# HG changeset patch
# User iuc
# Date 1524776566 14400
# Node ID 95a3b2c25bd1fd53c655e7c833827a168ba93802
# Parent  e36671a0f6461fdb71d8cfc1884f467b0e79aab7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b75b9e79cf3186a22dc2e1e9d27c1a080b891b59

diff -r e36671a0f646 -r 95a3b2c25bd1 annotateBed.xml
--- a/annotateBed.xml	Fri Apr 20 05:30:23 2018 -0400
+++ b/annotateBed.xml	Thu Apr 26 17:02:46 2018 -0400
@@ -33,7 +33,7 @@
 ]]>
     </command>
     <inputs>
-        <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file" />
+        <param format="@STD_BEDTOOLS_INPUTS@" name="inputA" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file" />
         <!-- Additional files, if the user needs more -->
          <conditional name="names">
             <param name="names_select" type="select" label="Specify names for each file">
@@ -73,7 +73,7 @@
 <![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.
+bedtools annotate, well, annotates one @STD_BEDTOOLS_INPUT_LABEL@ file with the coverage and number of overlaps observed from multiple other @STD_BEDTOOLS_INPUT_LABEL@ 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@
 ]]>
diff -r e36671a0f646 -r 95a3b2c25bd1 bedToIgv.xml
--- a/bedToIgv.xml	Fri Apr 20 05:30:23 2018 -0400
+++ b/bedToIgv.xml	Thu Apr 26 17:02:46 2018 -0400
@@ -20,7 +20,7 @@
 ]]>
     </command>
     <inputs>
-        <param format="bed,gff,gff3,vcf" name="input" type="data" label="Create IGV batch script the following BED file"/>
+        <param format="@STD_BEDTOOLS_INPUTS@" name="input" type="data" label="Create IGV batch script for this @STD_BEDTOOLS_INPUT_LABEL@ file"/>
         <param name="sort" type="select" label="Sort BAM file by" help="The type of BAM sorting you would like to apply to each image.">
             <option value="">No sorting at all (default)</option>
             <option value="base">base</option>
@@ -52,7 +52,7 @@
 <![CDATA[
 **What it does**
 
-Creates a batch script to create IGV images at each interval defined in a BED/GFF/VCF file.
+Creates a batch script to create IGV images at each interval defined in a @STD_BEDTOOLS_INPUT_LABEL@ file.
 
 **Notes**
 
diff -r e36671a0f646 -r 95a3b2c25bd1 bedpeToBam.xml
--- a/bedpeToBam.xml	Fri Apr 20 05:30:23 2018 -0400
+++ b/bedpeToBam.xml	Thu Apr 26 17:02:46 2018 -0400
@@ -15,7 +15,7 @@
 ]]>
     </command>
     <inputs>
-        <param name="input" format="bed,gff,vcf" type="data" label="BED/VCF/GFF file"/>
+        <param name="input" format="bed,gff,vcf" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
         <expand macro="input_conditional_genome_file" />
         <param name="mapq" type="integer" value="255"
             label="Set a mapping quality (SAM MAPQ field) value for all BED entries"
diff -r e36671a0f646 -r 95a3b2c25bd1 closestBed.xml
--- a/closestBed.xml	Fri Apr 20 05:30:23 2018 -0400
+++ b/closestBed.xml	Thu Apr 26 17:02:46 2018 -0400
@@ -30,11 +30,11 @@
 > '$output'
     ]]></command>
     <inputs>
-        <param name="inputA" type="data" format="bed,vcf,gff,gff3" label="BED/VCF/GFF file"/>
+        <param name="inputA" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
         <!-- overlap with file (inputB) -->
         <conditional name="overlap_with">
-            <param name="source" type="select" label="Overlap with: will you select a BED/VCF/GFF file from your history or use a built-in GFF file?" help="Built-in GFF files contain full annotation of a reference genome">
-                <option value="history" selected="true">Use a BED/VCF/GFF file from the history</option>
+            <param name="source" type="select" label="Overlap with: will you select a @STD_BEDTOOLS_INPUT_LABEL@ file from your history or use a built-in GFF file?" help="Built-in GFF files contain full annotation of a reference genome">
+                <option value="history" selected="true">Use a @STD_BEDTOOLS_INPUT_LABEL@ file from the history</option>
                 <option value="data_table">Use a built-in GFF file</option>
             </param>
             <when value="data_table">
@@ -46,7 +46,7 @@
                 </param>
             </when>
             <when value="history">
-                <param name="inputB" type="data" format="bed,gff,vcf,gff3" multiple="true" label="Select a BED/VCF/GFF file" />
+                <param name="inputB" type="data" format="@STD_BEDTOOLS_INPUTS@" multiple="true" label="Select a @STD_BEDTOOLS_INPUT_LABEL@ file" />
             </when>
         </conditional>
 
