# HG changeset patch
# User iuc
# Date 1616530994 0
# Node ID ce3c7f062223dadfc8259cfcd1ff453fa0f3c9d6
# Parent  0a5c785ac6db3796fb7d8bdab73b102317190734
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 8e072170dd8f7b68fabbf29b1b0d7d14974b8b22"

diff -r 0a5c785ac6db -r ce3c7f062223 coverageBed.xml
--- a/coverageBed.xml	Mon Jun 15 16:55:13 2020 -0400
+++ b/coverageBed.xml	Tue Mar 23 20:23:14 2021 +0000
@@ -24,15 +24,13 @@
 -a '$inputA'
 #if str($reduce_or_iterate.reduce_or_iterate_selector) == 'iterate':
     -b '$reduce_or_iterate.inputB'
-    #if $reduce_or_iterate.inputB.is_of_type('bam'):
-        -sorted -g <(samtools view -H $reduce_or_iterate.inputB | grep '^@SQ' |  sed $'s/\tSN:/\tSN\t/' | sed $'s/\tLN:/\tLN\t/' | cut -f 3,5)
-    #end if
 #else:
     -b
     #for $file in $reduce_or_iterate.inputB
         '$file'
     #end for
 #end if
+@SORTED@
 #if $inputA.is_of_type('gff'):
     | sort -k1,1 -k4,2n
 #else:
@@ -73,6 +71,8 @@
         <param name="a_or_b" argument="-e" type="boolean" truevalue="-e" falsevalue="" checked="false"
             label="Require that the minimum fraction be satisfied for A OR B."
             help="If -e is used with -f 0.90 and -F 0.10 this requires that either 90% of A is covered OR 10% of  B is covered. Without -e, both fractions would have to be satisfied" />
+        <!-- -sorted -g  -->
+        <expand macro="sorted" />
     </inputs>
     <outputs>
         <data name="output" format="bed" metadata_source="inputA" label="Count of overlaps on ${inputA.name}"/>
@@ -86,12 +86,14 @@
         <test>
             <param name="inputA" value="multiCov1.bed" ftype="bed" />
             <param name="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="sorted" value="true"/>
             <output name="output" file="multicov1_by_srma_in3.cov.bed" ftype="bed" />
         </test>
         <test>
@@ -107,6 +109,18 @@
             <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="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" />
+            <output name="output" file="coverageBed_result5_unsorted.bed" ftype="bed" />
+        </test>
     </tests>
     <help><![CDATA[
 **What it does**
diff -r 0a5c785ac6db -r ce3c7f062223 intersectBed.xml
--- a/intersectBed.xml	Mon Jun 15 16:55:13 2020 -0400
+++ b/intersectBed.xml	Tue Mar 23 20:23:14 2021 +0000
@@ -16,11 +16,7 @@
 #end if
 
 bedtools intersect
-#if $inputA.is_of_type('bam'):
-    -abam '${inputA}'
-#else:
-    -a '${inputA}'
-#end if
+-a '${inputA}'
 
 #if str($reduce_or_iterate.reduce_or_iterate_selector) == 'iterate':
     -b '$reduce_or_iterate.inputB'
@@ -53,14 +49,7 @@
 $once
 $header
 $modes
-$sorted
-#if str($sorted) != '':
-    #if str($reduce_or_iterate.reduce_or_iterate_selector) == 'iterate' and $reduce_or_iterate.inputB.is_of_type('bam'):
-        -g <(samtools view -H $reduce_or_iterate.inputB | tr ':' '\t' | grep SN | cut -f 3,5)
-    #else if str($reduce_or_iterate.reduce_or_iterate_selector) == 'reduce' and str($reduce_or_iterate.inputB) != 'None' and $reduce_or_iterate.inputB[0].is_of_type('bam'):
-        -g <(samtools view -H $reduce_or_iterate.inputB[0] | tr ':' '\t' | grep SN | cut -f 3,5)
-    #end if
-#end if
+@SORTED@
 $bed
 $count
 > '${output}'
@@ -124,10 +113,9 @@
             help="Reports 0 for A entries that have no overlap with B" />
