diff intersectBed.xml @ 42:d279800f4ff9 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b75b9e79cf3186a22dc2e1e9d27c1a080b891b59

--- a/intersectBed.xml	Fri Apr 20 05:30:04 2018 -0400
+++ b/intersectBed.xml	Thu Apr 26 17:02:24 2018 -0400
@@ -37,19 +37,19 @@
 ]]>
     </command>
     <inputs>
-        <param format="bed,bam,vcf,gff,gff3" name="inputA" type="data" label="File A to intersect with B" help="BAM/BED/GFF/VCF format" />
+        <param format="bam,@STD_BEDTOOLS_INPUTS@" name="inputA" type="data" label="File A to intersect with B" help="BAM/@STD_BEDTOOLS_INPUT_LABEL@ format" />
         <conditional name="reduce_or_iterate">
             <param name='reduce_or_iterate_selector' type='select' label='Combined or separate output files'>
                 <option value='iterate' selected='true'>One output file per 'input B' file</option>
                 <option value='reduce'>Single output containing intersections of any 'input B' lines with A </option>
             </param>
             <when value='iterate'>
-                <param format="bam,bed,gff,gff3,vcf" name="inputB" type="data"
-                       label="File(s) B to intersect with A" help="BAM/BED/GFF/VCF format"/>
+                <param format="bam,@STD_BEDTOOLS_INPUTS@" name="inputB" type="data"
+                       label="File(s) B to intersect with A" help="BAM/@STD_BEDTOOLS_INPUT_LABEL@ format"/>
             </when>
             <when value='reduce'>
-                <param format="bam,bed,gff,gff3,vcf" name="inputB" type="data" multiple="true"
-                       label="File(s) B to intersect with A" help="BAM/BED/GFF/VCF format"/>
+                <param format="bam,@STD_BEDTOOLS_INPUTS@" name="inputB" type="data" multiple="true"
+                       label="File(s) B to intersect with A" help="BAM/@STD_BEDTOOLS_INPUT_LABEL@ format"/>
             </when>
         </conditional>
         <expand macro="strand2" />
@@ -112,7 +112,7 @@
 <![CDATA[
 **What it does**
 
-By far, the most common question asked of two sets of genomic features is whether or not any of the features in the two sets “overlap” with one another. This is known as feature intersection. bedtools intersect allows one to screen for overlaps between two sets of genomic features. Moreover, it allows one to have fine control as to how the intersections are reported. bedtools intersect works with both BED/GFF/VCF and BAM files as input.
+By far, the most common question asked of two sets of genomic features is whether or not any of the features in the two sets “overlap” with one another. This is known as feature intersection. bedtools intersect allows one to screen for overlaps between two sets of genomic features. Moreover, it allows one to have fine control as to how the intersections are reported. bedtools intersect works with both @STD_BEDTOOLS_INPUT_LABEL@ and BAM files as input.
 
 .. image:: $PATH_TO_IMAGES/intersect-glyph.png