diff -r e36671a0f646 -r 95a3b2c25bd1 clusterBed.xml
--- a/clusterBed.xml	Fri Apr 20 05:30:23 2018 -0400
+++ b/clusterBed.xml	Thu Apr 26 17:02:46 2018 -0400
@@ -15,7 +15,7 @@
 ]]>
     </command>
     <inputs>
-        <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file"/>
+        <param format="@STD_BEDTOOLS_INPUTS@" name="inputA" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
         <param name="strand" type="boolean" checked="false" truevalue="-s" falsevalue="" label="Force strandedness."
             help="That is, only cluster features that are the same strand. By default, this is disabled." />
         <param name="distance" type="integer" value="0"
diff -r e36671a0f646 -r 95a3b2c25bd1 complementBed.xml
--- a/complementBed.xml	Fri Apr 20 05:30:23 2018 -0400
+++ b/complementBed.xml	Thu Apr 26 17:02:46 2018 -0400
@@ -14,7 +14,7 @@
 ]]>
     </command>
     <inputs>
-        <param format="bed,vcf,gff,gff3" name="input" type="data" label="BED/VCF/GFF file"/>
+        <param format="@STD_BEDTOOLS_INPUTS@" name="input" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
         <expand macro="input_conditional_genome_file" />
     </inputs>
     <outputs>
@@ -32,7 +32,7 @@
 <![CDATA[
 **What it does**
 
-bedtools complement returns all intervals in a genome that are not covered by at least one interval in the input BED/GFF/VCF file.
+bedtools complement returns all intervals in a genome that are not covered by at least one interval in the input @STD_BEDTOOLS_INPUT_LABEL@ file.
 