         <!-- -bed -->
         <param argument="-bed" type="boolean" truevalue="-bed" falsevalue="" checked="false"
-            label="When using BAM input (-abam), write output as BED instead of BAM." />
+            label="When using BAM input, write output as BED instead of BAM." />
         <!-- -sorted -g  -->
-        <param argument="-sorted" type="boolean" truevalue="-sorted" falsevalue="" checked="false"
-            label="For coordinate sorted input file the more efficient sweeping algorithm is enabled." />
+        <expand macro="sorted" />
         <expand macro="print_header" />
     </inputs>
     <outputs>
diff -r 0a5c785ac6db -r ce3c7f062223 macros.xml
--- a/macros.xml	Mon Jun 15 16:55:13 2020 -0400
+++ b/macros.xml	Tue Mar 23 20:23:14 2021 +0000
@@ -5,7 +5,7 @@
             <yield/>
         </requirements>
     </xml>
-    <token name="@TOOL_VERSION@">2.29.2</token>
+    <token name="@TOOL_VERSION@">2.30.0</token>
     <token name="@SAMTOOLS_VERSION@">1.9</token>
     <token name="@STD_BEDTOOLS_INPUTS@">bed,bedgraph,gff,vcf,encodepeak</token>
     <token name="@STD_BEDTOOLS_INPUT_LABEL@">BED/bedGraph/GFF/VCF/EncodePeak</token>
@@ -77,6 +77,19 @@
             </when>
         </conditional>
     </xml>
+    <xml name="input_optional_genome_file">
+        <conditional name="genome">
+            <param name="genome_choose" argument="-g" type="select"
+                label="Specify a genome file that defines the expected chromosome order in the input files." >
+                <option value="" selected="true">No</option>
+                <option value="-g">Yes</option>
+            </param>
+            <when value="-g">
+                <expand macro="input_conditional_genome_file" />
+            </when>
+            <when value="" />
+        </conditional>
+    </xml>
     <token name="@GENOME_FILE@">
 #if $genome_file_opts.genome_file_opts_selector == "loc":
     '$genome_file_opts.genome.fields.len_path'
@@ -223,6 +236,23 @@
         <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>
     </xml>
+    <xml name="sorted">
+        <!-- -sorted -g  -->
+        <param argument="-sorted" type="boolean" truevalue="-sorted" falsevalue="" checked="false"
+            label="For coordinate sorted input file the more efficient sweeping algorithm is enabled."/>
+    </xml>
+    <token name="@SORTED@">
+<![CDATA[
+$sorted
+#if str($sorted) != '':
+    #if str($reduce_or_iterate.reduce_or_iterate_selector) == 'iterate' and $reduce_or_iterate.inputB.is_of_type('bam'):
+        -g <(samtools view -H $reduce_or_iterate.inputB | tr ':' '\t' | grep SN | cut -f 3,5)
+    #else if str($reduce_or_iterate.reduce_or_iterate_selector) == 'reduce' and str($reduce_or_iterate.inputB) != 'None' and $reduce_or_iterate.inputB[0].is_of_type('bam'):
+        -g <(samtools view -H $reduce_or_iterate.inputB[0] | tr ':' '\t' | grep SN | cut -f 3,5)
+    #end if
+#end if
+]]>
+    </token>
     <token name="@REFERENCES@">
 <![CDATA[
 ------
diff -r 0a5c785ac6db -r ce3c7f062223 mapBed.xml
--- a/mapBed.xml	Mon Jun 15 16:55:13 2020 -0400
+++ b/mapBed.xml	Tue Mar 23 20:23:14 2021 +0000
@@ -35,17 +35,7 @@
         </expand>
         <expand macro="split" />
         <expand macro="print_header" />
-        <conditional name="genome">
