diff multiCov.xml @ 34:dde39ba9c031 draft

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

--- a/multiCov.xml	Mon Dec 17 14:23:31 2018 -0500
+++ b/multiCov.xml	Mon Apr 29 05:55:48 2019 -0400
@@ -1,75 +1,70 @@
-<tool id="bedtools_multicovtbed" name="bedtools MultiCovBed" version="@WRAPPER_VERSION@">
+<tool id="bedtools_multicovtbed" name="bedtools MultiCovBed" version="@TOOL_VERSION@">
     <description>counts coverage from multiple BAMs at specific intervals</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
     <expand macro="stdio" />
-    <command>
-<![CDATA[
-        #for $i, $bam in enumerate( $bams ):
-            ln -s -f $bam ${i}.bam &&
-            ln -s -f $bam.metadata.bam_index ${i}.bam.bai &&
-        #end for
+    <command><![CDATA[
+#for $i, $bam in enumerate($bams):
+    ln -s -f '$bam' ${i}.bam &&
+    ln -s -f '$bam.metadata.bam_index' ${i}.bam.bai &&
+#end for
 
-        bedtools multicov
-            -bed '$input'
-            -bams
-            #for $i, $bam in enumerate( $bams ):
-                '${i}.bam'
-            #end for
-            $strand
-            -f $overlap
-            $reciprocal
-            $split
-            -q $q
-            $duplicate
-            $failed
-            $proper
-            > '$output'
-]]>
-    </command>
+bedtools multicov
+-bed '$input'
+-bams
+#for $i, $bam in enumerate($bams):
+    '${i}.bam'
+#end for
+$strand
+@OVERLAP@
+$reciprocal
+$split
+-q $q
+$duplicate
+$failed
+$proper
+> '$output'
+    ]]></command>
     <inputs>
-        <param name="input" format="@STD_BEDTOOLS_INPUTS@" type="data" label="Sorted @STD_BEDTOOLS_INPUT_LABEL@ file" />
+        <param name="input" argument="-bed" type="data" format="@STD_BEDTOOLS_INPUTS@" label="Sorted @STD_BEDTOOLS_INPUT_LABEL@ file" />
         <!-- Additional files, if the user needs more -->
-        <param name="bams" format="bam" type="data" multiple="True" label="BAM file" />
+        <param argument="-bams" type="data" format="bam" multiple="true" label="BAM file" />
 
         <expand macro="strand2" />
         <expand macro="overlap" />
         <expand macro="reciprocal" />
         <expand macro="split" />
-        <param name="q" type="integer" value="0" label="Minimum mapping quality (MAPQ) allowed" help="(-q)" />
-        <param name="duplicate" type="boolean" checked="False" truevalue="-D" falsevalue=""
+        <param argument="-q" type="integer" value="0" label="Minimum mapping quality (MAPQ) allowed" />
+        <param name="duplicate" argument="-D" type="boolean" truevalue="-D" falsevalue="" checked="false"
             label="Include duplicate reads"
-            help="Default counts non-duplicates only. (-D)" />
-        <param name="failed" type="boolean" checked="false" truevalue="-F" falsevalue=""
+            help="Default counts non-duplicates only" />
+        <param name="failed" argument="-F" type="boolean" truevalue="-F" falsevalue="" checked="false"
             label="Include failed-QC reads"
-            help="Default counts pass-QC reads only (-F)"/>
-        <param name="proper" type="boolean" checked="false" truevalue="-p" falsevalue=""
+            help="Default counts pass-QC reads only"/>
+        <param name="proper" argument="-p" type="boolean" truevalue="-p" falsevalue="" checked="false"
             label="Only count proper pairs"
-            help="Default counts all alignments with MAPQ > -q argument, regardless of the BAM FLAG field. (-p)" />
+            help="Default counts all alignments with MAPQ > -q argument, regardless of the BAM FLAG field" />
     </inputs>
     <outputs>
-        <data name="output" metadata_source="input" format_source="input" />
+        <data name="output" format_source="input" metadata_source="input" />
     </outputs>
     <tests>
         <test>
             <param name="input" value="multiCov1.bed" ftype="bed" />
             <param name="bams" value="srma_in3.bam,srma_in3.bam" ftype="bam"/>
             <param name="q" value="1"/>
-            <param name="split" value="False"/>
+            <param name="split" value=""/>
             <output name="output" file="multiCovBed_result1.bed" ftype="bed" />
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 **What it does**
 
 bedtools multicov, reports the count of alignments from multiple position-sorted and indexed BAM files that overlap intervals in a BED file. Specifically, for each BED interval provided, it reports a separate count of overlapping alignments from each BAM file.
 
-
 @REFERENCES@
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations" />
 </tool>