# HG changeset patch
# User iuc
# Date 1636025706 0
# Node ID 539958feb49cacda37c7b2f08bd107b9af935f00
# Parent  ed6f66aed1f9c2600039c91c0f0f2e1b0536b203
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 500a03281ea704abc7a16d9af63d67dbdcc5cd0b"

diff -r ed6f66aed1f9 -r 539958feb49c annotateBed.xml
--- a/annotateBed.xml	Thu Sep 09 13:02:16 2021 +0000
+++ b/annotateBed.xml	Thu Nov 04 11:35:06 2021 +0000
@@ -1,9 +1,9 @@
 <tool id="bedtools_annotatebed" name="bedtools AnnotateBed" version="@TOOL_VERSION@" profile="@PROFILE@">
     <description>annotate coverage of features from multiple files</description>
-    <expand macro="bio_tools" />
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools" />
     <expand macro="requirements" />
     <expand macro="stdio" />
     <command><![CDATA[
@@ -66,7 +66,7 @@
         <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" />
+            <param name="beds" value="annotateBed2.bed,annotateBed3.bed,annotateBed4.bed"/>
             <output name="output" file="annotateBed_result.bed" ftype="bed" />
         </test>
     </tests>
diff -r ed6f66aed1f9 -r 539958feb49c bamToBed.xml
--- a/bamToBed.xml	Thu Sep 09 13:02:16 2021 +0000
+++ b/bamToBed.xml	Thu Nov 04 11:35:06 2021 +0000
@@ -1,16 +1,16 @@
-<tool id="bedtools_bamtobed" name="bedtools BAM to BED" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
+<tool id="bedtools_bamtobed" name="bedtools BAM to BED" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@">
     <description>converter</description>
-    <expand macro="bio_tools" />
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools" />
     <expand macro="requirements">
         <requirement type="package" version="@SAMTOOLS_VERSION@">samtools</requirement>
     </expand>
     <expand macro="stdio" />
     <command><![CDATA[
 #if $input.extension in ['bam', 'unsorted.bam', 'qname_input_sorted.bam'] and $option == "-bedpe":
-    samtools sort -n -@ "\${GALAXY_SLOTS:-4}" -T "\${TMPDIR:-.}" '${input}' ./input &&
+    samtools sort -n -@ "\${GALAXY_SLOTS:-4}" -T "\${TMPDIR:-.}" '${input}' > ./input.bam &&
 #else
     ln -s '${input}' ./input.bam &&
 #end if
@@ -54,6 +54,12 @@
             <param name="tag" value="NM" />
             <output name="output" file="bamToBed_result2.bed" ftype="bed" />
         </test>
+        <test>
+            <param name="input" value="bedpeToBam_result1.bam" ftype="bam" />
+            <param name="option" value="-bedpe" />
+            <param name="tag" value="" />
+            <output name="output" file="bamToBed_result3.bed" ftype="bed" />
+        </test>
     </tests>
     <help><![CDATA[
 **What it does**
diff -r ed6f66aed1f9 -r 539958feb49c bed12ToBed6.xml
--- a/bed12ToBed6.xml	Thu Sep 09 13:02:16 2021 +0000
+++ b/bed12ToBed6.xml	Thu Nov 04 11:35:06 2021 +0000
@@ -1,9 +1,9 @@
 <tool id="bedtools_bed12tobed6" name="bedtools BED12 to BED6" version="@TOOL_VERSION@" profile="@PROFILE@">
     <description>converter</description>
-    <expand macro="bio_tools" />
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools" />
     <expand macro="requirements" />
     <expand macro="stdio" />
     <command><![CDATA[
diff -r ed6f66aed1f9 -r 539958feb49c bedToBam.xml
--- a/bedToBam.xml	Thu Sep 09 13:02:16 2021 +0000
+++ b/bedToBam.xml	Thu Nov 04 11:35:06 2021 +0000
@@ -1,9 +1,9 @@
 <tool id="bedtools_bedtobam" name="bedtools BED to BAM" version="@TOOL_VERSION@" profile="@PROFILE@">
