diff mapBed.xml @ 2:457b09031d57 draft

Uploaded

--- a/mapBed.xml	Thu Jan 08 14:25:51 2015 -0500
+++ b/mapBed.xml	Tue May 19 07:05:36 2015 -0400
@@ -1,4 +1,4 @@
-<tool id="bedtools_map" name="MapBed" version="@WRAPPER_VERSION@.0">
+<tool id="bedtools_map" name="MapBed" version="@WRAPPER_VERSION@.1">
     <description></description>
     <macros>
         <import>macros.xml</import>
@@ -11,8 +11,7 @@
         -a "${inputA}"
         -b "${inputB}"
         $strand
-        -o $operation
-        -c "${cols}"
+        @C_AND_O_ARGUMENT@
         -f $overlap
         $reciprocal
         $split
@@ -26,16 +25,12 @@
     <inputs>
         <param format="bam,bed,vcf,gff,gff3" name="inputA" type="data" label="File A (BAM/BED/VCF/GFF)" />
         <param format="bam,bed,gff,vcf,gff3" name="inputB" type="data" label="File B (BAM/BED/VCF/GFF)" />
-        <expand macro="choose_columns" /> 
         <expand macro="overlap" />
         <param name="reciprocal" type="boolean" checked="false" truevalue="-r" falsevalue="" 
             label="Require reciprocal overlap"
             help="If set, the overlap between the BAM alignment and the BED interval must affect the above fraction of both the alignment and the BED interval. (-r)" />
         <expand macro="strand2" />
-        <expand macro="choose_operations">
-            <expand macro="math_options" />
-            <expand macro="additional_math_options" />
-        </expand>
+        <expand macro="c_and_o_argument" />
         <expand macro="split" />
         <expand macro="print_header" />
         <conditional name="genome">
@@ -53,30 +48,38 @@
         <test>
             <param name="inputA" value="mapBed1.bed" ftype="bed" />
             <param name="inputB" value="mapBed2.bed" ftype="bed" />
-            <param name="cols" value="5" />
-            <param name="operation" value="mean" />
+            <repeat name="c_and_o_argument_repeat">
+                <param name="cols" value="5" />
+                <param name="operation" value="mean" />
+            </repeat>
             <output name="output" file="mapBed_result1.bed" ftype="bed" />
         </test>
         <test>
             <param name="inputA" value="mapBed1.bed" ftype="bed" />
             <param name="inputB" value="mapBed2.bed" ftype="bed" />
-            <param name="cols" value="5" />
-            <param name="operation" value="collapse" />
+            <repeat name="c_and_o_argument_repeat">
+                <param name="col" value="5" />
+                <param name="operation" value="collapse" />
+            </repeat>
             <output name="output" file="mapBed_result2.bed" ftype="bed" />
         </test>
         <test>
             <param name="inputA" value="mapBed1.bed" ftype="bed" />
             <param name="inputB" value="mapBed2.bed" ftype="bed" />
-            <param name="cols" value="5" />
-            <param name="operation" value="collapse" />
+            <repeat name="c_and_o_argument_repeat">
+                <param name="cols" value="5" />
+                <param name="operation" value="collapse" />
+            </repeat>
             <param name="strand" value="-S" />
             <output name="output" file="mapBed_result3.bed" ftype="bed" />
         </test>
         <test>
             <param name="inputA" value="mapBed1.bed" ftype="bed" />
             <param name="inputB" value="mapBed2.bed" ftype="bed" />
-            <param name="cols" value="5" />
-            <param name="operation" value="collapse" />
+            <repeat name="c_and_o_argument_repeat">
+                <param name="cols" value="5" />
+                <param name="operation" value="collapse" />
+            </repeat>
             <param name="strand" value="-s" />
             <output name="output" file="mapBed_result4.bed" ftype="bed" />
         </test>