-            <param name="genome_choose" argument="-g" type="select"
-                label="Specify a genome file the defines the expected chromosome order in the input files." >
-                <option value="" selected="true">No</option>
-                <option value="-g">Yes</option>
-            </param>
-            <when value="-g">
-                <expand macro="input_conditional_genome_file" />
-            </when>
-            <when value="" />
-        </conditional>
+        <expand macro="input_optional_genome_file" />
     </inputs>
     <outputs>
         <data name="output" format_source="inputA" metadata_source="inputA" label="Mapping of ${inputB.name} into ${inputA.name}" />
diff -r 0a5c785ac6db -r ce3c7f062223 shuffleBed.xml
--- a/shuffleBed.xml	Mon Jun 15 16:55:13 2020 -0400
+++ b/shuffleBed.xml	Tue Mar 23 20:23:14 2021 +0000
@@ -87,7 +87,10 @@
             <param name="inputA" value="shuffleBed1.bed" ftype="bed" />
             <param name="genome_file_opts_selector" value="hist" />
             <param name="genome" value="shuffleBed.len" ftype="tabular" />
-            <param name="excl" value="shuffleBed2.bed" ftype="bed" />
+            <conditional name="add_bed">
+                <param name="add_bed_select" value="not_be"/>
+                <param name="excl" value="shuffleBed2.bed" ftype="bed" />
+            </conditional>
             <param name="seed_choose" value="True" />
             <param name="seed" value="1" />
             <output name="output" file="shuffleBed_result3.bed" ftype="bed" />
@@ -98,7 +101,7 @@
             <param name="genome" value="shuffleBed.len" ftype="bed" />
             <param name="allow_beyond" value="True" />
             <param name="seed_choose" value="True" />
-            <param name="seed" value="1" />
+            <param name="seed" value="3" />
             <output name="output" file="shuffleBed_result4.bed" ftype="bed" />
         </test>
     </tests>
diff -r 0a5c785ac6db -r ce3c7f062223 sortBed.xml
--- a/sortBed.xml	Mon Jun 15 16:55:13 2020 -0400
+++ b/sortBed.xml	Tue Mar 23 20:23:14 2021 +0000
@@ -9,6 +9,7 @@
 sortBed
 -i '$input'
 $option
+@GENOME_FILE_MAPBED@
 > '$output'
     ]]></command>
     <inputs>
@@ -23,6 +24,7 @@
             <option value="-chrThenScoreA">chromosome, then by score (asc).</option>
             <option value="-chrThenScoreD">chromosome, then by score (desc).</option>
         </param>
+        <expand macro="input_optional_genome_file" />
     </inputs>
     <outputs>
         <data name="output" format_source="input" metadata_source="input" label="SortBed on ${input.name}"/>
@@ -33,6 +35,19 @@
             <param name="option" value="" />
             <output name="output" file="sortBed_result1.bed" ftype="bed" />
         </test>
+        <test>
+            <param name="input" value="sortBed2.bed" ftype="bed" />
+            <param name="option" value="" />
+            <output name="output" file="sortBed_result2.bed" ftype="bed" />
+        </test>
+        <test>
+            <param name="input" value="sortBed2.bed" ftype="bed" />
+            <param name="option" value="" />
+            <param name="genome_choose" value="-g" />
+            <param name="genome_file_opts_selector" value="hist" />
