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changeset 35:b28e0cfa7ba1 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"
author iuc
date Fri, 06 Sep 2019 14:29:59 -0400
parents dde39ba9c031
children 0a5c785ac6db
files annotateBed.xml bamToBed.xml bamToFastq.xml bedpeToBam.xml coverageBed.xml fisherBed.xml intersectBed.xml jaccardBed.xml macros.xml makeWindowsBed.xml multiIntersectBed.xml tagBed.xml test-data/bamToFastq_result1.fastq test-data/jaccardBed_result1.bed test-data/jaccardBed_result2.bed test-data/srma_in3.bam
diffstat 16 files changed, 17 insertions(+), 93 deletions(-) [+]
line wrap: on
line diff
--- a/annotateBed.xml	Mon Apr 29 05:55:48 2019 -0400
+++ b/annotateBed.xml	Fri Sep 06 14:29:59 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="bedtools_annotatebed" name="bedtools AnnotateBed" version="@TOOL_VERSION@+galaxy1">
+<tool id="bedtools_annotatebed" name="bedtools AnnotateBed" version="@TOOL_VERSION@">
     <description>annotate coverage of features from multiple files</description>
     <macros>
         <import>macros.xml</import>
--- a/bamToBed.xml	Mon Apr 29 05:55:48 2019 -0400
+++ b/bamToBed.xml	Fri Sep 06 14:29:59 2019 -0400
@@ -9,7 +9,7 @@
     <expand macro="stdio" />
     <command><![CDATA[
 #if $input.extension == 'bam' and $option == "-bedpe":
-    samtools sort -n '${input}' ./input &&
+    samtools sort -n -T "\${TMPDIR:-.}" '${input}' ./input &&
 #else
     ln -s '${input}' ./input.bam &&
 #end if
--- a/bamToFastq.xml	Mon Apr 29 05:55:48 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,43 +0,0 @@
-<tool id="bedtools_bamtofastq" name="bedtools Convert from BAM to FastQ" version="@TOOL_VERSION@">
-    <description></description>
-    <macros>
-        <import>macros.xml</import>
-    </macros>
-    <expand macro="requirements" />
-    <expand macro="stdio" />
-    <command><![CDATA[
-bedtools bamtofastq
-$tags
--i '$input'
--fq '$output'
-#if $fq2:
-    -fq2 '$output2'
-#end if
-    ]]></command>
-    <inputs>
-        <param name="input" type="data" format="bam" label="Convert the following BAM file to FASTQ"/>
-        <param argument="-tags" type="boolean" truevalue="-tags" falsevalue="" checked="false" label="Create FASTQ based on the mate info in the BAM R2 and Q2 tags."/>
-        <param argument="-fq2" type="boolean" truevalue="-fq2" falsevalue="" checked="false" label="FASTQ for second end"
-            help="Used if BAM contains paired-end data. BAM should be sorted by query name if creating paired FASTQ with this option."/>
-    </inputs>
-    <outputs>
-        <data name="output" format="fastq" metadata_source="input" label="${input.name} (as FASTQ)"/>
-        <data name="output2" format="fastq" metadata_source="input" label="${input.name} (as FASTQ)">
-            <filter>fq2 is True</filter>
-        </data>
-    </outputs>
-    <tests>
-        <test>
-            <param name="input" value="srma_in3.bam" ftype="bam" />
-            <output name="output" file="bamToFastq_result1.fastq" ftype="fastq" />
-        </test>
-    </tests>
-    <help><![CDATA[
-**What it does**
-
-bedtools bamtofastq is a conversion utility for extracting FASTQ records from sequence alignments in BAM format.
