# HG changeset patch
# User iuc
# Date 1740173914 0
# Node ID f6c88d2e9ae53d85cddda961915e9ff573a1db57
# Parent  7411007544bf90d426cf08e0021e3ddd8547e6f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 73ebd55430874a3c1483b6dd6cce0482175482f9

diff -r 7411007544bf -r f6c88d2e9ae5 annotateBed.xml
--- a/annotateBed.xml	Thu Mar 02 08:50:31 2023 +0000
+++ b/annotateBed.xml	Fri Feb 21 21:38:34 2025 +0000
@@ -65,8 +65,8 @@
     <tests>
         <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="names|names_select" value="no" />
+            <param name="names|beds" value="annotateBed2.bed,annotateBed3.bed,annotateBed4.bed"/>
             <output name="output" file="annotateBed_result.bed" ftype="bed" />
         </test>
     </tests>
diff -r 7411007544bf -r f6c88d2e9ae5 bamToBed.xml
--- a/bamToBed.xml	Thu Mar 02 08:50:31 2023 +0000
+++ b/bamToBed.xml	Fri Feb 21 21:38:34 2025 +0000
@@ -1,11 +1,11 @@
-<tool id="bedtools_bamtobed" name="bedtools BAM to BED" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@">
+<tool id="bedtools_bamtobed" name="bedtools BAM to BED" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
     <description>converter</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="bio_tools" />
     <expand macro="requirements">
-        <requirement type="package" version="@SAMTOOLS_VERSION@">samtools</requirement>
+        <requirement type="package" version="1.18">samtools</requirement>
     </expand>
     <expand macro="stdio" />
     <command><![CDATA[
diff -r 7411007544bf -r f6c88d2e9ae5 bedToBam.xml
--- a/bedToBam.xml	Thu Mar 02 08:50:31 2023 +0000
+++ b/bedToBam.xml	Fri Feb 21 21:38:34 2025 +0000
@@ -1,4 +1,4 @@
-<tool id="bedtools_bedtobam" name="bedtools BED to BAM" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
+<tool id="bedtools_bedtobam" name="bedtools BED to BAM" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
     <description>converter</description>
     <macros>
         <import>macros.xml</import>
@@ -29,8 +29,8 @@
     <tests>
         <test>
             <param name="input" value="bedToBam1.bed" ftype="bed" />
-            <param name="genome_file_opts_selector" value="hist" />
-            <param name="genome" value="mm9_chr1.len" ftype="tabular" />
+            <param name="genome_file_opts|genome_file_opts_selector" value="hist" />
+            <param name="genome_file_opts|genome" value="mm9_chr1.len" ftype="tabular" />
             <output name="output" file="bedToBam_result.bam" lines_diff="4" ftype="bam" />
         </test>
     </tests>
diff -r 7411007544bf -r f6c88d2e9ae5 bedpeToBam.xml
--- a/bedpeToBam.xml	Thu Mar 02 08:50:31 2023 +0000
+++ b/bedpeToBam.xml	Fri Feb 21 21:38:34 2025 +0000
@@ -1,4 +1,4 @@
-<tool id="bedtools_bedpetobam" name="bedtools BEDPE to BAM" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
+<tool id="bedtools_bedpetobam" name="bedtools BEDPE to BAM" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
     <description>converter</description>
     <macros>
         <import>macros.xml</import>
@@ -6,7 +6,7 @@
     <expand macro="bio_tools" />
     <!-- bedtobam broken in 2.29.0 <expand macro="requirements" /> -->
     <requirements>
-        <requirement type="package" version="2.27.1">bedtools</requirement>
+        <requirement type="package" version="2.31.1">bedtools</requirement>
     </requirements>
     <expand macro="stdio" />
     <command><![CDATA[
@@ -28,8 +28,8 @@
     <tests>
         <test>
             <param name="input" value="bedpeToBamBed1.bed" ftype="bed" />
-            <param name="genome_file_opts_selector" value="hist" />
-            <param name="genome" value="mm9.len"/>
+            <param name="genome_file_opts|genome_file_opts_selector" value="hist" />
+            <param name="genome_file_opts|genome" value="mm9.len"/>
             <output name="output" file="bedpeToBam_result1.bam" lines_diff="72" ftype="unsorted.bam" />
         </test>
     </tests>
diff -r 7411007544bf -r f6c88d2e9ae5 closestBed.xml
--- a/closestBed.xml	Thu Mar 02 08:50:31 2023 +0000
+++ b/closestBed.xml	Fri Feb 21 21:38:34 2025 +0000
@@ -1,4 +1,4 @@
-<tool id="bedtools_closestbed" name="bedtools ClosestBed" version="@TOOL_VERSION@" profile="@PROFILE@">
+<tool id="bedtools_closestbed" name="bedtools ClosestBed" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
     <description>find the closest, potentially non-overlapping interval</description>
     <macros>
         <import>macros.xml</import>
@@ -14,6 +14,8 @@
     -D $addition2.addition2_select
     $addition2.iu
     $addition2.id
+    $addition2.fu
+    $addition2.fd
 #end if
 $io
 -mdb $mdb
@@ -109,50 +111,50 @@
     <tests>
         <test>
             <param name="inputA" value="closestBedA.bed" ftype="bed" />
-            <param name="source" value="history" />
-            <param name="inputB" value="closestBedB.bed" ftype="bed" />
+            <param name="overlap_with|source" value="history" />
+            <param name="overlap_with|inputB" value="closestBedB.bed" ftype="bed" />
             <output name="output" file="closestBed_result1.bed" ftype="bed" />
         </test>
         <test>
             <param name="inputA" value="closestBed_a.bed" ftype="bed" />
-            <param name="source" value="history" />
-            <param name="inputB" value="closestBed_b1.bed,closestBed_b2.bed" ftype="bed" />
+            <param name="overlap_with|source" value="history" />
+            <param name="overlap_with|inputB" value="closestBed_b1.bed,closestBed_b2.bed" ftype="bed" />
             <param name="addition" value="true" />
             <output name="output" file="closestBed_result2.bed" ftype="bed" />
         </test>
         <test>
             <param name="inputA" value="closestBed_a.bed" ftype="bed" />
-            <param name="source" value="history" />
-            <param name="inputB" value="closestBed_b1.bed,closestBed_b2.bed" ftype="bed" />
+            <param name="overlap_with|source" value="history" />
+            <param name="overlap_with|inputB" value="closestBed_b1.bed,closestBed_b2.bed" ftype="bed" />
             <param name="addition" value="True" />
             <param name="mdb" value="all" />
             <output name="output" file="closestBed_result3.bed" ftype="bed" />
         </test>
         <test>
             <param name="inputA" value="closestBed_c.bed" ftype="bed" />
-            <param name="source" value="history" />
-            <param name="inputB" value="closestBed_d.bed" ftype="bed" />
-            <param name="addition2_select" value="ref" />
+            <param name="overlap_with|source" value="history" />
+            <param name="overlap_with|inputB" value="closestBed_d.bed" ftype="bed" />
+            <param name="addition2|addition2_select" value="ref" />
             <output name="output" file="closestBed_result4.bed" ftype="bed" />
         </test>
         <test>
             <param name="inputA" value="closestBed_c.bed" ftype="bed" />
-            <param name="source" value="history" />
-            <param name="inputB" value="closestBed_d.bed" ftype="bed" />
-            <param name="addition2_select" value="a" />
+            <param name="overlap_with|source" value="history" />
