement type="package" version="2.0.0">sqlitedict</requirement>
+        <requirement type="package" version="1.7.0">sqlitedict</requirement>
         <requirement type="package" version="3.37.1">sqlite</requirement>
     </requirements>
     <command><![CDATA[
-        python $__tool_directory__/bam_to_sqlite.py $input1 $input2 $input3
+        python $__tool_directory__/bam_to_sqlite.py $input1 $input2 $input3 $output1
     ]]></command>
     <inputs>
         <param name="input1" type="data" format="bam" label="Sorted (samtools -n) BAM file" />