     <description>converter</description>
-    <expand macro="bio_tools" />
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools" />
     <expand macro="requirements" />
     <expand macro="stdio" />
     <command><![CDATA[
diff -r ed6f66aed1f9 -r 539958feb49c bedToIgv.xml
--- a/bedToIgv.xml	Thu Sep 09 13:02:16 2021 +0000
+++ b/bedToIgv.xml	Thu Nov 04 11:35:06 2021 +0000
@@ -1,9 +1,9 @@
 <tool id="bedtools_bedtoigv" name="bedtools BED to IGV" version="@TOOL_VERSION@" profile="@PROFILE@">
     <description>create batch script for taking IGV screenshots</description>
-    <expand macro="bio_tools" />
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools" />
     <expand macro="requirements" />
     <expand macro="stdio" />
     <command><![CDATA[
diff -r ed6f66aed1f9 -r 539958feb49c bedpeToBam.xml
--- a/bedpeToBam.xml	Thu Sep 09 13:02:16 2021 +0000
+++ b/bedpeToBam.xml	Thu Nov 04 11:35:06 2021 +0000
@@ -1,9 +1,9 @@
 <tool id="bedtools_bedpetobam" name="bedtools BEDPE to BAM" version="@TOOL_VERSION@" profile="@PROFILE@">
     <description>converter</description>
-    <expand macro="bio_tools" />
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools" />
     <!-- bedtobam broken in 2.29.0 <expand macro="requirements" /> -->
     <requirements>
         <requirement type="package" version="2.27.1">bedtools</requirement>
diff -r ed6f66aed1f9 -r 539958feb49c closestBed.xml
--- a/closestBed.xml	Thu Sep 09 13:02:16 2021 +0000
+++ b/closestBed.xml	Thu Nov 04 11:35:06 2021 +0000
@@ -1,9 +1,9 @@
 <tool id="bedtools_closestbed" name="bedtools ClosestBed" version="@TOOL_VERSION@" profile="@PROFILE@">
     <description>find the closest, potentially non-overlapping interval</description>
-    <expand macro="bio_tools" />
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools" />
     <expand macro="requirements" />
     <expand macro="stdio" />
     <command><![CDATA[
diff -r ed6f66aed1f9 -r 539958feb49c clusterBed.xml
--- a/clusterBed.xml	Thu Sep 09 13:02:16 2021 +0000
+++ b/clusterBed.xml	Thu Nov 04 11:35:06 2021 +0000
@@ -1,9 +1,9 @@
 <tool id="bedtools_clusterbed" name="bedtools ClusterBed" version="@TOOL_VERSION@" profile="@PROFILE@">
     <description>cluster overlapping/nearby intervals</description>
-    <expand macro="bio_tools" />
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools" />
     <expand macro="requirements" />
     <expand macro="stdio" />
     <command><![CDATA[
diff -r ed6f66aed1f9 -r 539958feb49c complementBed.xml
--- a/complementBed.xml	Thu Sep 09 13:02:16 2021 +0000
+++ b/complementBed.xml	Thu Nov 04 11:35:06 2021 +0000
@@ -1,9 +1,9 @@
 <tool id="bedtools_complementbed" name="bedtools ComplementBed" version="@TOOL_VERSION@" profile="@PROFILE@">
     <description>Extract intervals not represented by an interval file</description>
-    <expand macro="bio_tools" />
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools" />
     <expand macro="requirements" />
     <expand macro="stdio" />
     <command><![CDATA[
@@ -23,7 +23,7 @@
         <test>
             <param name="input" value="a.bed" ftype="bed" />
             <param name="genome_file_opts_selector" value="hist" />
-            <param name="genome" value="mm9_chr1.len" />
+            <param name="genome" value="mm9_chr1.len" ftype="tabular" />
             <output name="output" file="complementBed_result1.bed" ftype="bed" />
