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changeset 59:539958feb49c draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 500a03281ea704abc7a16d9af63d67dbdcc5cd0b"
author iuc
date Thu, 04 Nov 2021 11:35:06 +0000
parents ed6f66aed1f9
children 36d57dc82aa6
files annotateBed.xml bamToBed.xml bed12ToBed6.xml bedToBam.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 makeWindowsBed.xml mapBed.xml maskFastaBed.xml mergeBed.xml multiCov.xml multiIntersectBed.xml nucBed.xml overlapBed.xml randomBed.xml reldist.xml shuffleBed.xml slopBed.xml sortBed.xml spacingBed.xml subtractBed.xml tagBed.xml test-data/annotateBed4.bed test-data/bamToBed_result3.bed unionBedGraphs.xml windowBed.xml
diffstat 39 files changed, 62 insertions(+), 54 deletions(-) [+]
line wrap: on
line diff
--- 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>
--- 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**
--- 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[
--- 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[
--- 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[
--- 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>
--- 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[
--- 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[
--- 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>
--- 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>
--- 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[
--- 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[
--- 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"/>
--- 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[
--- 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[
--- 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>
--- 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>
--- 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[
--- 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[
--- 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[
--- 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[
--- 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[
--- 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[
--- 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[
--- 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>
--- 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[
--- 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[
--- 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" />
--- 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[
--- 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[
--- 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[
--- 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[
--- 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[
--- 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[
--- 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[
--- 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	+
 
--- /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	+	-
--- 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>
--- 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[