diff bamToBed.xml @ 34:dde39ba9c031 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95

--- a/bamToBed.xml	Mon Dec 17 14:23:31 2018 -0500
+++ b/bamToBed.xml	Mon Apr 29 05:55:48 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="bedtools_bamtobed" name="bedtools BAM to BED" version="@WRAPPER_VERSION@">
+<tool id="bedtools_bamtobed" name="bedtools BAM to BED" version="@TOOL_VERSION@">
     <description>converter</description>
     <macros>
         <import>macros.xml</import>
@@ -7,41 +7,38 @@
         <requirement type="package" version="@SAMTOOLS_VERSION@">samtools</requirement>
     </expand>
     <expand macro="stdio" />
-    <command>
-<![CDATA[
-
-        #if $input.extension == 'bam' and $option == "-bedpe":
-            samtools sort -n "${input}" ./input &&
-        #else
-            ln -s "${input}" ./input.bam &&
-        #end if
+    <command><![CDATA[
+#if $input.extension == 'bam' and $option == "-bedpe":
+    samtools sort -n '${input}' ./input &&
+#else
+    ln -s '${input}' ./input.bam &&
+#end if
 
-        bedtools bamtobed
-        $option
-        $ed_score
-        $split
-        #if $tag and str($tag).strip():
-          -tag "${tag}"
-        #end if
-        -i ./input.bam
-        > "${output}"
-]]>
-    </command>
+bedtools bamtobed
+$option
+$ed_score
+$split
+#if $tag and str($tag).strip():
+    -tag '${tag}'
+#end if
+-i ./input.bam
+> '${output}'
+    ]]></command>
     <inputs>
-        <param format="bam" name="input" type="data" label="Convert the following BAM file to BED"/>
+        <param name="input" type="data" format="bam" label="Convert the following BAM file to BED"/>
         <param name="option" type="select" label="What type of BED output would you like">
             <option value="">Create a 6-column BED file</option>
             <option value="-bed12">Create a full, 12-column "blocked" BED file</option>
             <option value="-bedpe">Create a paired-end, BEDPE format</option>
         </param>
         <expand macro="split" />
-        <param name="ed_score" type="boolean" truevalue="-ed" falsevalue="" checked="false"
-            label="Use alignment's edit-distance for BED score" help="(-ed)" />
-        <param name="tag" type="text" optional="true" label="Use other NUMERIC BAM alignment tag as the BED score"
-            help="(-tag)"/>
+        <param name="ed_score" argument="-ed" type="boolean" truevalue="-ed" falsevalue="" checked="false"
+            label="Use alignment's edit-distance for BED score" />
+        <param argument="-tag" type="text" optional="true"
+            label="Use other NUMERIC BAM alignment tag as the BED score" />
     </inputs>
     <outputs>
-        <data format="bed" name="output" metadata_source="input" label="${input.name} (as BED)"/>
+        <data name="output" format="bed" metadata_source="input" label="${input.name} (as BED)"/>
     </outputs>
     <tests>
         <test>
@@ -57,8 +54,7 @@
             <output name="output" file="bamToBed_result2.bed" ftype="bed" />
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 **What it does**
 
 bedtools bamtobed is a conversion utility that converts sequence alignments in BAM format into BED, BED12, and/or BEDPE records.
@@ -77,7 +73,6 @@
 
 
 @REFERENCES@
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations" />
 </tool>