         </test>
     </tests>
diff -r ed6f66aed1f9 -r 539958feb49c coverageBed.xml
--- a/coverageBed.xml	Thu Sep 09 13:02:16 2021 +0000
+++ b/coverageBed.xml	Thu Nov 04 11:35:06 2021 +0000
@@ -1,9 +1,9 @@
 <tool id="bedtools_coveragebed" name="bedtools Compute both the depth and breadth of coverage" version="@TOOL_VERSION@" profile="@PROFILE@">
     <description>of features in file B on the features in file A (bedtools coverage)</description>
-    <expand macro="bio_tools" />
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools" />
     <expand macro="requirements">
         <requirement type="package" version="@SAMTOOLS_VERSION@">samtools</requirement>
     </expand>
diff -r ed6f66aed1f9 -r 539958feb49c expandBed.xml
--- a/expandBed.xml	Thu Sep 09 13:02:16 2021 +0000
+++ b/expandBed.xml	Thu Nov 04 11:35:06 2021 +0000
@@ -1,9 +1,9 @@
 <tool id="bedtools_expandbed" name="bedtools ExpandBed" version="@TOOL_VERSION@" profile="@PROFILE@">
     <description>replicate lines based on lists of values in columns</description>
-    <expand macro="bio_tools" />
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools" />
     <expand macro="requirements" />
     <expand macro="stdio" />
     <command><![CDATA[
diff -r ed6f66aed1f9 -r 539958feb49c fisherBed.xml
--- a/fisherBed.xml	Thu Sep 09 13:02:16 2021 +0000
+++ b/fisherBed.xml	Thu Nov 04 11:35:06 2021 +0000
@@ -1,9 +1,9 @@
 <tool id="bedtools_fisher" name="bedtools FisherBed" version="@TOOL_VERSION@" profile="@PROFILE@">
     <description>calculate Fisher statistic between two feature files</description>
-    <expand macro="bio_tools" />
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools" />
     <expand macro="requirements" />
     <expand macro="stdio" />
     <command><![CDATA[
diff -r ed6f66aed1f9 -r 539958feb49c flankBed.xml
--- a/flankBed.xml	Thu Sep 09 13:02:16 2021 +0000
+++ b/flankBed.xml	Thu Nov 04 11:35:06 2021 +0000
@@ -1,9 +1,9 @@
 <tool id="bedtools_flankbed" name="bedtools FlankBed" version="@TOOL_VERSION@" profile="@PROFILE@">
     <description>create new intervals from the flanks of existing intervals</description>
-    <expand macro="bio_tools" />
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools" />
     <expand macro="requirements" />
     <expand macro="stdio" />
     <command><![CDATA[
@@ -39,7 +39,7 @@
         <test>
             <param name="input" value="a.bed" ftype="bed" />
             <param name="genome_file_opts_selector" value="hist" />
-            <param name="genome" value="mm9_chr1.len"/>
+            <param name="genome" value="mm9_chr1.len" ftype="tabular"/>
             <param name="addition_select" value="b"/>
             <param name="b" value="5"/>
             <output name="output" file="flankBed_result1.bed" ftype="bed" />
@@ -47,7 +47,7 @@
         <test>
             <param name="input" value="a.bed" ftype="bed" />
             <param name="genome_file_opts_selector" value="hist" />
-            <param name="genome" value="mm9_chr1.len"/>
+            <param name="genome" value="mm9_chr1.len" ftype="tabular"/>
             <param name="addition_select" value="lr"/>
             <param name="l" value="2"/>
             <param name="r" value="3"/>
diff -r ed6f66aed1f9 -r 539958feb49c genomeCoverageBed.xml
--- a/genomeCoverageBed.xml	Thu Sep 09 13:02:16 2021 +0000
+++ b/genomeCoverageBed.xml	Thu Nov 04 11:35:06 2021 +0000