 .. image:: $PATH_TO_IMAGES/complement-glyph.png
 
diff -r e36671a0f646 -r 95a3b2c25bd1 coverageBed.xml
--- a/coverageBed.xml	Fri Apr 20 05:30:23 2018 -0400
+++ b/coverageBed.xml	Thu Apr 26 17:02:46 2018 -0400
@@ -39,19 +39,19 @@
 ]]>
     </command>
     <inputs>
-        <param format="bam,bed,gff,gff3,vcf" name="inputA" type="data" label="File A (on which coverage is calculated)" help="BAM/BED/GFF/VCF format" />
+        <param format="bam,@STD_BEDTOOLS_INPUTS@" name="inputA" type="data" label="File A (on which coverage is calculated)" 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 results for all 'input B' files</option>
             </param>
             <when value='iterate'>
-                <param format="bam,bed,gff,gff3,vcf" name="inputB" type="data"
-                       label="File(s) B (for which coverage is calculated)" help="BAM/BED/GFF/VCF format"/>
+                <param format="bam,@STD_BEDTOOLS_INPUTS@" name="inputB" type="data"
+                       label="File(s) B (for which coverage is calculated)" 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 (for which coverage is calculated)" help="BAM/BED/GFF/VCF format"/>
+                <param format="bam,@STD_BEDTOOLS_INPUTS@" name="inputB" type="data" multiple="true"
+                       label="File(s) B (for which coverage is calculated)" help="BAM/@STD_BEDTOOLS_INPUT_LABEL@ format"/>
             </when>
         </conditional>
         <expand macro="split" />
@@ -69,14 +69,14 @@
             <sanitizer invalid_char="">
                 <valid initial="string.digits"><add value=",."/></valid>
             </sanitizer>
-	</param>
+        </param>
         <param name="overlap_b" type="text"
             label="Minimum overlap required as a fraction of B."
             help="Default is 1E-9 (i.e., 1bp). (-F)">
             <sanitizer invalid_char="">
                 <valid initial="string.digits"><add value=",."/></valid>
             </sanitizer>
-	</param>
+        </param>
         <param name="reciprocal_overlap" type="boolean" checked="false" truevalue="-r" falsevalue=""
             label="Require that the fraction overlap be reciprocal for A AND B."
             help="if -f is 0.90 and -r is used, this requires that B overlap 90% of A and A _also_ overlaps 90% of B (-r)" />
diff -r e36671a0f646 -r 95a3b2c25bd1 expandBed.xml
--- a/expandBed.xml	Fri Apr 20 05:30:23 2018 -0400
+++ b/expandBed.xml	Thu Apr 26 17:02:46 2018 -0400
@@ -14,7 +14,7 @@
 ]]>
     </command>
     <inputs>
-        <param format="bed,vcf,gff,gff3" name="input" type="data" label="BED/VCF/GFF file"/>
+        <param format="@STD_BEDTOOLS_INPUTS@" name="input" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
         <expand macro="choose_columns" />
     </inputs>
     <outputs>
diff -r e36671a0f646 -r 95a3b2c25bd1 fisherBed.xml
--- a/fisherBed.xml	Fri Apr 20 05:30:23 2018 -0400
+++ b/fisherBed.xml	Thu Apr 26 17:02:46 2018 -0400
@@ -20,8 +20,8 @@
 ]]>
     </command>
     <inputs>
-        <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file"/>
-        <param format="bed,gff,vcf,gff3" name="inputB" type="data" label="BED/VCF/GFF file"/>
+        <param format="@STD_BEDTOOLS_INPUTS@" name="inputA" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
+        <param format="@STD_BEDTOOLS_INPUTS@" name="inputB" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
         <expand macro="input_conditional_genome_file" />
         <expand macro="strand2" />
         <expand macro="split" />
diff -r e36671a0f646 -r 95a3b2c25bd1 flankBed.xml
--- a/flankBed.xml	Fri Apr 20 05:30:23 2018 -0400
+++ b/flankBed.xml	Thu Apr 26 17:02:46 2018 -0400
@@ -23,7 +23,7 @@
 ]]>
     </command>
     <inputs>
-        <param format="bed,vcf,gff,gff3" name="input" type="data" label="BED/VCF/GFF file"/>
+        <param format="@STD_BEDTOOLS_INPUTS@" name="input" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
         <expand macro="input_conditional_genome_file" />
         <param name="pct" type="boolean" checked="false" truevalue="-pct" falsevalue=""
             label="Define -l and -r as a fraction of the feature’s length"
diff -r e36671a0f646 -r 95a3b2c25bd1 genomeCoverageBed.xml
--- a/genomeCoverageBed.xml	Fri Apr 20 05:30:23 2018 -0400
+++ b/genomeCoverageBed.xml	Thu Apr 26 17:02:46 2018 -0400
@@ -39,11 +39,11 @@
     <inputs>
         <conditional name="input_type">
             <param name="input_type_select" type="select" label="Input type">
-                <option value="bed">BED/VCF/GFF</option>
+                <option value="bed">@STD_BEDTOOLS_INPUT_LABEL@</option>
                 <option value="bam">BAM</option>
             </param>
             <when value="bed">
-                <param format="bed,vcf,gff,gff3" name="input" type="data" label="BED/VCF/GFF file" />
+                <param format="@STD_BEDTOOLS_INPUTS@" name="input" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file" />
                 <expand macro="input_conditional_genome_file" />
             </when>
             <when value="bam">
diff -r e36671a0f646 -r 95a3b2c25bd1 getfastaBed.xml
--- a/getfastaBed.xml	Fri Apr 20 05:30:23 2018 -0400
+++ b/getfastaBed.xml	Thu Apr 26 17:02:46 2018 -0400
@@ -23,7 +23,7 @@
 ]]>
     </command>
     <inputs>
-        <param format="bed,vcf,gff,gff3" name="input" type="data" label="BED/VCF/GFF file" />
+        <param format="@STD_BEDTOOLS_INPUTS@" name="input" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file" />
         <conditional name="fasta_source">
             <param name="fasta_source_selector" type="select" label="Choose the source for the fasta file">
                 <option value="history" selected="True">History</option>
diff -r e36671a0f646 -r 95a3b2c25bd1 groupbyBed.xml
--- a/groupbyBed.xml	Fri Apr 20 05:30:23 2018 -0400
+++ b/groupbyBed.xml	Thu Apr 26 17:02:46 2018 -0400
@@ -16,7 +16,7 @@
 ]]>
     </command>
     <inputs>
-        <param format="bed" name="inputA" type="data" label="BED file"/>
+        <param format="@STD_BEDTOOLS_INPUTS@" name="inputA" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
         <expand macro="choose_columns" />
         <param name="group" type="text" value="1,2,3"
             label="Specifies which column(s) (1-based) should be used to group the input"
diff -r e36671a0f646 -r 95a3b2c25bd1 intersectBed.xml
--- a/intersectBed.xml	Fri Apr 20 05:30:23 2018 -0400
+++ b/intersectBed.xml	Thu Apr 26 17:02:46 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
 