+            <param name="overlap_with|inputB" value="closestBed_d.bed" ftype="bed" />
+            <param name="addition2|addition2_select" value="a" />
             <output name="output" file="closestBed_result5.bed" ftype="bed" />
         </test>
         <test>
             <param name="inputA" value="closestBedA.bed" ftype="bed" />
-            <param name="source" value="history" />
-            <param name="inputB" value="a.bed" ftype="bed" />
+            <param name="overlap_with|source" value="history" />
+            <param name="overlap_with|inputB" value="a.bed" ftype="bed" />
             <param name="k" value="3" />
             <output name="output" file="closestBed_result6.bed" ftype="bed" />
         </test>
         <test>
             <param name="inputA" value="closestBedA.bed" ftype="bed" />
-            <param name="source" value="data_table" />
-            <param name="inputB" value="testid" />
+            <param name="overlap_with|source" value="data_table" />
+            <param name="overlap_with|table" value="testid" />
             <param name="k" value="3" />
             <output name="output" file="closestBed_result6.bed" ftype="bed" />
         </test>
diff -r 7411007544bf -r f6c88d2e9ae5 complementBed.xml
--- a/complementBed.xml	Thu Mar 02 08:50:31 2023 +0000
+++ b/complementBed.xml	Fri Feb 21 21:38:34 2025 +0000
@@ -1,11 +1,11 @@
-<tool id="bedtools_complementbed" name="bedtools ComplementBed" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
+<tool id="bedtools_complementbed" name="bedtools ComplementBed" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
     <description>Extract intervals not represented by an interval file</description>
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="bio_tools" />
-    <expand macro="requirements" />
-    <expand macro="stdio" />
+    <expand macro="bio_tools"/>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
     <command><![CDATA[
 complementBed
 -i '$input'
@@ -14,17 +14,17 @@
     ]]></command>
     <inputs>
         <param name="input" argument="-i" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
-        <expand macro="input_conditional_genome_file" />
+        <expand macro="input_conditional_genome_file"/>
     </inputs>
     <outputs>
         <data name="output" format_source="input" metadata_source="input" label="Complement of ${input.name}"/>
     </outputs>
     <tests>
         <test>
-            <param name="input" value="a.bed" ftype="bed" />
-            <param name="genome_file_opts_selector" value="hist" />
-            <param name="genome" value="mm9_chr1.len" ftype="tabular" />
-            <output name="output" file="complementBed_result1.bed" ftype="bed" />
+            <param name="input" value="a.bed" ftype="bed"/>
+            <param name="genome_file_opts|genome_file_opts_selector" value="hist"/>
+            <param name="genome_file_opts|genome" value="mm9_chr1.len" ftype="tabular"/>
+            <output name="output" file="complementBed_result1.bed" ftype="bed"/>
         </test>
     </tests>
     <help><![CDATA[
@@ -36,5 +36,5 @@
 
 @REFERENCES@
     ]]></help>
-    <expand macro="citations" />
+    <expand macro="citations"/>
 </tool>
diff -r 7411007544bf -r f6c88d2e9ae5 coverageBed.xml
--- a/coverageBed.xml	Thu Mar 02 08:50:31 2023 +0000
+++ b/coverageBed.xml	Fri Feb 21 21:38:34 2025 +0000
@@ -1,13 +1,13 @@
-<tool id="bedtools_coveragebed" name="bedtools Compute both the depth and breadth of coverage" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
+<tool id="bedtools_coveragebed" name="bedtools Compute both the depth and breadth of coverage" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
     <description>of features in file B on the features in file A (bedtools coverage)</description>
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="bio_tools" />
+    <expand macro="bio_tools"/>
     <expand macro="requirements">
-        <requirement type="package" version="@SAMTOOLS_VERSION@">samtools</requirement>
+        <requirement type="package" version="1.18">samtools</requirement>
     </expand>
-    <expand macro="stdio" />
+    <expand macro="stdio"/>
     <command><![CDATA[
 bedtools coverage
 $d
@@ -41,95 +41,83 @@
 > '$output'
     ]]></command>
     <inputs>
-        <param name="inputA" argument="-a" type="data" format="bam,@STD_BEDTOOLS_INPUTS@" label="File A (on which coverage is calculated)" help="BAM/@STD_BEDTOOLS_INPUT_LABEL@ format" />
+        <param name="inputA" argument="-a" type="data" format="bam,@STD_BEDTOOLS_INPUTS@" 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 name="inputB" argument="-b" type="data" format="bam,@STD_BEDTOOLS_INPUTS@"
-                       label="File B (for which coverage is calculated)" help="BAM/@STD_BEDTOOLS_INPUT_LABEL@ format"/>
+                <param name="inputB" argument="-b" type="data" format="bam,@STD_BEDTOOLS_INPUTS@" label="File B (for which coverage is calculated)" help="BAM/@STD_BEDTOOLS_INPUT_LABEL@ format"/>
             </when>
             <when value="reduce">
-                <param name="inputB" argument="-b" type="data" format="bam,@STD_BEDTOOLS_INPUTS@" multiple="true"
-                       label="File(s) B (for which coverage is calculated)" help="BAM/@STD_BEDTOOLS_INPUT_LABEL@ format"/>
+                <param name="inputB" argument="-b" type="data" format="bam,@STD_BEDTOOLS_INPUTS@" label="File(s) B (for which coverage is calculated)" help="BAM/@STD_BEDTOOLS_INPUT_LABEL@ format" multiple="true"/>
             </when>
         </conditional>
-        <expand macro="split" />
-        <param name="strandedness" argument="-s" type="boolean" label="Force strandedness" truevalue="-s" falsevalue="" checked="false"
-            help="Only report hits in B that overlap A on the same strand. By default, overlaps are reported without respect to strand"/>
-        <param argument="-d" type="boolean" truevalue="-d" falsevalue="" checked="false"
-            label="Report the depth at each position in each A feature"
-            help="Positions reported are one based. Each position and depth follow the complete B feature" />
-        <param argument="-hist" type="boolean" truevalue="-hist" falsevalue="" checked="false"
-            label="Report a histogram of coverage for each feature in A as well as a summary histogram for all features in A"
-            help="Additional columns after each feature in A: 1) depth 2) # bases at depth 3) size of A 4) % of A at depth" />
-        <param name="mean" argument="-mean" type="boolean" label="Mean depth" truevalue="-mean" falsevalue="" checked="false"
-            help="Report the mean depth of all positions in each A feature."/>
-        <expand macro="overlap" name="overlap_a" />
-        <expand macro="overlap" name="overlap_b" argument="-F" fracof="B" />
-        <param name="reciprocal_overlap" argument="-r" type="boolean" truevalue="-r" falsevalue="" checked="false"
-            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" />
-        <param name="a_or_b" argument="-e" type="boolean" truevalue="-e" falsevalue="" checked="false"
-            label="Require that the minimum fraction be satisfied for A OR B."