@@ -1,9 +1,9 @@
 <tool id="bedtools_genomecoveragebed" name="bedtools Genome Coverage" version="@TOOL_VERSION@" profile="@PROFILE@">
     <description>compute the coverage over an entire genome</description>
-    <expand macro="bio_tools" />
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools" />
     <expand macro="requirements" />
     <expand macro="stdio" />
     <command><![CDATA[
diff -r ed6f66aed1f9 -r 539958feb49c getfastaBed.xml
--- a/getfastaBed.xml	Thu Sep 09 13:02:16 2021 +0000
+++ b/getfastaBed.xml	Thu Nov 04 11:35:06 2021 +0000
@@ -1,9 +1,9 @@
 <tool id="bedtools_getfastabed" name="bedtools GetFastaBed" version="@TOOL_VERSION@" profile="@PROFILE@">
     <description>use intervals to extract sequences from a FASTA file</description>
-    <expand macro="bio_tools" />
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools" />
     <expand macro="requirements" />
     <expand macro="stdio" />
     <command><![CDATA[
diff -r ed6f66aed1f9 -r 539958feb49c groupbyBed.xml
--- a/groupbyBed.xml	Thu Sep 09 13:02:16 2021 +0000
+++ b/groupbyBed.xml	Thu Nov 04 11:35:06 2021 +0000
@@ -1,9 +1,9 @@
 <tool id="bedtools_groupbybed" name="bedtools GroupByBed" version="@TOOL_VERSION@" profile="@PROFILE@">
     <description>group by common cols and summarize other cols</description>
-    <expand macro="bio_tools" />
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools" />
     <expand macro="requirements" />
     <expand macro="stdio" />
     <command><![CDATA[
@@ -25,7 +25,7 @@
             </sanitizer>
         </param>
         <param name="operation" argument="-o" type="select" label="Specify the operation">
-            <option value="sum" selected="true">Sum - numeric only</option>
+            <!-- <option value="sum" selected="true">Sum - numeric only</option> This is already in math-->
             <option value="stdev">Stdev - numeric only</option>
             <option value="sstdev">Sstdev - numeric only</option>
             <option value="freqasc">Freqasc - comma separated list of values observed and the number of times they were observed (ascending)</option>
diff -r ed6f66aed1f9 -r 539958feb49c intersectBed.xml
--- a/intersectBed.xml	Thu Sep 09 13:02:16 2021 +0000
+++ b/intersectBed.xml	Thu Nov 04 11:35:06 2021 +0000
@@ -1,9 +1,9 @@
 <tool id="bedtools_intersectbed" name="bedtools Intersect intervals" version="@TOOL_VERSION@" profile="@PROFILE@">
     <description>find overlapping intervals in various ways</description>
-    <expand macro="bio_tools" />
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools" />
     <expand macro="requirements">
         <requirement type="package" version="@SAMTOOLS_VERSION@">samtools</requirement>
     </expand>
diff -r ed6f66aed1f9 -r 539958feb49c jaccardBed.xml
--- a/jaccardBed.xml	Thu Sep 09 13:02:16 2021 +0000
+++ b/jaccardBed.xml	Thu Nov 04 11:35:06 2021 +0000
@@ -1,9 +1,9 @@
 <tool id="bedtools_jaccard" name="bedtools JaccardBed" version="@TOOL_VERSION@" profile="@PROFILE@">
     <description>calculate the distribution of relative distances between two files</description>
-    <expand macro="bio_tools" />
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools" />
     <expand macro="requirements" />
     <expand macro="stdio" />
     <command><![CDATA[
diff -r ed6f66aed1f9 -r 539958feb49c linksBed.xml
--- a/linksBed.xml	Thu Sep 09 13:02:16 2021 +0000
