diff annotateBed.xml @ 8:0d3aa592ce27 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/annotateBed.xml	Tue Apr 28 22:56:34 2015 -0400
@@ -0,0 +1,79 @@
+<tool id="bedtools_annotatebed" name="AnnotateBed" version="@WRAPPER_VERSION@.0">
+    <description></description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <command>
+<![CDATA[
+        bedtools annotate
+        -i "${inputA}"
+        #if $names.names_select == 'yes':
+            -files
+            #for $bed in $names.beds:
+                "${bed.input}"
+            #end for
+
+            -names
+            #for $bed in $names.beds:
+                "${bed.inputName}"
+            #end for
+        #else:
+            #set files = '" "'.join( [ str( $file ) for $file in $names.beds ] )
+            -files "${files}"
+        #end if
+        $strand
+        $counts
+        $both
+        > "${output}"
+]]>
+    </command>
+    <inputs>
+        <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file" />
+        <!-- Additional files, if the user needs more -->
+         <conditional name="names">
+            <param name="names_select" type="select" label="Specify names for each file">
+                <option value="no" selected="True">No</option>
+                <option value="yes">Yes</option>
+            </param>
+            <when value="yes">
+                <repeat name="beds" title="Add BED files and names" >
+                    <param name="input" format="bed" type="data" label="BED file" />
+                    <param name="inputName" type="text" label="Name of the file" />
+                </repeat>
+            </when>
+            <when value="no">
+                <param name="beds" format="bed" multiple="True" type="data" label="BED file" />
+            </when>
+        </conditional>
+        <expand macro="strand2" />
+        <param name="counts" type="boolean" checked="false" truevalue="-counts" falsevalue=""
+            label="Report the count of features followed by the % coverage for each annotation file" 
+            help="Default is to report solely the fraction of -i covered by each file." />
+        <param name="both" type="boolean" checked="false" truevalue="-both" falsevalue=""
+            label="Report the count of features followed by the % coverage for each annotation file" 
+            help="Default is to report solely the fraction of the input file covered by each file." />
+    </inputs>
+    <outputs>
+        <data format="bed" name="output" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="inputA" value="annotateBed1.bed" ftype="bed" />
+            <param name="names_select" value="no" />
+            <param name="beds" value="annotateBed2.bed,annotateBed3.bed,annotateBed4.bed" />
+            <output name="output" file="annotateBed_result.bed" ftype="bed" />
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+**What it does**
+
+bedtools annotate, well, annotates one BED/VCF/GFF file with the coverage and number of overlaps observed from multiple other BED/VCF/GFF files. In this way, it allows one to ask to what degree one feature coincides with multiple other feature types with a single command.
+
+@REFERENCES@
+]]>
+    </help>
+    <expand macro="citations" />
+</tool>