diff -r e36671a0f646 -r 95a3b2c25bd1 jaccardBed.xml
--- a/jaccardBed.xml	Fri Apr 20 05:30:23 2018 -0400
+++ b/jaccardBed.xml	Thu Apr 26 17:02:46 2018 -0400
@@ -18,8 +18,8 @@
 ]]>
     </command>
     <inputs>
-        <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file"/>
-        <param format="bed,vcf,gff,gff3" name="inputB" type="data" label="BED/VCF/GFF file"/>
+        <param format="@STD_BEDTOOLS_INPUTS@" name="inputA" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
+        <param format="@STD_BEDTOOLS_INPUTS@" name="inputB" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
         <expand macro="overlap" />
         <expand macro="reciprocal" />
         <param name="strand" type="boolean" checked="false" truevalue="-s" falsevalue=""
diff -r e36671a0f646 -r 95a3b2c25bd1 linksBed.xml
--- a/linksBed.xml	Fri Apr 20 05:30:23 2018 -0400
+++ b/linksBed.xml	Thu Apr 26 17:02:46 2018 -0400
@@ -16,7 +16,7 @@
 ]]>
     </command>
     <inputs>
-        <param format="bed,vcf,gff,gff3" name="input" type="data" label="BED/VCF/GFF file"/>
+        <param format="@STD_BEDTOOLS_INPUTS@" name="input" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
         <param name="basename" type="text" value="http://genome.ucsc.edu"
             label="The 'basename' for the UCSC genome browser" />
         <param name="org" type="text" value="human" label="Organism name" help="e.g. mouse, human (-org)" />
diff -r e36671a0f646 -r 95a3b2c25bd1 macros.xml
--- a/macros.xml	Fri Apr 20 05:30:23 2018 -0400
+++ b/macros.xml	Thu Apr 26 17:02:46 2018 -0400
@@ -6,6 +6,8 @@
         </requirements>
     </xml>
     <token name="@WRAPPER_VERSION@">2.27.0</token>
+    <token name="@STD_BEDTOOLS_INPUTS@">bed,bedgraph,gff,vcf</token>
+    <token name="@STD_BEDTOOLS_INPUT_LABEL@">bed,bedgraph,gff,vcf</token>
     <xml name="stdio">
         <stdio>
             <!-- Anything other than zero is an error -->
@@ -131,7 +133,7 @@
     <xml name="addition">
         <conditional name="addition">
             <param name="addition_select" type="select" label="Choose what you want to do">
-                <option value="b" selected="True">Increase the BED/GFF/VCF entry by the same number base pairs in each direction.</option>
+                <option value="b" selected="True">Increase the @STD_BEDTOOLS_INPUT_LABEL@ entry by the same number base pairs in each direction.</option>
                 <option value="lr">Increase by Start Coordinate and End Coordinate</option>
             </param>
             <when value="b">
diff -r e36671a0f646 -r 95a3b2c25bd1 makeWindowsBed.xml
--- a/makeWindowsBed.xml	Fri Apr 20 05:30:23 2018 -0400
+++ b/makeWindowsBed.xml	Thu Apr 26 17:02:46 2018 -0400
@@ -33,7 +33,7 @@
                 <option value="genome">Genome File</option>
             </param>
             <when value="bed">
-                <param  name="input" format="bed,vcf,gff,gff3" type="data" label="BED/VCF/GFF file"/>
+                <param  name="input" format="@STD_BEDTOOLS_INPUTS@" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
             </when>
             <when value="genome">
                 <expand macro="input_conditional_genome_file" />
diff -r e36671a0f646 -r 95a3b2c25bd1 mapBed.xml
--- a/mapBed.xml	Fri Apr 20 05:30:23 2018 -0400
+++ b/mapBed.xml	Thu Apr 26 17:02:46 2018 -0400
@@ -21,8 +21,8 @@
 ]]>
     </command>
     <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)" />
+        <param format="bam,@STD_BEDTOOLS_INPUTS@" name="inputA" type="data" label="File A (BAM/@STD_BEDTOOLS_INPUT_LABEL@)" />
+        <param format="bam,@STD_BEDTOOLS_INPUTS@" name="inputB" type="data" label="File B (BAM/@STD_BEDTOOLS_INPUT_LABEL@)" />
         <expand macro="overlap" />
         <param name="reciprocal" type="boolean" checked="false" truevalue="-r" falsevalue=""
             label="Require reciprocal overlap"
diff -r e36671a0f646 -r 95a3b2c25bd1 maskFastaBed.xml
--- a/maskFastaBed.xml	Fri Apr 20 05:30:23 2018 -0400
+++ b/maskFastaBed.xml	Thu Apr 26 17:02:46 2018 -0400
@@ -17,7 +17,7 @@
 ]]>
     </command>
     <inputs>
-        <param format="bed,vcf,gff,gff3" name="input" type="data" label="BED/VCF/GFF file"/>
+        <param format="@STD_BEDTOOLS_INPUTS@" name="input" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
         <param format="fasta" name="fasta" type="data" label="Fasta file"/>
         <param name="soft" type="boolean" checked="false" truevalue="-soft" falsevalue=""
             label="Soft-mask (that is, convert to lower-case bases) the FASTA sequence"
diff -r e36671a0f646 -r 95a3b2c25bd1 mergeBed.xml
--- a/mergeBed.xml	Fri Apr 20 05:30:23 2018 -0400
+++ b/mergeBed.xml	Thu Apr 26 17:02:46 2018 -0400
@@ -17,7 +17,7 @@
 ]]>
     </command>
     <inputs>
-        <param  name="input" format="bam,bed,gff,vcf" type="data" label="Sort the following BAM/BED/VCF/GFF file"/>
+        <param  name="input" format="bam,@STD_BEDTOOLS_INPUTS@" type="data" label="Sort the following BAM/@STD_BEDTOOLS_INPUT_LABEL@ file"/>
         <param name="strand" type="select" label="Calculation based on strandedness?">
             <option value="" selected="True">Overlaps on either strand</option>
             <option value="-s">Force strandedness. That is, only merge features that are the same strand.</option>
diff -r e36671a0f646 -r 95a3b2c25bd1 multiCov.xml
--- a/multiCov.xml	Fri Apr 20 05:30:23 2018 -0400
+++ b/multiCov.xml	Thu Apr 26 17:02:46 2018 -0400
@@ -30,7 +30,7 @@
 ]]>
     </command>
     <inputs>
-        <param name="input" format="bed" type="data" label="Sorted BED file" />
+        <param name="input" format="@STD_BEDTOOLS_INPUTS@" type="data" label="Sorted @STD_BEDTOOLS_INPUT_LABEL@ file" />
         <!-- Additional files, if the user needs more -->
         <param name="bams" format="bam" type="data" multiple="True" label="BAM file" />
 