+++ b/linksBed.xml	Thu Nov 04 11:35:06 2021 +0000
@@ -1,9 +1,9 @@
 <tool id="bedtools_links" name="bedtools LinksBed" version="@TOOL_VERSION@" profile="@PROFILE@">
     <description>create a HTML page of links to UCSC locations</description>
-    <expand macro="bio_tools" />
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools" />
     <expand macro="requirements" />
     <expand macro="stdio" />
     <command><![CDATA[
diff -r ed6f66aed1f9 -r 539958feb49c makeWindowsBed.xml
--- a/makeWindowsBed.xml	Thu Sep 09 13:02:16 2021 +0000
+++ b/makeWindowsBed.xml	Thu Nov 04 11:35:06 2021 +0000
@@ -1,9 +1,9 @@
 <tool id="bedtools_makewindowsbed" name="bedtools MakeWindowsBed" version="@TOOL_VERSION@" profile="@PROFILE@">
     <description>make interval windows across a genome</description>
-    <expand macro="bio_tools" />
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools" />
     <expand macro="requirements" />
     <expand macro="stdio" />
     <command><![CDATA[
diff -r ed6f66aed1f9 -r 539958feb49c mapBed.xml
--- a/mapBed.xml	Thu Sep 09 13:02:16 2021 +0000
+++ b/mapBed.xml	Thu Nov 04 11:35:06 2021 +0000
@@ -1,9 +1,9 @@
 <tool id="bedtools_map" name="bedtools MapBed" version="@TOOL_VERSION@.2" profile="@PROFILE@">
     <description>apply a function to a column for each overlapping interval</description>
-    <expand macro="bio_tools" />
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools" />
     <expand macro="requirements" />
     <expand macro="stdio" />
     <command><![CDATA[
diff -r ed6f66aed1f9 -r 539958feb49c maskFastaBed.xml
--- a/maskFastaBed.xml	Thu Sep 09 13:02:16 2021 +0000
+++ b/maskFastaBed.xml	Thu Nov 04 11:35:06 2021 +0000
@@ -1,9 +1,9 @@
 <tool id="bedtools_maskfastabed" name="bedtools MaskFastaBed" version="@TOOL_VERSION@" profile="@PROFILE@">
     <description>use intervals to mask sequences from a FASTA file</description>
-    <expand macro="bio_tools" />
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools" />
     <expand macro="requirements" />
     <expand macro="stdio" />
     <command><![CDATA[
diff -r ed6f66aed1f9 -r 539958feb49c mergeBed.xml
--- a/mergeBed.xml	Thu Sep 09 13:02:16 2021 +0000
+++ b/mergeBed.xml	Thu Nov 04 11:35:06 2021 +0000
@@ -1,9 +1,9 @@
 <tool id="bedtools_mergebed" name="bedtools MergeBED" version="@TOOL_VERSION@" profile="@PROFILE@">
     <description>combine overlapping/nearby intervals into a single interval</description>
-    <expand macro="bio_tools" />
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools" />
     <expand macro="requirements" />
     <expand macro="stdio" />
     <command><![CDATA[
diff -r ed6f66aed1f9 -r 539958feb49c multiCov.xml
--- a/multiCov.xml	Thu Sep 09 13:02:16 2021 +0000
+++ b/multiCov.xml	Thu Nov 04 11:35:06 2021 +0000
@@ -1,9 +1,9 @@
 <tool id="bedtools_multicovtbed" name="bedtools MultiCovBed" version="@TOOL_VERSION@" profile="@PROFILE@">
     <description>counts coverage from multiple BAMs at specific intervals</description>
-    <expand macro="bio_tools" />
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools" />
     <expand macro="requirements" />
     <expand macro="stdio" />
     <command><![CDATA[
diff -r ed6f66aed1f9 -r 539958feb49c multiIntersectBed.xml
--- a/multiIntersectBed.xml	Thu Sep 09 13:02:16 2021 +0000
+++ b/multiIntersectBed.xml	Thu Nov 04 11:35:06 2021 +0000
@@ -1,9 +1,9 @@
