diff mapBed.xml @ 17:44867b59dbf2 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174

--- a/mapBed.xml	Fri Aug 18 15:33:08 2017 -0400
+++ b/mapBed.xml	Tue Sep 05 15:40:14 2017 -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>apply a function to a column for each overlapping interval</description>
     <macros>
         <import>macros.xml</import>
@@ -8,17 +8,15 @@
     <command>
 <![CDATA[
         bedtools map
-        -a "${inputA}"
-        -b "${inputB}"
+        -a '${inputA}'
+        -b '${inputB}'
         $strand
         @C_AND_O_ARGUMENT@
         -f $overlap
         $reciprocal
         $split
         $header
-        #if $genome.genome_choose == "-g" :
-            -g $genome.genome
-        #end if
+        @GENOME_FILE_MAPBED@
         > "${output}"
 ]]>
     </command>
@@ -36,16 +34,19 @@
         <expand macro="split" />
         <expand macro="print_header" />
         <conditional name="genome">
-            <param name="genome_choose" type="boolean" checked="false" truevalue="-g" falsevalue=""
-                label="Treat split/spliced BAM or BED12 entries as distinct BED intervals when computing coverage." help="(-g)" />
+            <param name="genome_choose" argument="-g" type="select" 
+                label="Specify a genome file the defines the expected chromosome order in the input files." >
+                <option value="" selected="true">No</option>
+                <option value="-g">Yes</option>
+            </param>
             <when value="-g">
-                <expand macro="genome" />
+                <expand macro="input_conditional_genome_file" />
             </when>
             <when value="" />
         </conditional>
     </inputs>
     <outputs>
-        <data format_source="inputA" name="output" metadata_source="inputA" label="Mapping of ${inputB.name} into ${inputA.name}"/>
+        <data format_source="inputA" name="output" metadata_source="inputA" label="Mapping of ${inputB.name} into ${inputA.name}" />
     </outputs>
     <tests>
         <test>
@@ -86,6 +87,19 @@
             <param name="strand" value="-s" />
             <output name="output" file="mapBed_result4.bed" ftype="bed" />
         </test>
+        <test>
+            <param name="inputA" value="mapBed3.bed" ftype="bed" />
+            <param name="inputB" value="mapBed4.bed" ftype="bed" />
+            <repeat name="c_and_o_argument_repeat">
+                <param name="col" value="5" />
+                <param name="operation" value="collapse" />
+            </repeat>
+            <param name="strand" value="-s" />
+            <param name="genome_choose" value="-g" />
+            <param name="genome_file_opts_selector" value="hist" />
+            <param name="genome" value="mm9.len" ftype="bed" />
+            <output name="output" file="mapBed_result5.bed" ftype="bed" />
+        </test>
     </tests>
     <help>
 <![CDATA[