-            help="If -e is used with -f 0.90 and -F 0.10 this requires that either 90% of A is covered OR 10% of  B is covered. Without -e, both fractions would have to be satisfied" />
+        <expand macro="split"/>
+        <param name="strandedness" argument="-s" type="boolean" truevalue="-s" falsevalue="" checked="false" label="Force strandedness" help="Only report hits in B that overlap A on the same strand. By default, overlaps are reported without respect to strand"/>
+        <param argument="-d" type="boolean" truevalue="-d" falsevalue="" checked="false" label="Report the depth at each position in each A feature" help="Positions reported are one based. Each position and depth follow the complete B feature"/>
+        <param argument="-hist" type="boolean" truevalue="-hist" falsevalue="" checked="false" label="Report a histogram of coverage for each feature in A as well as a summary histogram for all features in A" help="Additional columns after each feature in A: 1) depth 2) # bases at depth 3) size of A 4) % of A at depth"/>
+        <param argument="-mean" type="boolean" truevalue="-mean" falsevalue="" checked="false" label="Mean depth" help="Report the mean depth of all positions in each A feature."/>
+        <expand macro="overlap" name="overlap_a"/>
+        <expand macro="overlap" name="overlap_b" argument="-F" fracof="B"/>
+        <param name="reciprocal_overlap" argument="-r" type="boolean" truevalue="-r" falsevalue="" checked="false" 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"/>
+        <param name="a_or_b" argument="-e" type="boolean" truevalue="-e" falsevalue="" checked="false" label="Require that the minimum fraction be satisfied for A OR B." help="If -e is used with -f 0.90 and -F 0.10 this requires that either 90% of A is covered OR 10% of  B is covered. Without -e, both fractions would have to be satisfied"/>
         <!-- -sorted -g  -->
-        <expand macro="sorted" />
+        <expand macro="sorted"/>
     </inputs>
     <outputs>
         <data name="output" format="bed" metadata_source="inputA" label="Count of overlaps on ${inputA.name}"/>
     </outputs>
     <tests>
         <test>
-            <param name="inputA" value="coverageBedA.bed" ftype="bed" />
-            <param name="inputB" value="coverageBedB.bed" ftype="bed" />
-            <output name="output" file="coverageBed_result1.bed" ftype="bed" />
+            <param name="inputA" value="coverageBedA.bed" ftype="bed"/>
+            <param name="reduce_or_iterate|inputB" value="coverageBedB.bed" ftype="bed"/>
+            <output name="output" file="coverageBed_result1.bed" ftype="bed"/>
         </test>
         <test>
-            <param name="inputA" value="multiCov1.bed" ftype="bed" />
-            <param name="inputB" value="srma_in3.bam" ftype="bam" />
+            <param name="inputA" value="multiCov1.bed" ftype="bed"/>
+            <param name="reduce_or_iterate|inputB" value="srma_in3.bam" ftype="bam"/>
             <param name="sorted" value="true"/>
-            <output name="output" file="multicov1_by_srma_in3.cov.bed" ftype="bed" />
+            <output name="output" file="multicov1_by_srma_in3.cov.bed" ftype="bed"/>
         </test>
         <test>
-            <param name="inputA" value="multiCov1.bed" ftype="bed" />
-            <param name="reduce_or_iterate_selector" value="reduce" />
-            <param name="inputB" value="srma_in3.bam" ftype="bam" />
+            <param name="inputA" value="multiCov1.bed" ftype="bed"/>
+            <param name="reduce_or_iterate|reduce_or_iterate_selector" value="reduce"/>
+            <param name="reduce_or_iterate|inputB" value="srma_in3.bam" ftype="bam"/>
             <param name="sorted" value="true"/>
-            <output name="output" file="multicov1_by_srma_in3.cov.bed" ftype="bed" />
+            <output name="output" file="multicov1_by_srma_in3.cov.bed" ftype="bed"/>
         </test>
         <test>
-            <param name="inputA" value="coverageBedA.bed" ftype="bed" />
-            <param name="inputB" value="coverageBedB.bed" ftype="bed" />
-            <param name="overlap_b" value="1"  />
-            <output name="output" file="coverageBed_result2_F1.bed" ftype="bed" />
+            <param name="inputA" value="coverageBedA.bed" ftype="bed"/>
+            <param name="reduce_or_iterate|inputB" value="coverageBedB.bed" ftype="bed"/>
+            <param name="overlap_b" value="1"/>
+            <output name="output" file="coverageBed_result2_F1.bed" ftype="bed"/>
         </test>
         <test>
-            <param name="inputA" value="coverageBedA.bed" ftype="bed" />
-            <param name="inputB" value="coverageBedB.bed" ftype="bed" />
-            <param name="overlap_a" value="1E-5"  />
-            <param name="reciprocal_overlap" value="true"  />
-            <output name="output" file="coverageBed_result3_f1r.bed" ftype="bed" />
+            <param name="inputA" value="coverageBedA.bed" ftype="bed"/>
+            <param name="reduce_or_iterate|inputB" value="coverageBedB.bed" ftype="bed"/>
+            <param name="overlap_a" value="1E-5"/>
+            <param name="reciprocal_overlap" value="true"/>
+            <output name="output" file="coverageBed_result3_f1r.bed" ftype="bed"/>
         </test>
         <test>
-            <param name="inputA" value="multiCov1.bed" ftype="bed" />
-            <param name="reduce_or_iterate_selector" value="reduce" />
-            <param name="inputB" value="srma_in3.bam,coverageBed.bam" ftype="bam" />
+            <param name="inputA" value="multiCov1.bed" ftype="bed"/>
+            <param name="reduce_or_iterate|reduce_or_iterate_selector" value="reduce"/>
+            <param name="reduce_or_iterate|inputB" value="srma_in3.bam,coverageBed.bam" ftype="bam"/>
             <param name="sorted" value="true"/>
-            <output name="output" file="coverageBed_result4_2bam.bed" ftype="bed" />
+            <output name="output" file="coverageBed_result4_2bam.bed" ftype="bed"/>
         </test>
         <test>
-            <param name="inputA" value="coverageBedA2.bed" ftype="bed" />
-            <param name="inputB" value="coverageBed.bam" ftype="bam" />
-            <output name="output" file="coverageBed_result5_unsorted.bed" ftype="bed" />
+            <param name="inputA" value="coverageBedA2.bed" ftype="bed"/>
+            <param name="reduce_or_iterate|inputB" value="coverageBed.bam" ftype="bam"/>
+            <output name="output" file="coverageBed_result5_unsorted.bed" ftype="bed"/>
         </test>
         <test>
-            <param name="inputA" value="coverageBedA2.bed" ftype="bed" />
-            <param name="inputB" value="coverageBed.bam" ftype="bam" />
+            <param name="inputA" value="coverageBedA2.bed" ftype="bed"/>
+            <param name="reduce_or_iterate|inputB" value="coverageBed.bam" ftype="bam"/>
             <param name="mean" value="true"/>
-            <output name="output" file="mean_coverage.bed" ftype="bed" />
+            <output name="output" file="mean_coverage.bed" ftype="bed"/>
         </test>
     </tests>
     <help><![CDATA[
@@ -155,5 +143,5 @@
 
 @REFERENCES@
     ]]></help>
-    <expand macro="citations" />
+    <expand macro="citations"/>
 </tool>
diff -r 7411007544bf -r f6c88d2e9ae5 fisherBed.xml
--- a/fisherBed.xml	Thu Mar 02 08:50:31 2023 +0000
+++ b/fisherBed.xml	Fri Feb 21 21:38:34 2025 +0000
@@ -1,4 +1,4 @@
-<tool id="bedtools_fisher" name="bedtools FisherBed" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
+<tool id="bedtools_fisher" name="bedtools FisherBed" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
     <description>calculate Fisher statistic between two feature files</description>
     <macros>
         <import>macros.xml</import>
@@ -36,8 +36,8 @@
         <test>
             <param name="inputA" value="fisherBed1.bed" ftype="bed" />
             <param name="inputB" value="fisherBed2.bed" ftype="bed" />
-            <param name="genome_file_opts_selector" value="hist" />
-            <param name="genome" value="fisherBed.len" ftype="tabular" />
+            <param name="genome_file_opts|genome_file_opts_selector" value="hist" />
+            <param name="genome_file_opts|genome" value="fisherBed.len" ftype="tabular" />
             <output name="output" file="fisherBed_result1.bed" ftype="bed" />
         </test>
     </tests>
diff -r 7411007544bf -r f6c88d2e9ae5 flankBed.xml
--- a/flankBed.xml	Thu Mar 02 08:50:31 2023 +0000
+++ b/flankBed.xml	Fri Feb 21 21:38:34 2025 +0000
@@ -1,4 +1,4 @@
-<tool id="bedtools_flankbed" name="bedtools FlankBed" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