diff -r e36671a0f646 -r 95a3b2c25bd1 multiIntersectBed.xml
--- a/multiIntersectBed.xml	Fri Apr 20 05:30:23 2018 -0400
+++ b/multiIntersectBed.xml	Thu Apr 26 17:02:46 2018 -0400
@@ -38,11 +38,11 @@
                 <option value="custom">Enter custom name per file</option>
             </param>
             <when value="tag">
-                <param name="inputs" format="bed" type="data" multiple="True" label="BED files" />
+                <param name="inputs" format="@STD_BEDTOOLS_INPUTS@" type="data" multiple="True" label="@STD_BEDTOOLS_INPUT_LABEL@ files" />
             </when>
             <when value="custom">
                 <repeat name="beds" title="Add BED files" min="2" >
-                    <param name="input" format="bed" type="data" multiple="True" label="BED file" />
+                    <param name="input" format="@STD_BEDTOOLS_INPUTS@" type="data" multiple="True" label="@STD_BEDTOOLS_INPUT_LABEL@ file" />
                     <param name="custom_name" type="text" area="false" label="Custom sample name" />
                 </repeat>
             </when>
diff -r e36671a0f646 -r 95a3b2c25bd1 nucBed.xml
--- a/nucBed.xml	Fri Apr 20 05:30:23 2018 -0400
+++ b/nucBed.xml	Thu Apr 26 17:02:46 2018 -0400
@@ -20,7 +20,7 @@
 ]]>
     </command>
     <inputs>
-        <param format="bed,vcf,gff,gff3" name="input" type="data" label="BED/VCF/GFF file"/>
+        <param format="@STD_BEDTOOLS_INPUTS@" name="input" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
         <param format="fasta" name="fasta" type="data" label="FASTA file"/>
 