 <tool id="bedtools_multiintersectbed" name="bedtools Multiple Intersect" version="@TOOL_VERSION@" profile="@PROFILE@">
     <description>identifies common intervals among multiple interval files</description>
-    <expand macro="bio_tools" />
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools" />
     <expand macro="requirements" />
     <expand macro="stdio" />
     <command><![CDATA[
@@ -86,7 +86,7 @@
             <param name="inputs" value="multiIntersectBed1.bed,multiIntersectBed2.bed,multiIntersectBed3.bed" ftype="bed" />
             <param name="empty_selector" value="-empty" />
             <param name="genome_file_opts_selector" value="hist" />
-            <param name="genome" value="multiIntersectBed1.len" />
+            <param name="genome" value="multiIntersectBed1.len" ftype="tabular" />
             <output name="output" file="multiIntersectBed_result3.bed" ftype="bed" />
         </test>
     </tests>
diff -r ed6f66aed1f9 -r 539958feb49c nucBed.xml
--- a/nucBed.xml	Thu Sep 09 13:02:16 2021 +0000
+++ b/nucBed.xml	Thu Nov 04 11:35:06 2021 +0000
@@ -1,9 +1,9 @@
 <tool id="bedtools_nucbed" name="bedtools NucBed" version="@TOOL_VERSION@" profile="@PROFILE@">
     <description>profile the nucleotide content of intervals in a FASTA file</description>
-    <expand macro="bio_tools" />
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools" />
     <expand macro="requirements" />
     <expand macro="stdio" />
     <command><![CDATA[
diff -r ed6f66aed1f9 -r 539958feb49c overlapBed.xml
--- a/overlapBed.xml	Thu Sep 09 13:02:16 2021 +0000
+++ b/overlapBed.xml	Thu Nov 04 11:35:06 2021 +0000
@@ -1,9 +1,9 @@
 <tool id="bedtools_overlapbed" name="bedtools OverlapBed" version="@TOOL_VERSION@" profile="@PROFILE@">
     <description>computes the amount of overlap from two intervals</description>
-    <expand macro="bio_tools" />
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools" />
     <expand macro="requirements" />
     <expand macro="stdio" />
     <command><![CDATA[
diff -r ed6f66aed1f9 -r 539958feb49c randomBed.xml
--- a/randomBed.xml	Thu Sep 09 13:02:16 2021 +0000
+++ b/randomBed.xml	Thu Nov 04 11:35:06 2021 +0000
@@ -1,9 +1,9 @@
 <tool id="bedtools_randombed" name="bedtools RandomBed" version="@TOOL_VERSION@" profile="@PROFILE@">
     <description>generate random intervals in a genome</description>
-    <expand macro="bio_tools" />
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools" />
     <expand macro="requirements" />
     <expand macro="stdio" />
     <command><![CDATA[
@@ -28,7 +28,7 @@
     <tests>
         <test>
             <param name="genome_file_opts_selector" value="hist" />
-            <param name="genome" value="mm9_chr1.len" />
+            <param name="genome" value="mm9_chr1.len" ftype="tabular" />
             <param name="seed_choose" value="False" />
             <param name="length" value="5" />
             <param name="intervals" value="3" />
diff -r ed6f66aed1f9 -r 539958feb49c reldist.xml
--- a/reldist.xml	Thu Sep 09 13:02:16 2021 +0000
+++ b/reldist.xml	Thu Nov 04 11:35:06 2021 +0000
@@ -1,9 +1,9 @@
 <tool id="bedtools_reldistbed" name="bedtools ReldistBed" version="@TOOL_VERSION@" profile="@PROFILE@">
     <description>calculate the distribution of relative distances</description>
-    <expand macro="bio_tools" />
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools" />
     <expand macro="requirements" />