+<tool id="bedtools_flankbed" name="bedtools FlankBed" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
     <description>create new intervals from the flanks of existing intervals</description>
     <macros>
         <import>macros.xml</import>
@@ -38,19 +38,19 @@
     <tests>
         <test>
             <param name="input" value="a.bed" ftype="bed" />
-            <param name="genome_file_opts_selector" value="hist" />
-            <param name="genome" value="mm9_chr1.len" ftype="tabular"/>
-            <param name="addition_select" value="b"/>
-            <param name="b" value="5"/>
+            <param name="genome_file_opts|genome_file_opts_selector" value="hist" />
+            <param name="genome_file_opts|genome" value="mm9_chr1.len" ftype="tabular"/>
+            <param name="addition|addition_select" value="b"/>
+            <param name="addition|b" value="5"/>
             <output name="output" file="flankBed_result1.bed" ftype="bed" />
         </test>
         <test>
             <param name="input" value="a.bed" ftype="bed" />
-            <param name="genome_file_opts_selector" value="hist" />
-            <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"/>
+            <param name="genome_file_opts|genome_file_opts_selector" value="hist" />
+            <param name="genome_file_opts|genome" value="mm9_chr1.len" ftype="tabular"/>
+            <param name="addition|addition_select" value="lr"/>
+            <param name="addition|l" value="2"/>
+            <param name="addition|r" value="3"/>
             <output name="output" file="flankBed_result2.bed" ftype="bed" />
         </test>
     </tests>
diff -r 7411007544bf -r f6c88d2e9ae5 genomeCoverageBed.xml
--- a/genomeCoverageBed.xml	Thu Mar 02 08:50:31 2023 +0000
+++ b/genomeCoverageBed.xml	Fri Feb 21 21:38:34 2025 +0000
@@ -90,11 +90,11 @@
     </outputs>
     <tests>
         <test>
-            <param name="input_type_select" value="bed" />
-            <param name="input" value="genomeCoverageBed1.bed" ftype="bed" />
-            <param name="genome_file_opts_selector" value="hist" />
-            <param name="genome" value="genomeCoverageBed1.len" ftype="tabular" />
-            <param name="report_select" value="hist" />
+            <param name="input_type|input_type_select" value="bed" />
+            <param name="input_type|input" value="genomeCoverageBed1.bed" ftype="bed" />
+            <param name="input_type|genome_file_opts|genome_file_opts_selector" value="hist" />
+            <param name="input_type|genome_file_opts|genome" value="genomeCoverageBed1.len" ftype="tabular" />
+            <param name="report|report_select" value="hist" />
             <output name="output" file="genomeCoverageBed_result1.bed" ftype="tabular" />
         </test>
     </tests>
diff -r 7411007544bf -r f6c88d2e9ae5 getfastaBed.xml
--- a/getfastaBed.xml	Thu Mar 02 08:50:31 2023 +0000
+++ b/getfastaBed.xml	Fri Feb 21 21:38:34 2025 +0000
@@ -1,4 +1,4 @@
-<tool id="bedtools_getfastabed" name="bedtools getfasta" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
+<tool id="bedtools_getfastabed" name="bedtools getfasta" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
     <description>use intervals to extract sequences from a FASTA file</description>
     <macros>
         <import>macros.xml</import>
@@ -61,7 +61,7 @@
     <tests>
         <test>
             <param name="input" value="nucBed1.bed" ftype="bed" />
-            <param name="fasta" value="nucBed1.fasta" ftype="fasta" />
+            <param name="fasta_source|fasta" value="nucBed1.fasta" ftype="fasta" />
             <param name="tab" value="False" />
             <param name="split" value="False" />
             <param name="nameOnly" value="False" />
@@ -69,7 +69,7 @@
         </test>
         <test>
             <param name="input" value="nucBed1.bed" ftype="bed" />
-            <param name="fasta" value="nucBed1.fasta" ftype="fasta" />
+            <param name="fasta_source|fasta" value="nucBed1.fasta" ftype="fasta" />
             <param name="tab" value="True" />
             <param name="split" value="False" />
             <param name="nameOnly" value="False" />
@@ -77,7 +77,7 @@
         </test>
         <test>
             <param name="input" value="nucBed1.bed" ftype="bed" />
-            <param name="fasta" value="nucBed1.fasta" ftype="fasta" />
+            <param name="fasta_source|fasta" value="nucBed1.fasta" ftype="fasta" />
             <param name="tab" value="False" />
             <param name="split" value="False" />
             <param name="name" value="True" />
@@ -85,7 +85,7 @@
         </test>
         <test>
             <param name="input" value="nucBed2.bed" ftype="bed" />
-            <param name="fasta" value="nucBed1.fasta" ftype="fasta" />
+            <param name="fasta_source|fasta" value="nucBed1.fasta" ftype="fasta" />
             <param name="tab" value="False" />
             <param name="split" value="False" />
             <param name="nameOnly" value="True" />
@@ -93,8 +93,8 @@
         </test>
         <test>
             <param name="input" value="nucBed2.bed" ftype="bed" />
-            <param name="fasta_source_selector" value="preloaded"/>
-            <param name="fasta_id" value="testid" />
+            <param name="fasta_source|fasta_source_selector" value="preloaded"/>
+            <param name="fasta_source|fasta_id" value="testid" />
             <param name="tab" value="False" />
             <param name="split" value="False" />
             <param name="nameOnly" value="True" />
diff -r 7411007544bf -r f6c88d2e9ae5 groupbyBed.xml
--- a/groupbyBed.xml	Thu Mar 02 08:50:31 2023 +0000
+++ b/groupbyBed.xml	Fri Feb 21 21:38:34 2025 +0000
@@ -1,4 +1,4 @@
-<tool id="bedtools_groupbybed" name="bedtools GroupByBed" version="@TOOL_VERSION@" profile="@PROFILE@">
+<tool id="bedtools_groupbybed" name="bedtools GroupByBed" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
     <description>group by common cols and summarize other cols</description>
     <macros>
         <import>macros.xml</import>
@@ -25,13 +25,8 @@
             </sanitizer>
         </param>
         <param name="operation" argument="-o" type="select" label="Specify the operation">
-            <!-- <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>
             <option value="freqdesc">Freqdesc - comma separated list of values observed and the number of times they were observed (descending)</option>
-            <option value="first">First - numeric or text</option>
-            <option value="last">Last - numeric or text</option>
             <expand macro="math_options" />
             <expand macro="additional_math_options" />
         </param>
diff -r 7411007544bf -r f6c88d2e9ae5 intersectBed.xml
--- a/intersectBed.xml	Thu Mar 02 08:50:31 2023 +0000
+++ b/intersectBed.xml	Fri Feb 21 21:38:34 2025 +0000
@@ -1,11 +1,11 @@
-<tool id="bedtools_intersectbed" name="bedtools Intersect intervals" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
+<tool id="bedtools_intersectbed" name="bedtools Intersect intervals" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
     <description>find overlapping intervals in various ways</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="bio_tools" />
     <expand macro="requirements">
-        <requirement type="package" version="@SAMTOOLS_VERSION@">samtools</requirement>
+        <requirement type="package" version="1.18">samtools</requirement>
     </expand>
     <expand macro="stdio" />
     <command><![CDATA[
@@ -93,13 +93,13 @@
                 <expand macro="overlap" />
                 <conditional name="reciprocal_cond">
                     <expand macro="reciprocal" />
-                <when value="-r"/>
-                <when value="">
-                    <expand macro="overlap" name="overlapB" argument="-F" fracof="B"/>
-                    <param name="disjoint" argument="-e" type="boolean" truevalue="-e"  falsevalue="" checked="false"
-                        label="Require that the fraction of overlap is fulfilled for A OR B." help="If enabled, then for -f 0.90 and -F 0.10 this requires that either 90% of A is covered OR 10% of B is covered, otherwise, both fractions would have to be satisfied."/>
-                </when>
-            </conditional>
+                    <when value="-r"/>
+                    <when value="">
+                        <expand macro="overlap" name="overlapB" argument="-F" fracof="B"/>
+                        <param name="disjoint" argument="-e" type="boolean" truevalue="-e"  falsevalue="" checked="false"
+                            label="Require that the fraction of overlap is fulfilled for A OR B." help="If enabled, then for -f 0.90 and -F 0.10 this requires that either 90% of A is covered OR 10% of B is covered, otherwise, both fractions would have to be satisfied."/>
