Mercurial > repos > iuc > bedtools

diff bedpeToBam.xml @ 35:b28e0cfa7ba1 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
author iuc
date Fri, 06 Sep 2019 14:29:59 -0400
parents dde39ba9c031
children 3e38c9b3214f
line wrap: on
line diff
--- a/bedpeToBam.xml	Mon Apr 29 05:55:48 2019 -0400
+++ b/bedpeToBam.xml	Fri Sep 06 14:29:59 2019 -0400
@@ -3,7 +3,10 @@
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements" />
+    <!-- bedtobam broken in 2.29.0 <expand macro="requirements" /> -->
+    <requirements>
+        <requirement type="package" version="2.27.1">bedtools</requirement>
+    </requirements>
     <expand macro="stdio" />
     <command><![CDATA[
 bedtools bedpetobam
@@ -19,14 +22,14 @@
             label="Set a mapping quality (SAM MAPQ field) value for all BED entries" />
     </inputs>
     <outputs>
-        <data name="output" format="bam" metadata_source="input"/>
+        <data name="output" format="unsorted.bam" metadata_source="input"/>
     </outputs>
     <tests>
         <test>
             <param name="input" value="bedpeToBamBed1.bed" ftype="bed" />
             <param name="genome_file_opts_selector" value="hist" />
             <param name="genome" value="mm9.len"/>
-            <output name="output" file="bedpeToBam_result1.bam" lines_diff="72" ftype="bam" />
+            <output name="output" file="bedpeToBam_result1.bam" lines_diff="72" ftype="unsorted.bam" />
         </test>
     </tests>
     <help><![CDATA[