Mercurial > repos > iuc > bam_to_scidx

changeset 1:ebbf2a6a4c55 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit f33b04533bca91242b8a0a4077e1d593f5a874e0
author iuc
date Tue, 19 Apr 2016 18:10:09 -0400
parents 741b8af6386c
children bd79c4d39af0
files bam_to_scidx.xml test-data/output.scidx
diffstat 2 files changed, 4 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/bam_to_scidx.xml	Sat Dec 12 15:46:03 2015 -0500
+++ b/bam_to_scidx.xml	Tue Apr 19 18:10:09 2016 -0400
@@ -1,5 +1,8 @@
 <tool id="bam_to_scidx" name="Convert BAM to ScIdx" version="1.0.0">
     <description></description>
+    <requirements>
+        <requirement type="package" version="8.0.45">java-jdk</requirement>
+    </requirements>
     <command>
         <![CDATA[
             ln -f -s "${input_bam.metadata.bam_index}" "${input_bam}.bai" &&
@@ -28,7 +31,7 @@
             <param name="input_bam" value="input.bam" ftype="bam" />
             <param name="require_proper_mate_pairing" value="1" />
             <param name="read" value="0" />
-            <output name="output" file="output.scidx" lines_diff="1" ftype="scidx" />
+            <output name="output" file="output.scidx" lines_diff="1" ftype="scidx" compare="contains" />
         </test>
     </tests>
     <help>
--- a/test-data/output.scidx	Sat Dec 12 15:46:03 2015 -0500
+++ b/test-data/output.scidx	Tue Apr 19 18:10:09 2016 -0400
@@ -1,4 +1,3 @@
-#2015-11-23 20:18:56.51;input.bam;READ1
 chrom	index	forward	reverse	value
 chr17	1820100	0	1	1
 chr17	1849175	1	0	1