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changeset 47:2892111d91f8 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 73ebd55430874a3c1483b6dd6cce0482175482f9
author iuc
date Fri, 21 Feb 2025 21:40:09 +0000
parents 64e2edfe7a2c
children
files annotateBed.xml bedToBam.xml bedpeToBam.xml closestBed.xml complementBed.xml coverageBed.xml fisherBed.xml flankBed.xml genomeCoverageBed.xml getfastaBed.xml groupbyBed.xml intersectBed.xml macros.xml makeWindowsBed.xml mergeBed.xml multiCov.xml multiIntersectBed.xml randomBed.xml shuffleBed.xml slopBed.xml unionBedGraphs.xml windowBed.xml
diffstat 22 files changed, 217 insertions(+), 197 deletions(-) [+]
line wrap: on
line diff
--- a/annotateBed.xml	Sat May 18 23:28:38 2024 +0000
+++ b/annotateBed.xml	Fri Feb 21 21:40:09 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>
--- a/bedToBam.xml	Sat May 18 23:28:38 2024 +0000
+++ b/bedToBam.xml	Fri Feb 21 21:40:09 2025 +0000
@@ -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>
--- a/bedpeToBam.xml	Sat May 18 23:28:38 2024 +0000
+++ b/bedpeToBam.xml	Fri Feb 21 21:40:09 2025 +0000
@@ -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>
--- a/closestBed.xml	Sat May 18 23:28:38 2024 +0000
+++ b/closestBed.xml	Fri Feb 21 21:40:09 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>
--- a/complementBed.xml	Sat May 18 23:28:38 2024 +0000
+++ b/complementBed.xml	Fri Feb 21 21:40:09 2025 +0000
@@ -22,8 +22,8 @@
     <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="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>
--- a/coverageBed.xml	Sat May 18 23:28:38 2024 +0000
+++ b/coverageBed.xml	Fri Feb 21 21:40:09 2025 +0000
@@ -72,50 +72,50 @@
     <tests>
         <test>
             <param name="inputA" value="coverageBedA.bed" ftype="bed"/>
-            <param name="inputB" value="coverageBedB.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="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"/>
         </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="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"/>
         </test>
         <test>
             <param name="inputA" value="coverageBedA.bed" ftype="bed"/>
-            <param name="inputB" value="coverageBedB.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="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="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"/>
         </test>
         <test>
             <param name="inputA" value="coverageBedA2.bed" ftype="bed"/>
-            <param name="inputB" value="coverageBed.bam" ftype="bam"/>
+            <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="reduce_or_iterate|inputB" value="coverageBed.bam" ftype="bam"/>
             <param name="mean" value="true"/>
             <output name="output" file="mean_coverage.bed" ftype="bed"/>
         </test>
--- a/fisherBed.xml	Sat May 18 23:28:38 2024 +0000
+++ b/fisherBed.xml	Fri Feb 21 21:40:09 2025 +0000
@@ -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>
--- a/flankBed.xml	Sat May 18 23:28:38 2024 +0000
+++ b/flankBed.xml	Fri Feb 21 21:40:09 2025 +0000
@@ -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>
--- a/genomeCoverageBed.xml	Sat May 18 23:28:38 2024 +0000
+++ b/genomeCoverageBed.xml	Fri Feb 21 21:40:09 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>
--- a/getfastaBed.xml	Sat May 18 23:28:38 2024 +0000
+++ b/getfastaBed.xml	Fri Feb 21 21:40:09 2025 +0000
@@ -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" />
--- a/groupbyBed.xml	Sat May 18 23:28:38 2024 +0000
+++ b/groupbyBed.xml	Fri Feb 21 21:40:09 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>
--- a/intersectBed.xml	Sat May 18 23:28:38 2024 +0000
+++ b/intersectBed.xml	Fri Feb 21 21:40:09 2025 +0000
@@ -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" />
--- a/macros.xml	Sat May 18 23:28:38 2024 +0000
+++ b/macros.xml	Fri Feb 21 21:40:09 2025 +0000
@@ -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  -->
--- a/makeWindowsBed.xml	Sat May 18 23:28:38 2024 +0000
+++ b/makeWindowsBed.xml	Fri Feb 21 21:40:09 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>
--- a/mergeBed.xml	Sat May 18 23:28:38 2024 +0000
+++ b/mergeBed.xml	Fri Feb 21 21:40:09 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[
--- a/multiCov.xml	Sat May 18 23:28:38 2024 +0000
+++ b/multiCov.xml	Fri Feb 21 21:40:09 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>
--- a/multiIntersectBed.xml	Sat May 18 23:28:38 2024 +0000
+++ b/multiIntersectBed.xml	Fri Feb 21 21:40:09 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>
--- a/randomBed.xml	Sat May 18 23:28:38 2024 +0000
+++ b/randomBed.xml	Fri Feb 21 21:40:09 2025 +0000
@@ -1,4 +1,4 @@
-<tool id="bedtools_randombed" name="bedtools RandomBed" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
+<tool id="bedtools_randombed" name="bedtools RandomBed" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
     <description>generate random intervals in a genome</description>
     <macros>
         <import>macros.xml</import>
@@ -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">
--- a/shuffleBed.xml	Sat May 18 23:28:38 2024 +0000
+++ b/shuffleBed.xml	Fri Feb 21 21:40:09 2025 +0000
@@ -1,4 +1,4 @@
-<tool id="bedtools_shufflebed" name="bedtools ShuffleBed" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
+<tool id="bedtools_shufflebed" name="bedtools ShuffleBed" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
     <description>randomly redistrubute intervals in a genome</description>
     <macros>
         <import>macros.xml</import>
@@ -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>
--- a/slopBed.xml	Sat May 18 23:28:38 2024 +0000
+++ b/slopBed.xml	Fri Feb 21 21:40:09 2025 +0000
@@ -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>
--- a/unionBedGraphs.xml	Sat May 18 23:28:38 2024 +0000
+++ b/unionBedGraphs.xml	Fri Feb 21 21:40:09 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>
--- a/windowBed.xml	Sat May 18 23:28:38 2024 +0000
+++ b/windowBed.xml	Fri Feb 21 21:40:09 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>