diff unionBedGraphs.xml @ 17:44867b59dbf2 draft

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

--- a/unionBedGraphs.xml	Fri Aug 18 15:33:08 2017 -0400
+++ b/unionBedGraphs.xml	Tue Sep 05 15:40:14 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="bedtools_unionbedgraph" name="Merge BedGraph files" version="@WRAPPER_VERSION@.0">
+<tool id="bedtools_unionbedgraph" name="Merge BedGraph files" version="@WRAPPER_VERSION@.1">
     <description>combines coverage intervals from multiple BEDGRAPH files</description>
     <macros>
         <import>macros.xml</import>
@@ -10,10 +10,8 @@
     unionBedGraphs
         $header
         -filler "${filler}"
-        #if $zero.value == True:
-            -empty
-            -g $genome
-        #end if
+        $empty.empty_selector
+        @GENOME_FILE_UNION@
 
         #if str($tag.tag_select) == "tag":
             #set files = '" "'.join( [ str( $file ) for $file in $tag.inputs ] )
@@ -43,14 +41,20 @@
             <when value="custom">
                 <repeat name="bedgraphs" title="Add BedGraph files" min="2" >
                     <param name="input" format="bedgraph" type="data" multiple="True" label="BedGraph file" />
-                    <param name="custom_name" type="text" area="false" label="Custom sample name"/>
+                    <param name="custom_name" type="text" area="false" label="Custom sample name" />
                 </repeat>
             </when>
         </conditional>
-        <expand macro="genome" />
-        <param name="zero" type="boolean" checked="true"
-            label="Report regions with zero coverage"
-            help="If set, regions without any coverage will also be reported. Requires a valid organism key for all input datasets" />
+        <conditional name="empty">
+            <param name="empty_selector" argument="-empty" type="select" label="Report empty regions" help="Include regions that have zero coverage in all BedGraph datasets">
+                <option value="-empty">Yes</option>
+                <option value="">No</option>
+            </param>
+            <when value="-empty">
+                <expand macro="input_conditional_genome_file" />
+            </when>
+            <when value="" />
+        </conditional>
         <param name="filler" type="text" value="N/A"
             label="Text to use for no-coverage value"
             help="Can be 0.0, N/A, - or any other value. (-filler)" />
@@ -61,27 +65,28 @@
     </outputs>
     <tests>
         <test>
-            <param name="tag_select" value="tag"/>
+            <param name="tag_select" value="tag" />
             <param name="inputs" value="unionBedGraphs1.bg,unionBedGraphs2.bg,unionBedGraphs3.bg" ftype="bedgraph" />
-            <param name="zero" value="False"/>
+            <param name="empty_selector" value="" />
             <output name="output" file="unionBedGraphs_result1.bg" ftype="bedgraph" />
         </test>
         <test>
-            <param name="tag_select" value="tag"/>
+            <param name="tag_select" value="tag" />
             <param name="inputs" value="unionBedGraphs1.bg,unionBedGraphs2.bg,unionBedGraphs3.bg" ftype="bedgraph" />
-            <param name="header" value="True"/>
-            <param name="zero" value="False"/>
+            <param name="header" value="True" />
+            <param name="empty_selector" value="" />
             <output name="output" file="unionBedGraphs_result2.bg" ftype="bedgraph" />
         </test>
         <test>
-            <param name="tag_select" value="tag"/>
+            <param name="tag_select" value="tag" />
             <param name="inputs" value="unionBedGraphs1.bg,unionBedGraphs2.bg,unionBedGraphs3.bg" ftype="bedgraph" />
-            <param name="zero" value="True"/>
-            <param name="genome" value="unionBedGraphs1.len"/>
+            <param name="empty_selector" value="-empty" />
+            <param name="genome_file_opts_selector" value="hist" />
+            <param name="genome" value="unionBedGraphs1.len" />
             <output name="output" file="unionBedGraphs_result3.bg" ftype="bedgraph" />
         </test>
         <test>
-            <param name="tag_select" value="custom"/>
+            <param name="tag_select" value="custom" />
             <repeat name="bedgraphs">
                 <param name="input" value="unionBedGraphs1.bg" />
                 <param name="custom_name" value="first" />
@@ -94,8 +99,9 @@
                 <param name="input" value="unionBedGraphs3.bg" />
                 <param name="custom_name" value="third" />
             </repeat>
-            <param name="zero" value="True"/>
-            <param name="genome" value="unionBedGraphs1.len"/>
+            <param name="empty_selector" value="-empty" />
+            <param name="genome_file_opts_selector" value="hist" />
+            <param name="genome" value="unionBedGraphs1.len" />
             <output name="output" file="unionBedGraphs_result4.bg" ftype="bedgraph" />
         </test>
     </tests>