     <expand macro="stdio" />
     <command><![CDATA[
diff -r ed6f66aed1f9 -r 539958feb49c shuffleBed.xml
--- a/shuffleBed.xml	Thu Sep 09 13:02:16 2021 +0000
+++ b/shuffleBed.xml	Thu Nov 04 11:35:06 2021 +0000
@@ -1,9 +1,9 @@
 <tool id="bedtools_shufflebed" name="bedtools ShuffleBed" version="@TOOL_VERSION@" profile="@PROFILE@">
     <description>randomly redistrubute intervals in a genome</description>
-    <expand macro="bio_tools" />
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools" />
     <expand macro="requirements" />
     <expand macro="stdio" />
     <command><![CDATA[
diff -r ed6f66aed1f9 -r 539958feb49c slopBed.xml
--- a/slopBed.xml	Thu Sep 09 13:02:16 2021 +0000
+++ b/slopBed.xml	Thu Nov 04 11:35:06 2021 +0000
@@ -1,9 +1,9 @@
 <tool id="bedtools_slopbed" name="bedtools SlopBed" version="@TOOL_VERSION@" profile="@PROFILE@">
     <description>adjust the size of intervals</description>
-    <expand macro="bio_tools" />
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools" />
     <expand macro="requirements" />
     <expand macro="stdio" />
     <command><![CDATA[
diff -r ed6f66aed1f9 -r 539958feb49c sortBed.xml
--- a/sortBed.xml	Thu Sep 09 13:02:16 2021 +0000
+++ b/sortBed.xml	Thu Nov 04 11:35:06 2021 +0000
@@ -1,9 +1,9 @@
 <tool id="bedtools_sortbed" name="bedtools SortBED" version="@TOOL_VERSION@" profile="@PROFILE@">
     <description>order the intervals</description>
-    <expand macro="bio_tools" />
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools" />
     <expand macro="requirements" />
     <expand macro="stdio" />
     <command><![CDATA[
diff -r ed6f66aed1f9 -r 539958feb49c spacingBed.xml
--- a/spacingBed.xml	Thu Sep 09 13:02:16 2021 +0000
+++ b/spacingBed.xml	Thu Nov 04 11:35:06 2021 +0000
@@ -1,9 +1,9 @@
 <tool id="bedtools_spacingbed" name="bedtools SpacingBed" version="@TOOL_VERSION@" profile="@PROFILE@">
     <description>reports the distances between features</description>
-    <expand macro="bio_tools" />
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools" />
     <expand macro="requirements" />
     <expand macro="stdio" />
     <command><![CDATA[
diff -r ed6f66aed1f9 -r 539958feb49c subtractBed.xml
--- a/subtractBed.xml	Thu Sep 09 13:02:16 2021 +0000
+++ b/subtractBed.xml	Thu Nov 04 11:35:06 2021 +0000
@@ -1,9 +1,9 @@
 <tool id="bedtools_subtractbed" name="bedtools SubtractBed" version="@TOOL_VERSION@" profile="@PROFILE@">
     <description>remove intervals based on overlaps</description>
-    <expand macro="bio_tools" />
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools" />
     <expand macro="requirements" />
     <expand macro="stdio" />
     <command><![CDATA[
diff -r ed6f66aed1f9 -r 539958feb49c tagBed.xml
--- a/tagBed.xml	Thu Sep 09 13:02:16 2021 +0000
+++ b/tagBed.xml	Thu Nov 04 11:35:06 2021 +0000
@@ -1,9 +1,9 @@
 <tool id="bedtools_tagbed" name="bedtools TagBed" version="@TOOL_VERSION@" profile="@PROFILE@">
     <description>tag BAM alignments based on overlaps with interval files</description>
-    <expand macro="bio_tools" />
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools" />
     <expand macro="requirements" />
     <expand macro="stdio" />
     <command><![CDATA[
diff -r ed6f66aed1f9 -r 539958feb49c test-data/annotateBed4.bed
--- a/test-data/annotateBed4.bed	Thu Sep 09 13:02:16 2021 +0000
+++ b/test-data/annotateBed4.bed	Thu Nov 04 11:35:06 2021 +0000