+                    </when>
+                </conditional>
             </when>
         </conditional>
         <!-- -v -->
@@ -157,7 +157,6 @@
             <output name="output" file="intersect-multiple-wa-wb.bed" ftype="bed" />
         </test>
         <test>
-            <param name="inputB" value="intersect-d1.bed,intersect-d2.bed,intersect-d3.bed" ftype="bed" />
             <param name="inputA" value="intersect-query.bed" ftype="bed" />
             <conditional name="reduce_or_iterate">
                 <param name="reduce_or_iterate_selector" value="reduce" />
@@ -174,7 +173,7 @@
                 <param name="reduce_or_iterate_selector" value="reduce" />
                 <param name="inputB" value="intersect-d1.bed,intersect-d2.bed,intersect-d3.bed" ftype="bed" />
             </conditional>
-            <param name="invert" value="-v" />
+            <param name="invert" value="true" />
             <param name="sorted" value="true" />
             <output name="output" file="intersect-multiple-invert.bed" ftype="bed" />
         </test>
@@ -252,7 +251,7 @@
                 <param name="reduce_or_iterate_selector" value="iterate" />
                 <param name="inputB" value="intersect-B.bed" ftype="bed" />
             </conditional>
-            <param name="once" value="-u" />
+            <param name="once" value="true" />
             <output name="output" file="intersect-unique.bed" ftype="bed" />
         </test>
         <test>
@@ -261,7 +260,7 @@
                 <param name="reduce_or_iterate_selector" value="iterate" />
                 <param name="inputB" value="intersect-B.bed" ftype="bed" />
             </conditional>
-            <param name="count" value="-c"/>
+            <param name="count" value="true"/>
             <output name="output" file="intersect-count.bed" ftype="bed" />
         </test>
         <test>
@@ -270,7 +269,7 @@
                 <param name="reduce_or_iterate_selector" value="iterate" />
                 <param name="inputB" value="intersect-B.bed" ftype="bed" />
             </conditional>
-            <param name="invert" value="-v"/>
+            <param name="invert" value="true"/>
             <output name="output" file="intersect-invert.bed" ftype="bed" />
         </test>
         <test>
@@ -330,7 +329,7 @@
                 <param name="overlap" value="0.5" />
                 <conditional name="reciprocal_cond">
                     <param name="overlapB" value="0.5" />
-                    <param name="disjoint" value="-e" />
+                    <param name="disjoint" value="true" />
                 </conditional>
             </conditional>
             <output name="output" file="intersect-fracA.bed" ftype="bed" />
@@ -338,21 +337,27 @@
         <!-- old tests -->
         <test>
             <param name="inputA" value="intersectBed1.bed" ftype="bed" />
-            <param name="inputB" value="intersectBed2.bed" ftype="bed" />
+            <conditional name="reduce_or_iterate">
+                <param name="inputB" value="intersectBed2.bed" ftype="bed" />
+            </conditional>
             <param name="overlap_mode" value="-wa" />
             <param name="split" value="False" />
             <output name="output" file="intersectBed_result1.bed" ftype="bed" />
         </test>
         <test>
             <param name="inputA" value="intersectBed1.bed" ftype="bed" />
-            <param name="inputB" value="intersectBed2.bed" ftype="bed" />
+            <conditional name="reduce_or_iterate">
+                <param name="inputB" value="intersectBed2.bed" ftype="bed" />
+            </conditional>
             <param name="overlap_mode" value="-wa,-wb" />
             <param name="split" value="False" />
             <output name="output" file="intersectBed_result2.bed" ftype="bed" />
         </test>
         <test>
             <param name="inputA" value="intersectBed1.bed" ftype="bed" />
-            <param name="inputB" value="intersectBed2.bed" ftype="bed" />
+            <conditional name="reduce_or_iterate">
+                <param name="inputB" value="intersectBed2.bed" ftype="bed" />
+            </conditional>
             <param name="invert" value="True" />
             <param name="split" value="False" />
             <output name="output" file="intersectBed_result3.bed" ftype="bed" />
diff -r 7411007544bf -r f6c88d2e9ae5 jaccardBed.xml
--- a/jaccardBed.xml	Thu Mar 02 08:50:31 2023 +0000
+++ b/jaccardBed.xml	Fri Feb 21 21:38:34 2025 +0000
@@ -3,9 +3,9 @@
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="bio_tools" />
-    <expand macro="requirements" />
-    <expand macro="stdio" />
+    <expand macro="bio_tools"/>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
     <command><![CDATA[
 bedtools jaccard
 $strand
@@ -22,29 +22,33 @@
     <inputs>
         <param name="inputA" argument="-a" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
         <param name="inputB" argument="-b" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
-        <expand macro="overlap" />
+        <expand macro="overlap"/>
         <expand macro="overlap" name="overlapB" argument="-F" fracof="B"/>
-        <expand macro="reciprocal" />
-        <param name="strand" argument="-s" type="boolean" truevalue="-s" falsevalue="" checked="false"
-            label="Force strandedness"
-            help="That is, only report hits in B that overlap A on the same strand. By default, overlaps are reported without respect to strand." />
-        <expand macro="strand2" />
-        <expand macro="split" />
+        <expand macro="reciprocal"/>
+        <param name="strand" argument="-s" type="boolean" truevalue="-s" falsevalue="" checked="false" label="Force strandedness" help="That is, only report hits in B that overlap A on the same strand. By default, overlaps are reported without respect to strand."/>
+        <expand macro="split"/>
     </inputs>
     <outputs>
-        <data name="output" format_source="inputA" metadata_source="inputA" label="Intersection of ${inputA.name} and ${inputB.name}" />
+        <data name="output" format_source="inputA" metadata_source="inputA" label="Intersection of ${inputA.name} and ${inputB.name}"/>
     </outputs>
     <tests>
         <test>
-            <param name="inputA" value="jaccardBed1.bed" ftype="bed" />
-            <param name="inputB" value="jaccardBed2.bed" ftype="bed" />
-            <output name="output" file="jaccardBed_result1.bed" ftype="bed" />
+            <param name="inputA" value="jaccardBed1.bed" ftype="bed"/>
+            <param name="inputB" value="jaccardBed2.bed" ftype="bed"/>
+            <output name="output" file="jaccardBed_result1.bed" ftype="bed"/>
         </test>
         <test>
-            <param name="inputA" value="jaccardBed1.bed" ftype="bed" />
-            <param name="inputB" value="jaccardBed2.bed" ftype="bed" />
-            <param name="overlap" value="0.1" />
-            <output name="output" file="jaccardBed_result2.bed" ftype="bed" />
+            <param name="inputA" value="jaccardBed1.bed" ftype="bed"/>
+            <param name="inputB" value="jaccardBed2.bed" ftype="bed"/>
+            <param name="overlap" value="0.1"/>
+            <output name="output" file="jaccardBed_result2.bed" ftype="bed"/>
+        </test>
+        <test>
+            <param name="inputA" value="jaccardBed1.bed" ftype="bed"/>
+            <param name="inputB" value="jaccardBed2.bed" ftype="bed"/>
+            <param name="overlap" value="0.1"/>
+            <param name="strand" value="true"/>
+            <output name="output" file="jaccardBed_strand_result2.bed" ftype="bed"/>
         </test>
     </tests>
     <help><![CDATA[
@@ -61,5 +65,5 @@
 
 @REFERENCES@
     ]]></help>
-    <expand macro="citations" />
+    <expand macro="citations"/>
 </tool>
diff -r 7411007544bf -r f6c88d2e9ae5 macros.xml
--- a/macros.xml	Thu Mar 02 08:50:31 2023 +0000
+++ b/macros.xml	Fri Feb 21 21:38:34 2025 +0000
@@ -10,7 +10,7 @@
             <xref type="bio.tools">bedtools</xref>
         </xrefs>
     </xml>
-    <token name="@TOOL_VERSION@">2.30.0</token>
+    <token name="@TOOL_VERSION@">2.31.1</token>
     <token name="@SAMTOOLS_VERSION@">1.9</token>
     <token name="@STD_BEDTOOLS_INPUTS@">bed,bedgraph,gff,vcf,encodepeak</token>
     <token name="@STD_BEDTOOLS_INPUT_LABEL@">BED/bedGraph/GFF/VCF/EncodePeak</token>
@@ -51,16 +51,7 @@
         </param>
     </xml>
     <xml name="seed">
-        <conditional name="seed">
-            <param name="seed_choose" type="select" label="Choose Seed?">