         <param argument="-s" type="boolean" checked="false" truevalue="-s" falsevalue=""
diff -r e36671a0f646 -r 95a3b2c25bd1 overlapBed.xml
--- a/overlapBed.xml	Fri Apr 20 05:30:23 2018 -0400
+++ b/overlapBed.xml	Thu Apr 26 17:02:46 2018 -0400
@@ -14,7 +14,7 @@
 ]]>
     </command>
     <inputs>
-        <param format="bed,vcf,gff,gff3" name="input" type="data" label="BED/VCF/GFF file"/>
+        <param format="@STD_BEDTOOLS_INPUTS@" name="input" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
         <param name="cols" type="data_column" multiple="True" data_ref="input"
             label="Specify the columns for the starts and ends of the features for which you’d like to compute the overlap/distance"
             help="The columns must be listed in the following order: start1,end1,start2,end2" />
diff -r e36671a0f646 -r 95a3b2c25bd1 reldist.xml
--- a/reldist.xml	Fri Apr 20 05:30:23 2018 -0400
+++ b/reldist.xml	Thu Apr 26 17:02:46 2018 -0400
@@ -15,8 +15,8 @@
 ]]>
     </command>
     <inputs>
-        <param format="bed,bam,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF/BAM file"/>
-        <param format="bed,gff,vcf,gff3" name="inputB" type="data" label="BED/VCF/GFF file"/>
+        <param format="bam,@STD_BEDTOOLS_INPUTS@" name="inputA" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@/BAM file"/>
+        <param format="@STD_BEDTOOLS_INPUTS@" name="inputB" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
         <param name="detail" type="boolean" checked="false" truevalue="-detail" falsevalue=""
             label="Instead of a summary, report the relative distance for each interval in A" help="(-detail)" />
     </inputs>
diff -r e36671a0f646 -r 95a3b2c25bd1 shuffleBed.xml
--- a/shuffleBed.xml	Fri Apr 20 05:30:23 2018 -0400
+++ b/shuffleBed.xml	Thu Apr 26 17:02:46 2018 -0400
@@ -29,7 +29,7 @@
 ]]>
     </command>
     <inputs>
-        <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file"/>
+        <param format="@STD_BEDTOOLS_INPUTS@" name="inputA" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
         <param name="bedpe" type="boolean" label="The file is in BEDPE format" checked="False" truevalue="-bedpe" falsevalue="" />
         <expand macro="input_conditional_genome_file" />
         <param name="chrom" type="boolean" checked="False" truevalue="-chrom" falsevalue=""
@@ -106,7 +106,7 @@
 <![CDATA[
 **What it does**
 
-bedtools shuffle will randomly permute the genomic locations of a feature file among a genome defined in a genome file. One can also provide an “exclusions” BED/GFF/VCF file that lists regions where you do not want the permuted features to be placed. For example, one might want to prevent features from being placed in known genome gaps. shuffle is useful as a null basis against which to test the significance of associations of one feature with another.
+bedtools shuffle will randomly permute the genomic locations of a feature file among a genome defined in a genome file. One can also provide an “exclusions” @STD_BEDTOOLS_INPUT_LABEL@ file that lists regions where you do not want the permuted features to be placed. For example, one might want to prevent features from being placed in known genome gaps. shuffle is useful as a null basis against which to test the significance of associations of one feature with another.
 