@@ -1,4 +1,4 @@
-chr1	0	120	known1	-
-chr1	150	160	known2	-
-chr2	0	10000	known3	+
+chr1	0	120	known	1	-
+chr1	150	160	known	2	-
+chr2	0	10000	known	3	+
 
diff -r ed6f66aed1f9 -r 539958feb49c test-data/bamToBed_result3.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bamToBed_result3.bed	Thu Nov 04 11:35:06 2021 +0000
@@ -0,0 +1,2 @@
+chr1	100	200	chr5	5000	5100	bedpe_example1	255	+	-
+chr9	1000	5000	chr9	3000	3800	bedpe_example2	255	+	-
diff -r ed6f66aed1f9 -r 539958feb49c unionBedGraphs.xml
--- a/unionBedGraphs.xml	Thu Sep 09 13:02:16 2021 +0000
+++ b/unionBedGraphs.xml	Thu Nov 04 11:35:06 2021 +0000
@@ -1,9 +1,9 @@
 <tool id="bedtools_unionbedgraph" name="bedtools Merge BedGraph files" version="@TOOL_VERSION@" profile="@PROFILE@">
     <description>combines coverage intervals from multiple BEDGRAPH files</description>
-    <expand macro="bio_tools" />
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools" />
     <expand macro="requirements" />
     <expand macro="stdio" />
     <command><![CDATA[
@@ -83,26 +83,26 @@
             <param name="inputs" value="unionBedGraphs1.bg,unionBedGraphs2.bg,unionBedGraphs3.bg" ftype="bedgraph" />
             <param name="empty_selector" value="-empty" />
             <param name="genome_file_opts_selector" value="hist" />
-            <param name="genome" value="unionBedGraphs1.len" />
+            <param name="genome" value="unionBedGraphs1.len" ftype="tabular" />
             <output name="output" file="unionBedGraphs_result3.bg" ftype="bedgraph" />
         </test>
         <test>
             <param name="tag_select" value="custom" />
             <repeat name="bedgraphs">
-                <param name="input" value="unionBedGraphs1.bg" />
+                <param name="input" value="unionBedGraphs1.bg" ftype="bedgraph" />
                 <param name="custom_name" value="first" />
             </repeat>
             <repeat name="bedgraphs">
-                <param name="input" value="unionBedGraphs2.bg" />
+                <param name="input" value="unionBedGraphs2.bg" ftype="bedgraph" />
                 <param name="custom_name" value="second" />
             </repeat>
             <repeat name="bedgraphs">
-                <param name="input" value="unionBedGraphs3.bg" />
+                <param name="input" value="unionBedGraphs3.bg" ftype="bedgraph" />
                 <param name="custom_name" value="third" />
             </repeat>
             <param name="empty_selector" value="-empty" />
             <param name="genome_file_opts_selector" value="hist" />
-            <param name="genome" value="unionBedGraphs1.len" />
+            <param name="genome" value="unionBedGraphs1.len" ftype="tabular" />
             <output name="output" file="unionBedGraphs_result4.bg" ftype="bedgraph" />
         </test>
     </tests>
diff -r ed6f66aed1f9 -r 539958feb49c windowBed.xml
--- a/windowBed.xml	Thu Sep 09 13:02:16 2021 +0000
+++ b/windowBed.xml	Thu Nov 04 11:35:06 2021 +0000
@@ -1,9 +1,9 @@
 <tool id="bedtools_windowbed" name="bedtools WindowBed" version="@TOOL_VERSION@" profile="@PROFILE@">
     <description>find overlapping intervals within a window around an interval</description>
-    <expand macro="bio_tools" />
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools" />
     <expand macro="requirements" />
     <expand macro="stdio" />
     <command><![CDATA[