diff bamToBed.xml @ 41:7ab85ac5f64b draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 500a03281ea704abc7a16d9af63d67dbdcc5cd0b"

--- a/bamToBed.xml	Thu Sep 09 13:04:07 2021 +0000
+++ b/bamToBed.xml	Thu Nov 04 11:36:55 2021 +0000
@@ -1,16 +1,16 @@
-<tool id="bedtools_bamtobed" name="bedtools BAM to BED" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
+<tool id="bedtools_bamtobed" name="bedtools BAM to BED" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@">
     <description>converter</description>
-    <expand macro="bio_tools" />
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools" />
     <expand macro="requirements">
         <requirement type="package" version="@SAMTOOLS_VERSION@">samtools</requirement>
     </expand>
     <expand macro="stdio" />
     <command><![CDATA[
 #if $input.extension in ['bam', 'unsorted.bam', 'qname_input_sorted.bam'] and $option == "-bedpe":
-    samtools sort -n -@ "\${GALAXY_SLOTS:-4}" -T "\${TMPDIR:-.}" '${input}' ./input &&
+    samtools sort -n -@ "\${GALAXY_SLOTS:-4}" -T "\${TMPDIR:-.}" '${input}' > ./input.bam &&
 #else
     ln -s '${input}' ./input.bam &&
 #end if
@@ -54,6 +54,12 @@
             <param name="tag" value="NM" />
             <output name="output" file="bamToBed_result2.bed" ftype="bed" />
         </test>
+        <test>
+            <param name="input" value="bedpeToBam_result1.bam" ftype="bam" />
+            <param name="option" value="-bedpe" />
+            <param name="tag" value="" />
+            <output name="output" file="bamToBed_result3.bed" ftype="bed" />
+        </test>
     </tests>
     <help><![CDATA[
 **What it does**