 .. image:: $PATH_TO_IMAGES/shuffle-glyph.png
 
diff -r e36671a0f646 -r 95a3b2c25bd1 slopBed.xml
--- a/slopBed.xml	Fri Apr 20 05:30:23 2018 -0400
+++ b/slopBed.xml	Thu Apr 26 17:02:46 2018 -0400
@@ -23,7 +23,7 @@
 ]]>
     </command>
     <inputs>
-        <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file"/>
+        <param format="@STD_BEDTOOLS_INPUTS@" name="inputA" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
         <expand macro="input_conditional_genome_file" />
         <param name="pct" type="boolean" checked="false" truevalue="-pct" falsevalue=""
             label="Define -l and -r as a fraction of the feature’s length"
diff -r e36671a0f646 -r 95a3b2c25bd1 sortBed.xml
--- a/sortBed.xml	Fri Apr 20 05:30:23 2018 -0400
+++ b/sortBed.xml	Thu Apr 26 17:02:46 2018 -0400
@@ -14,7 +14,7 @@
 ]]>
     </command>
     <inputs>
-        <param format="bed,gff,gff3,vcf" name="input" type="data" label="Sort the following BED file"/>
+        <param format="@STD_BEDTOOLS_INPUTS@" name="input" type="data" label="Sort the following @STD_BEDTOOLS_INPUT_LABEL@ file"/>
         <param name="option" type="select" label="Sort by">
             <!-- sort -k 1,1 -k2,2 -n a.bed -->
             <option value="">chromosome, then by start position (asc)</option>
diff -r e36671a0f646 -r 95a3b2c25bd1 spacingBed.xml
--- a/spacingBed.xml	Fri Apr 20 05:30:23 2018 -0400
+++ b/spacingBed.xml	Thu Apr 26 17:02:46 2018 -0400
@@ -13,7 +13,7 @@
 ]]>
     </command>
     <inputs>
-        <param format="bed,vcf,gff,gff3,bam" name="input" type="data" label="BED/VCF/GFF/BAM file"/>
+        <param format="bam,@STD_BEDTOOLS_INPUTS@" name="input" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@/BAM file"/>
     </inputs>
     <outputs>
         <data format_source="input" name="output" metadata_source="input" label="Spaces between intervals of ${input}"/>
diff -r e36671a0f646 -r 95a3b2c25bd1 subtractBed.xml
--- a/subtractBed.xml	Fri Apr 20 05:30:23 2018 -0400
+++ b/subtractBed.xml	Thu Apr 26 17:02:46 2018 -0400
@@ -17,8 +17,8 @@
 ]]>
     </command>
     <inputs>
-        <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file"/>
-        <param format="bed,gff,vcf,gff3" name="inputB" type="data" label="BED/VCF/GFF file"/>
+        <param format="@STD_BEDTOOLS_INPUTS@" name="inputA" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
+        <param format="@STD_BEDTOOLS_INPUTS@" name="inputB" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
         <expand macro="strand2" />
         <expand macro="overlap" />
         <param name="removeIfOverlap" type="select" label="Calculation based on strandedness?">
diff -r e36671a0f646 -r 95a3b2c25bd1 tagBed.xml
--- a/tagBed.xml	Fri Apr 20 05:30:23 2018 -0400
+++ b/tagBed.xml	Thu Apr 26 17:02:46 2018 -0400
@@ -20,7 +20,7 @@
     </command>
     <inputs>
         <param name="inputA" format="bam" type="data" label="BAM file"/>
-        <param name="inputB" format="bed,gff,vcf" multiple="True" type="data" label="BED/VCF/GFF file" />
+        <param name="inputB" format="@STD_BEDTOOLS_INPUTS@" multiple="True" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file" />
         <expand macro="strand2" />
         <expand macro="overlap" />
         <param name="tag" type="text" value="YB" label="Specify the tag to use" />
@@ -46,7 +46,7 @@
 <![CDATA[
 **What it does**
 
-Annotates a BAM file based on overlaps with multiple BED/GFF/VCF files on the intervals in an input bam file
+Annotates a BAM file based on overlaps with multiple @STD_BEDTOOLS_INPUT_LABEL@ files on the intervals in an input bam file
 
 @REFERENCES@
 ]]>
diff -r e36671a0f646 -r 95a3b2c25bd1 windowBed.xml
--- a/windowBed.xml	Fri Apr 20 05:30:23 2018 -0400
+++ b/windowBed.xml	Thu Apr 26 17:02:46 2018 -0400
@@ -30,8 +30,8 @@
 ]]>
     </command>
     <inputs>
-        <param format="bed,bam,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF/BAM file"/>
-        <param format="bed,gff,vcf,gff3" name="inputB" type="data" label="BED/VCF/GFF file"/>
+        <param format="bam,@STD_BEDTOOLS_INPUTS@" name="inputA" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@/BAM file"/>
+        <param format="@STD_BEDTOOLS_INPUTS@" name="inputB" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
         <param name="bed" type="boolean" checked="false" truevalue="-bed" falsevalue=""
             label="When using BAM input, write output as BED. The default is to write output in BAM when using a bam file"
             help="(-bed)" />