-                <option value="False" selected="true">Random Shuffling</option>
-                <option value="True">Choose fixed seed</option>
-            </param>
-            <when value="True">
-                <param argument="-seed" type="integer" value="12345" label="Enter Seed" />
-            </when>
-            <when value="False" />
-        </conditional>
+        <param argument="-seed" type="integer" value="" min="0" optional="true" label="Seed" help="For reproducible 'randomness'"/>
     </xml>
     <xml name="split">
         <param argument="-split" type="boolean" truevalue="-split" falsevalue="" checked="false"
@@ -215,13 +206,19 @@
         <option value="median">Median - numeric only</option>
         <option value="mode">Mode - numeric only</option>
         <option value="antimode">Antimode - numeric only</option>
+        <option value="stdev">Standard deviation - numeric only</option>
+        <option value="sstdev">Sample standard deviation - numeric only</option>
         <option value="collapse">collapse (i.e., print a comma separated list) - numeric or text</option>
     </xml>
     <xml name="additional_math_options">
         <option value="count">Count - numeric or text</option>
         <option value="count_disctinct">Count Distinct - numeric or text</option>
         <option value="distinct">distinct (i.e., print a comma separated list) - numeric or text</option>
-        <option value="concat">concat (i.e., print a comma separated list) - numeric or text</option>
+        <option value="distinct_sort_num">distinct sorted numerially (i.e., print a comma separated list) - numeric</option>
+        <option value="distinct_sort_num_desc">distinct sorted numerially descending (i.e., print a comma separated list) - numeric</option>
+        <option value="distinct_only">delimited list of only unique values - numeric or text</option>
+        <option value="first">just the first value in the column - numeric or text</option>
+        <option value="last">just the last value in the column - numeric or text</option>
     </xml>
     <xml name="sorted">
         <!-- -sorted -g  -->
diff -r 7411007544bf -r f6c88d2e9ae5 makeWindowsBed.xml
--- a/makeWindowsBed.xml	Thu Mar 02 08:50:31 2023 +0000
+++ b/makeWindowsBed.xml	Fri Feb 21 21:38:34 2025 +0000
@@ -1,4 +1,4 @@
-<tool id="bedtools_makewindowsbed" name="bedtools MakeWindowsBed" version="@TOOL_VERSION@" profile="@PROFILE@">
+<tool id="bedtools_makewindowsbed" name="bedtools MakeWindowsBed" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
     <description>make interval windows across a genome</description>
     <macros>
         <import>macros.xml</import>
@@ -15,8 +15,8 @@
 #end if
 #if $action.action_select == 'windowsize':
     -w $action.windowsize
-    #if $action.step_size.step_size_select == 'yes':
-        -s $action.step_size.step_size
+    #if $action.step_size != '':
+        -s $action.step_size
     #end if
 #else:
     -n $action.number
@@ -46,18 +46,7 @@
                 <param name="windowsize" argument="-w" type="integer" value="1"
                     label="Divide each input interval (either a chromosome or a BED interval) to fixed-sized windows"
                     help="i.e. same number of nucleotide in each window" />
-                 <conditional name="step_size">
-                    <param name="step_size_select" type="select"
-                        label="Specify Step size? i.e. how many base pairs to step before creating a new window"
-                        help="Used to create 'sliding' windows. Defaults to window size (non-sliding windows).">
-                        <option value="yes">Yes</option>
-                        <option value="no" selected="true">No</option>
-                    </param>
-                    <when value="yes">
-                        <param name="step_size" argument="-s" type="integer" value="100" label="Specify it" />
-                    </when>
-                    <when value="no" />
-                 </conditional>
+                <param name="step_size" argument="-s" type="integer" value="" optional="true" label="Step size" help="How many base pairs to step before creating a new window. Used to create 'sliding' windows. Defaults to window size (non-sliding windows)."/>
             </when>
             <when value="number">
                 <param name="number" argument="-n" type="integer" value="1"
@@ -77,36 +66,35 @@
     </outputs>
     <tests>
         <test>
-            <param name="type_select" value="genome" />
-            <param name="genome_file_opts_selector" value="hist" />
-            <param name="genome" value="mm9_chr1.len" ftype="tabular" />
-            <param name="action_select" value="windowsize" />
-            <param name="windowsize" value="1000000" />
+            <param name="type|type_select" value="genome" />
+            <param name="type|genome_file_opts|genome_file_opts_selector" value="hist" />
+            <param name="type|genome_file_opts|genome" value="mm9_chr1.len" ftype="tabular" />
+            <param name="action|action_select" value="windowsize" />
+            <param name="action|windowsize" value="1000000" />
             <output name="output" file="makeWindowBed_result1.bed" ftype="bed" />
         </test>
         <test>
-            <param name="type_select" value="genome" />
-            <param name="genome_file_opts_selector" value="hist" />
-            <param name="genome" value="mm9_chr1.len" ftype="tabular" />
-            <param name="action_select" value="windowsize" />
-            <param name="windowsize" value="1000000" />
-            <param name="step_size_select" value="yes" />
-            <param name="step_size" value="50000" />
+            <param name="type|type_select" value="genome" />
+            <param name="type|genome_file_opts|genome_file_opts_selector" value="hist" />
+            <param name="type|genome_file_opts|genome" value="mm9_chr1.len" ftype="tabular" />
+            <param name="action|action_select" value="windowsize" />
+            <param name="action|windowsize" value="1000000" />
+            <param name="action|step_size" value="50000" />
             <output name="output" file="makeWindowBed_result2.bed" ftype="bed" />
         </test>
         <test>
-            <param name="type_select" value="genome" />
-            <param name="genome_file_opts_selector" value="hist" />
-            <param name="genome" value="mm9_chr1.len" ftype="tabular" />
-            <param name="action_select" value="number" />
-            <param name="number" value="100" />
+            <param name="type|type_select" value="genome" />
+            <param name="type|genome_file_opts|genome_file_opts_selector" value="hist" />
+            <param name="type|genome_file_opts|genome" value="mm9_chr1.len" ftype="tabular" />
+            <param name="action|action_select" value="number" />
+            <param name="action|number" value="100" />
             <output name="output" file="makeWindowBed_result3.bed" ftype="bed" />
         </test>
         <test>
-            <param name="type_select" value="bed" />
-            <param name="input" value="makeWindowBed1.bed" ftype="bed" />
-            <param name="action_select" value="number" />
-            <param name="number" value="15" />
+            <param name="type|type_select" value="bed" />
+            <param name="type|input" value="makeWindowBed1.bed" ftype="bed" />
+            <param name="action|action_select" value="number" />
+            <param name="action|number" value="15" />
             <output name="output" file="makeWindowBed_result4.bed" ftype="bed" />
         </test>
     </tests>
diff -r 7411007544bf -r f6c88d2e9ae5 mergeBed.xml
--- a/mergeBed.xml	Thu Mar 02 08:50:31 2023 +0000
+++ b/mergeBed.xml	Fri Feb 21 21:38:34 2025 +0000
@@ -1,4 +1,4 @@
-<tool id="bedtools_mergebed" name="bedtools MergeBED" version="@TOOL_VERSION@" profile="@PROFILE@">
+<tool id="bedtools_mergebed" name="bedtools MergeBED" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@">
     <description>combine overlapping/nearby intervals into a single interval</description>
     <macros>
         <import>macros.xml</import>
@@ -13,10 +13,13 @@
 -d $distance
 $header
 @C_AND_O_ARGUMENT@
+#if $input.ext == "bam"
+    -bed
+#end if
 > '${output}'
     ]]></command>
     <inputs>
-        <param  name="input" argument="-i" type="data" format="bam,@STD_BEDTOOLS_INPUTS@" label="Sort the following BAM/@STD_BEDTOOLS_INPUT_LABEL@ file"/>
+        <param  name="input" argument="-i" type="data" format="bam,@STD_BEDTOOLS_INPUTS@" label="Merge 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 (-s)</option>
