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changeset 26:95a3b2c25bd1 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b75b9e79cf3186a22dc2e1e9d27c1a080b891b59
author iuc
date Thu, 26 Apr 2018 17:02:46 -0400
parents e36671a0f646
children a33db97b220c
files annotateBed.xml bedToIgv.xml bedpeToBam.xml closestBed.xml clusterBed.xml complementBed.xml coverageBed.xml expandBed.xml fisherBed.xml flankBed.xml genomeCoverageBed.xml getfastaBed.xml groupbyBed.xml intersectBed.xml jaccardBed.xml linksBed.xml macros.xml makeWindowsBed.xml mapBed.xml maskFastaBed.xml mergeBed.xml multiCov.xml multiIntersectBed.xml nucBed.xml overlapBed.xml reldist.xml shuffleBed.xml slopBed.xml sortBed.xml spacingBed.xml subtractBed.xml tagBed.xml windowBed.xml
diffstat 33 files changed, 62 insertions(+), 60 deletions(-) [+]
line wrap: on
line diff
--- 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@
 ]]>
--- 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**
 
--- 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"
--- 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>
 
--- 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"
--- 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
 
--- 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)" />
--- 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>
--- 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" />
--- 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"
--- 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">
--- 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>
--- 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"
--- 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
 
--- 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=""
--- 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)" />
--- 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">
--- 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" />
--- 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"
--- 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"
--- 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>
--- 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" />
 
--- 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>
--- 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=""
--- 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" />
--- 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>
--- 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
 
--- 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"
--- 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>
--- 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}"/>
--- 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?">
--- 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@
 ]]>
--- 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)" />