+            <param name="genome" value="mm9.len" ftype="bed" />
+            <output name="output" file="sortBed_result3.bed" ftype="bed" />
+        </test>
     </tests>
     <help><![CDATA[
 **What it does**
diff -r 0a5c785ac6db -r ce3c7f062223 test-data/coverageBed.bam
Binary file test-data/coverageBed.bam has changed
diff -r 0a5c785ac6db -r ce3c7f062223 test-data/coverageBedA2.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/coverageBedA2.bed	Tue Mar 23 20:23:14 2021 +0000
@@ -0,0 +1,3 @@
+dummy_chr	1	100
+dummy_chr	1000	1000000
+super_dummy_chr	1	100
diff -r 0a5c785ac6db -r ce3c7f062223 test-data/coverageBed_result4_2bam.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/coverageBed_result4_2bam.bed	Tue Mar 23 20:23:14 2021 +0000
@@ -0,0 +1,2 @@
+dummy_chr	1	100	0	0	99	0.0000000
+dummy_chr	1000	1000000	4	152	999000	0.0001522
diff -r 0a5c785ac6db -r ce3c7f062223 test-data/coverageBed_result5_unsorted.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/coverageBed_result5_unsorted.bed	Tue Mar 23 20:23:14 2021 +0000
@@ -0,0 +1,3 @@
+dummy_chr	1	100	0	0	99	0.0000000
+dummy_chr	1000	1000000	2	152	999000	0.0001522
+super_dummy_chr	1	100	0	0	99	0.0000000
diff -r 0a5c785ac6db -r ce3c7f062223 test-data/shuffleBed2.bed
--- a/test-data/shuffleBed2.bed	Mon Jun 15 16:55:13 2020 -0400
+++ b/test-data/shuffleBed2.bed	Tue Mar 23 20:23:14 2021 +0000
@@ -1,1 +1,1 @@
-chr1	0	100
+chr1	0	10000
diff -r 0a5c785ac6db -r ce3c7f062223 test-data/shuffleBed_result1.bed
--- a/test-data/shuffleBed_result1.bed	Mon Jun 15 16:55:13 2020 -0400
+++ b/test-data/shuffleBed_result1.bed	Tue Mar 23 20:23:14 2021 +0000
@@ -1,2 +1,2 @@
-chr2	51	151	a1	1	+
-chr2	720	1720	a2	2	-
+chr2	1528	1628	a1	1	+
+chr1	7462	8462	a2	2	-
diff -r 0a5c785ac6db -r ce3c7f062223 test-data/shuffleBed_result2.bed
--- a/test-data/shuffleBed_result2.bed	Mon Jun 15 16:55:13 2020 -0400
+++ b/test-data/shuffleBed_result2.bed	Tue Mar 23 20:23:14 2021 +0000
@@ -1,2 +1,2 @@
-chr1	5845	5945	a1	1	+
-chr1	6139	7139	a2	2	-
+chr1	1528	1628	a1	1	+
+chr1	2462	3462	a2	2	-
diff -r 0a5c785ac6db -r ce3c7f062223 test-data/shuffleBed_result3.bed
--- a/test-data/shuffleBed_result3.bed	Mon Jun 15 16:55:13 2020 -0400
+++ b/test-data/shuffleBed_result3.bed	Tue Mar 23 20:23:14 2021 +0000
@@ -1,2 +1,2 @@
-chr2	51	151	a1	1	+
-chr2	720	1720	a2	2	-
+chr2	1528	1628	a1	1	+
+chr2	5665	6665	a2	2	-
diff -r 0a5c785ac6db -r ce3c7f062223 test-data/shuffleBed_result4.bed
--- a/test-data/shuffleBed_result4.bed	Mon Jun 15 16:55:13 2020 -0400
+++ b/test-data/shuffleBed_result4.bed	Tue Mar 23 20:23:14 2021 +0000
@@ -1,2 +1,2 @@
-chr2	51	151	a1	1	+
-chr2	720	1720	a2	2	-
+chr1	6467	6567	a1	1	+
+chr2	7167	8000	a2	2	-
diff -r 0a5c785ac6db -r ce3c7f062223 test-data/sortBed2.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sortBed2.bed	Tue Mar 23 20:23:14 2021 +0000
@@ -0,0 +1,3 @@
+chr1	800	1000
+chr10	80	180
+chr2	1	10
diff -r 0a5c785ac6db -r ce3c7f062223 test-data/sortBed_result2.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sortBed_result2.bed	Tue Mar 23 20:23:14 2021 +0000
@@ -0,0 +1,3 @@
+chr1	800	1000
+chr10	80	180
+chr2	1	10
diff -r 0a5c785ac6db -r ce3c7f062223 test-data/sortBed_result3.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sortBed_result3.bed	Tue Mar 23 20:23:14 2021 +0000
@@ -0,0 +1,3 @@
+chr1	800	1000
+chr2	1	10
+chr10	80	180