@@ -25,7 +28,7 @@
         </param>
         <param name="distance" argument="-d" type="integer" value="0"
             label="Maximum distance between features allowed for features to be merged"
-            help="That is, overlapping and/or book-ended features are merged"/>
+            help="Default 0: overlapping and/or book-ended features are merged. Note: negative values enforce the number of b.p. required for overlap."/>
         <expand macro="print_header" />
         <expand macro="c_and_o_argument">
             <param name="col" argument="-c" type="data_column" data_ref="input" label="Specify the column(s) that should be summarized" />
@@ -38,20 +41,48 @@
         <test>
             <param name="input" value="mergedBed1.bed" ftype="bed" />
             <output name="output" file="mergedBed_result1.bed" ftype="bed" />
+            <assert_command>
+                <not_has_text text="-s "/>
+                <not_has_text text="-S "/>
+                <has_text text="-d 0"/>
+                <not_has_text text="-c "/>
+                <not_has_text text="-o "/>
+            </assert_command>
         </test>
         <test>
             <param name="input" value="mergedBed2.bed" ftype="bed" />
             <param name="strand" value="-s" />
             <output name="output" file="mergedBed_result2.bed" ftype="bed" />
+            <assert_command>
+                <has_text text="-s "/>
+                <not_has_text text="-S "/>
+                <has_text text="-d 0"/>
+                <not_has_text text="-c "/>
+                <not_has_text text="-o "/>
+            </assert_command>
         </test>
         <test>
             <param name="input" value="mergedBed3.bed" ftype="bed" />
             <output name="output" file="mergedBed_result3.bed" ftype="bed" />
+            <assert_command>
+                <not_has_text text="-s "/>
+                <not_has_text text="-S "/>
+                <has_text text="-d 0"/>
+                <not_has_text text="-c "/>
+                <not_has_text text="-o "/>
+            </assert_command>
         </test>
         <test>
             <param name="input" value="mergedBed4.bed" ftype="bed" />
             <param name="distance" value="1000" />
             <output name="output" file="mergedBed_result4.bed" ftype="bed" />
+            <assert_command>
+                <not_has_text text="-s "/>
+                <not_has_text text="-S "/>
+                <has_text text="-d 1000"/>
+                <not_has_text text="-c "/>
+                <not_has_text text="-o "/>
+            </assert_command>
         </test>
         <test>
             <param name="input" value="mergedBed4.bed" ftype="bed" />
@@ -61,6 +92,13 @@
                 <param name="operation" value="count"/>
             </repeat>
             <output name="output" file="mergedBed_result5.bed" ftype="bed" />
+            <assert_command>
+                <not_has_text text="-s "/>
+                <not_has_text text="-S "/>
+                <has_text text="-d 1000"/>
+                <has_text text="-c 1"/>
+                <has_text text="-o count"/>
+            </assert_command>
         </test>
     </tests>
     <help><![CDATA[
diff -r 7411007544bf -r f6c88d2e9ae5 multiCov.xml
--- a/multiCov.xml	Thu Mar 02 08:50:31 2023 +0000
+++ b/multiCov.xml	Fri Feb 21 21:38:34 2025 +0000
@@ -56,7 +56,7 @@
             <param name="input" value="multiCov1.bed" ftype="bed" />
             <param name="bams" value="srma_in3.bam,srma_in3.bam" ftype="bam"/>
             <param name="q" value="1"/>
-            <param name="split" value=""/>
+            <param name="split" value="false"/>
             <output name="output" file="multiCovBed_result1.bed" ftype="bed" />
         </test>
     </tests>
diff -r 7411007544bf -r f6c88d2e9ae5 multiIntersectBed.xml
--- a/multiIntersectBed.xml	Thu Mar 02 08:50:31 2023 +0000
+++ b/multiIntersectBed.xml	Fri Feb 21 21:38:34 2025 +0000
@@ -69,24 +69,24 @@
     </outputs>
     <tests>
         <test>
-            <param name="tag_select" value="tag" />
-            <param name="inputs" value="multiIntersectBed1.bed,multiIntersectBed2.bed,multiIntersectBed3.bed" ftype="bed" />
-            <param name="empty_selector" value="" />
+            <param name="tag|tag_select" value="tag" />
+            <param name="tag|inputs" value="multiIntersectBed1.bed,multiIntersectBed2.bed,multiIntersectBed3.bed" ftype="bed" />
+            <param name="empty|empty_selector" value="" />
             <output name="output" file="multiIntersectBed_result1.bed" ftype="bed" />
         </test>
         <test>
-            <param name="tag_select" value="tag" />
-            <param name="inputs" value="multiIntersectBed1.bed,multiIntersectBed2.bed,multiIntersectBed3.bed" ftype="bed" />
-            <param name="header" value="True" />
-            <param name="empty_selector" value="" />
+            <param name="tag|tag_select" value="tag" />
+            <param name="tag|inputs" value="multiIntersectBed1.bed,multiIntersectBed2.bed,multiIntersectBed3.bed" ftype="bed" />
+            <param name="header" value="true" />
+            <param name="empty|empty_selector" value="" />
             <output name="output" file="multiIntersectBed_result2.bed" lines_diff="2" ftype="bed" />
         </test>
         <test>
-            <param name="tag_select" value="tag" />
-            <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" ftype="tabular" />
+            <param name="tag|tag_select" value="tag" />
+            <param name="tag|inputs" value="multiIntersectBed1.bed,multiIntersectBed2.bed,multiIntersectBed3.bed" ftype="bed" />
+            <param name="empty|empty_selector" value="-empty" />
+            <param name="empty|genome_file_opts|genome_file_opts_selector" value="hist" />
+            <param name="empty|genome_file_opts|genome" value="multiIntersectBed1.len" ftype="tabular" />
             <output name="output" file="multiIntersectBed_result3.bed" ftype="bed" />
         </test>
     </tests>
diff -r 7411007544bf -r f6c88d2e9ae5 randomBed.xml
--- a/randomBed.xml	Thu Mar 02 08:50:31 2023 +0000
+++ b/randomBed.xml	Fri Feb 21 21:38:34 2025 +0000
@@ -11,8 +11,8 @@
 @GENOME_FILE@
 -l $length
 -n $intervals
-#if str($seed.seed_choose) == "True":
-    -seed $seed.seed
+#if str($seed) != "":
+    -seed $seed
 #end if
 > '$output'
     ]]></command>
@@ -27,9 +27,8 @@
     </outputs>
     <tests>
         <test>
-            <param name="genome_file_opts_selector" value="hist" />
-            <param name="genome" value="mm9_chr1.len" ftype="tabular" />
-            <param name="seed_choose" value="False" />
+            <param name="genome_file_opts|genome_file_opts_selector" value="hist" />
+            <param name="genome_file_opts|genome" value="mm9_chr1.len" ftype="tabular" />
             <param name="length" value="5" />
             <param name="intervals" value="3" />
             <output name="output">
diff -r 7411007544bf -r f6c88d2e9ae5 shuffleBed.xml
--- a/shuffleBed.xml	Thu Mar 02 08:50:31 2023 +0000
+++ b/shuffleBed.xml	Fri Feb 21 21:38:34 2025 +0000
@@ -11,8 +11,8 @@
 @GENOME_FILE@
 -i '$inputA'
 $bedpe
-#if str($seed.seed_choose) == "True":
-    -seed $seed.seed
+#if str($seed) != "":
+    -seed $seed
 #end if
 #if str($add_bed.add_bed_select) == "not_be":
     -excl $add_bed.excl
@@ -68,40 +68,36 @@
     <tests>
         <test>
             <param name="inputA" value="shuffleBed1.bed" ftype="bed" />
-            <param name="genome_file_opts_selector" value="hist" />
-            <param name="genome" value="shuffleBed.len" ftype="tabular" />
-            <param name="chrom" value="" />
-            <param name="seed_choose" value="True" />
+            <param name="genome_file_opts|genome_file_opts_selector" value="hist" />
+            <param name="genome_file_opts|genome" value="shuffleBed.len" ftype="tabular" />
+            <param name="chrom" value="false" />
             <param name="seed" value="1" />
             <output name="output" file="shuffleBed_result1.bed" ftype="bed" />
         </test>
         <test>
             <param name="inputA" value="shuffleBed1.bed" ftype="bed" />
-            <param name="genome_file_opts_selector" value="hist" />
-            <param name="genome" value="shuffleBed.len" ftype="tabular" />
+            <param name="genome_file_opts|genome_file_opts_selector" value="hist" />
+            <param name="genome_file_opts|genome" value="shuffleBed.len" ftype="tabular" />
             <param name="chrom" value="True" />
-            <param name="seed_choose" value="True" />
             <param name="seed" value="1" />
