# HG changeset patch
# User iuc
# Date 1740174009 0
# Node ID 2892111d91f8a26b8a7e048d6cfc724d047b459f
# Parent 64e2edfe7a2c8116f078eb1a08d387783760b968
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 73ebd55430874a3c1483b6dd6cce0482175482f9
diff -r 64e2edfe7a2c -r 2892111d91f8 annotateBed.xml
--- 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>
diff -r 64e2edfe7a2c -r 2892111d91f8 bedToBam.xml
--- 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>
diff -r 64e2edfe7a2c -r 2892111d91f8 bedpeToBam.xml
--- 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>
diff -r 64e2edfe7a2c -r 2892111d91f8 closestBed.xml
--- 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>
diff -r 64e2edfe7a2c -r 2892111d91f8 complementBed.xml
--- 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>
diff -r 64e2edfe7a2c -r 2892111d91f8 coverageBed.xml
--- 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>
diff -r 64e2edfe7a2c -r 2892111d91f8 fisherBed.xml
--- 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>
diff -r 64e2edfe7a2c -r 2892111d91f8 flankBed.xml
--- 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>
diff -r 64e2edfe7a2c -r 2892111d91f8 genomeCoverageBed.xml
--- 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>
diff -r 64e2edfe7a2c -r 2892111d91f8 getfastaBed.xml
--- 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" />
diff -r 64e2edfe7a2c -r 2892111d91f8 groupbyBed.xml
--- 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>
diff -r 64e2edfe7a2c -r 2892111d91f8 intersectBed.xml
--- 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" />
diff -r 64e2edfe7a2c -r 2892111d91f8 macros.xml
--- 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 -->
diff -r 64e2edfe7a2c -r 2892111d91f8 makeWindowsBed.xml
--- 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>
diff -r 64e2edfe7a2c -r 2892111d91f8 mergeBed.xml
--- 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[
diff -r 64e2edfe7a2c -r 2892111d91f8 multiCov.xml
--- 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>
diff -r 64e2edfe7a2c -r 2892111d91f8 multiIntersectBed.xml
--- 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>
diff -r 64e2edfe7a2c -r 2892111d91f8 randomBed.xml
--- 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">
diff -r 64e2edfe7a2c -r 2892111d91f8 shuffleBed.xml
--- 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>
diff -r 64e2edfe7a2c -r 2892111d91f8 slopBed.xml
--- 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>
diff -r 64e2edfe7a2c -r 2892111d91f8 unionBedGraphs.xml
--- 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>
diff -r 64e2edfe7a2c -r 2892111d91f8 windowBed.xml
--- 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>