             <output name="output" file="shuffleBed_result2.bed" ftype="bed" />
         </test>
         <test>
             <param name="inputA" value="shuffleBed1.bed" ftype="bed" />
-            <param name="genome_file_opts_selector" value="hist" />
-            <param name="genome" value="shuffleBed.len" ftype="tabular" />
+            <param name="genome_file_opts|genome_file_opts_selector" value="hist" />
+            <param name="genome_file_opts|genome" value="shuffleBed.len" ftype="tabular" />
             <conditional name="add_bed">
                 <param name="add_bed_select" value="not_be"/>
                 <param name="excl" value="shuffleBed2.bed" ftype="bed" />
             </conditional>
-            <param name="seed_choose" value="True" />
             <param name="seed" value="1" />
             <output name="output" file="shuffleBed_result3.bed" ftype="bed" />
         </test>
         <test>
             <param name="inputA" value="shuffleBed1.bed" ftype="bed" />
-            <param name="genome_file_opts_selector" value="hist" />
-            <param name="genome" value="shuffleBed.len" ftype="bed" />
+            <param name="genome_file_opts|genome_file_opts_selector" value="hist" />
+            <param name="genome_file_opts|genome" value="shuffleBed.len" ftype="bed" />
             <param name="allow_beyond" value="True" />
-            <param name="seed_choose" value="True" />
             <param name="seed" value="3" />
             <output name="output" file="shuffleBed_result4.bed" ftype="bed" />
         </test>
diff -r 7411007544bf -r f6c88d2e9ae5 slopBed.xml
--- a/slopBed.xml	Thu Mar 02 08:50:31 2023 +0000
+++ b/slopBed.xml	Fri Feb 21 21:38:34 2025 +0000
@@ -1,4 +1,4 @@
-<tool id="bedtools_slopbed" name="bedtools SlopBed" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
+<tool id="bedtools_slopbed" name="bedtools SlopBed" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
     <description>adjust the size of intervals</description>
     <macros>
         <import>macros.xml</import>
@@ -39,19 +39,19 @@
     <tests>
         <test>
             <param name="inputA" value="a.bed" ftype="bed" />
-            <param name="genome_file_opts_selector" value="hist" />
-            <param name="genome" value="mm9_chr1.len" ftype="bed" />
-            <param name="addition_select" value="b" />
-            <param name="b" value="5" />
+            <param name="genome_file_opts|genome_file_opts_selector" value="hist" />
+            <param name="genome_file_opts|genome" value="mm9_chr1.len" ftype="bed" />
+            <param name="addition|addition_select" value="b" />
+            <param name="addition|b" value="5" />
             <output name="output" file="slopBed_result1.bed" ftype="bed" />
         </test>
         <test>
             <param name="inputA" value="a.bed" ftype="bed" />
-            <param name="genome_file_opts_selector" value="hist" />
-            <param name="genome" value="mm9_chr1.len" ftype="bed" />
-            <param name="addition_select" value="lr" />
-            <param name="l" value="2" />
-            <param name="r" value="3" />
+            <param name="genome_file_opts|genome_file_opts_selector" value="hist" />
+            <param name="genome_file_opts|genome" value="mm9_chr1.len" ftype="bed" />
+            <param name="addition|addition_select" value="lr" />
+            <param name="addition|l" value="2" />
+            <param name="addition|r" value="3" />
             <output name="output" file="slopBed_result2.bed" ftype="bed" />
         </test>
     </tests>
diff -r 7411007544bf -r f6c88d2e9ae5 sortBed.xml
--- a/sortBed.xml	Thu Mar 02 08:50:31 2023 +0000
+++ b/sortBed.xml	Fri Feb 21 21:38:34 2025 +0000
@@ -1,4 +1,4 @@
-<tool id="bedtools_sortbed" name="bedtools SortBED" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@">
+<tool id="bedtools_sortbed" name="bedtools SortBED" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
     <description>order the intervals</description>
     <macros>
         <import>macros.xml</import>
diff -r 7411007544bf -r f6c88d2e9ae5 test-data/jaccardBed_strand_result2.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/jaccardBed_strand_result2.bed	Fri Feb 21 21:38:34 2025 +0000
@@ -0,0 +1,2 @@
+intersection	union	jaccard	n_intersections
+0	0	-nan	0
diff -r 7411007544bf -r f6c88d2e9ae5 unionBedGraphs.xml
--- a/unionBedGraphs.xml	Thu Mar 02 08:50:31 2023 +0000
+++ b/unionBedGraphs.xml	Fri Feb 21 21:38:34 2025 +0000
@@ -66,43 +66,43 @@
     </outputs>
     <tests>
         <test>
-            <param name="tag_select" value="tag" />
-            <param name="inputs" value="unionBedGraphs1.bg,unionBedGraphs2.bg,unionBedGraphs3.bg" ftype="bedgraph" />
-            <param name="empty_selector" value="" />
+            <param name="tag|tag_select" value="tag" />
+            <param name="tag|inputs" value="unionBedGraphs1.bg,unionBedGraphs2.bg,unionBedGraphs3.bg" ftype="bedgraph" />
+            <param name="empty|empty_selector" value="" />
             <output name="output" file="unionBedGraphs_result1.bg" ftype="bedgraph" />
         </test>
         <test>
-            <param name="tag_select" value="tag" />
-            <param name="inputs" value="unionBedGraphs1.bg,unionBedGraphs2.bg,unionBedGraphs3.bg" ftype="bedgraph" />
-            <param name="header" value="True" />
-            <param name="empty_selector" value="" />
+            <param name="tag|tag_select" value="tag" />
+            <param name="tag|inputs" value="unionBedGraphs1.bg,unionBedGraphs2.bg,unionBedGraphs3.bg" ftype="bedgraph" />
+            <param name="header" value="true" />
+            <param name="empty|empty_selector" value="" />
             <output name="output" file="unionBedGraphs_result2.bg" ftype="bedgraph" />
         </test>
         <test>
-            <param name="tag_select" value="tag" />
-            <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" ftype="tabular" />
+            <param name="tag|tag_select" value="tag" />
+            <param name="tag|inputs" value="unionBedGraphs1.bg,unionBedGraphs2.bg,unionBedGraphs3.bg" ftype="bedgraph" />
+            <param name="empty|empty_selector" value="-empty" />
+            <param name="empty|genome_file_opts|genome_file_opts_selector" value="hist" />
+            <param name="empty|genome_file_opts|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="tag|tag_select" value="custom" />
+            <repeat name="tag|bedgraphs">
                 <param name="input" value="unionBedGraphs1.bg" ftype="bedgraph" />
                 <param name="custom_name" value="first" />
             </repeat>
-            <repeat name="bedgraphs">
+            <repeat name="tag|bedgraphs">
                 <param name="input" value="unionBedGraphs2.bg" ftype="bedgraph" />
                 <param name="custom_name" value="second" />
             </repeat>
-            <repeat name="bedgraphs">
+            <repeat name="tag|bedgraphs">
                 <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" ftype="tabular" />
+            <param name="empty|empty_selector" value="-empty" />
+            <param name="empty|genome_file_opts|genome_file_opts_selector" value="hist" />
+            <param name="empty|genome_file_opts|genome" value="unionBedGraphs1.len" ftype="tabular" />
             <output name="output" file="unionBedGraphs_result4.bg" ftype="bedgraph" />
         </test>
     </tests>
diff -r 7411007544bf -r f6c88d2e9ae5 windowBed.xml
--- a/windowBed.xml	Thu Mar 02 08:50:31 2023 +0000
+++ b/windowBed.xml	Fri Feb 21 21:38:34 2025 +0000
@@ -77,16 +77,16 @@
         <test>
             <param name="inputA" value="windowBedA.bed" ftype="bed" />
             <param name="inputB" value="windowBedB.bed" ftype="bed" />
-            <param name="addition_select" value="window" />
-            <param name="w" value="5000" />
+            <param name="addition|addition_select" value="window" />
+            <param name="addition|w" value="5000" />
             <output name="output" file="windowBed_result2.bed" ftype="bed" />
         </test>
         <test>
             <param name="inputA" value="windowBedA.bed" ftype="bed" />
             <param name="inputB" value="windowBedB.bed" ftype="bed" />
-            <param name="addition_select" value="lr" />
-            <param name="l" value="200" />
-            <param name="r" value="20000" />
+            <param name="addition|addition_select" value="lr" />
+            <param name="addition|l" value="200" />
+            <param name="addition|r" value="20000" />
             <output name="output" file="windowBed_result2.bed" ftype="bed" />
         </test>
     </tests>