-
-@REFERENCES@
-    ]]></help>
-    <expand macro="citations" />
-</tool>
--- a/bedpeToBam.xml	Mon Apr 29 05:55:48 2019 -0400
+++ b/bedpeToBam.xml	Fri Sep 06 14:29:59 2019 -0400
@@ -3,7 +3,10 @@
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements" />
+    <!-- bedtobam broken in 2.29.0 <expand macro="requirements" /> -->
+    <requirements>
+        <requirement type="package" version="2.27.1">bedtools</requirement>
+    </requirements>
     <expand macro="stdio" />
     <command><![CDATA[
 bedtools bedpetobam
@@ -19,14 +22,14 @@
             label="Set a mapping quality (SAM MAPQ field) value for all BED entries" />
     </inputs>
     <outputs>
-        <data name="output" format="bam" metadata_source="input"/>
+        <data name="output" format="unsorted.bam" metadata_source="input"/>
     </outputs>
     <tests>
         <test>
             <param name="input" value="bedpeToBamBed1.bed" ftype="bed" />
             <param name="genome_file_opts_selector" value="hist" />
             <param name="genome" value="mm9.len"/>
-            <output name="output" file="bedpeToBam_result1.bam" lines_diff="72" ftype="bam" />
+            <output name="output" file="bedpeToBam_result1.bam" lines_diff="72" ftype="unsorted.bam" />
         </test>
     </tests>
     <help><![CDATA[
--- a/coverageBed.xml	Mon Apr 29 05:55:48 2019 -0400
+++ b/coverageBed.xml	Fri Sep 06 14:29:59 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="bedtools_coveragebed" name="bedtools Compute both the depth and breadth of coverage" version="@TOOL_VERSION@+galaxy1">
+<tool id="bedtools_coveragebed" name="bedtools Compute both the depth and breadth of coverage" version="@TOOL_VERSION@">
     <description>of features in file B on the features in file A (bedtools coverage)</description>
     <macros>
         <import>macros.xml</import>
--- a/fisherBed.xml	Mon Apr 29 05:55:48 2019 -0400
+++ b/fisherBed.xml	Fri Sep 06 14:29:59 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="bedtools_fisher" name="bedtools FisherBed" version="@TOOL_VERSION@+galaxy1">
+<tool id="bedtools_fisher" name="bedtools FisherBed" version="@TOOL_VERSION@">
     <description>calculate Fisher statistic between two feature files</description>
     <macros>
         <import>macros.xml</import>
--- a/intersectBed.xml	Mon Apr 29 05:55:48 2019 -0400
+++ b/intersectBed.xml	Fri Sep 06 14:29:59 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="bedtools_intersectbed" name="bedtools Intersect intervals" version="@TOOL_VERSION@+galaxy1">
+<tool id="bedtools_intersectbed" name="bedtools Intersect intervals" version="@TOOL_VERSION@">
     <description>find overlapping intervals in various ways</description>
     <macros>
         <import>macros.xml</import>
--- a/jaccardBed.xml	Mon Apr 29 05:55:48 2019 -0400
+++ b/jaccardBed.xml	Fri Sep 06 14:29:59 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="bedtools_jaccard" name="bedtools JaccardBed" version="@TOOL_VERSION@+galaxy1">
+<tool id="bedtools_jaccard" name="bedtools JaccardBed" version="@TOOL_VERSION@">
     <description>calculate the distribution of relative distances between two files</description>
     <macros>
         <import>macros.xml</import>
--- a/macros.xml	Mon Apr 29 05:55:48 2019 -0400
+++ b/macros.xml	Fri Sep 06 14:29:59 2019 -0400
@@ -5,7 +5,7 @@
             <yield/>
         </requirements>
     </xml>
-    <token name="@TOOL_VERSION@">2.27.1</token>
+    <token name="@TOOL_VERSION@">2.29.0</token>
     <token name="@SAMTOOLS_VERSION@">1.9</token>
     <token name="@STD_BEDTOOLS_INPUTS@">bed,bedgraph,gff,vcf</token>
     <token name="@STD_BEDTOOLS_INPUT_LABEL@">BED/bedGraph/GFF/VCF</token>
--- a/makeWindowsBed.xml	Mon Apr 29 05:55:48 2019 -0400
+++ b/makeWindowsBed.xml	Fri Sep 06 14:29:59 2019 -0400
@@ -19,7 +19,6 @@
     #end if
 #else:
     -n $action.number
-    -s $action.step_size
 #end if
 $sourcename
 > '$output'
@@ -63,7 +62,6 @@
                 <param name="number" argument="-n" type="integer" value="1"
                     label="Divide each input interval (either a chromosome or a BED interval) to fixed number of windows"
                     help="I.e. same number of windows, with varying window sizes" />
-                <param name="step_size" argument="-s" type="integer" value="100" label="Specify it" />
             </when>
         </conditional>
         <param name="sourcename" type="select" label="ID Naming Options">
@@ -101,7 +99,6 @@
             <param name="genome" value="mm9_chr1.len" ftype="tabular" />
             <param name="action_select" value="number" />
             <param name="number" value="100" />
-            <param name="step_size" value="10000" />
             <output name="output" file="makeWindowBed_result3.bed" ftype="bed" />
         </test>
         <test>
@@ -109,7 +106,6 @@
             <param name="input" value="makeWindowBed1.bed" ftype="bed" />
             <param name="action_select" value="number" />
             <param name="number" value="15" />
-            <param name="step_size" value="100" />
             <output name="output" file="makeWindowBed_result4.bed" ftype="bed" />
         </test>
     </tests>
--- a/multiIntersectBed.xml	Mon Apr 29 05:55:48 2019 -0400
+++ b/multiIntersectBed.xml	Fri Sep 06 14:29:59 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="bedtools_multiintersectbed" name="bedtools Multiple Intersect" version="@TOOL_VERSION@+galaxy1">
+<tool id="bedtools_multiintersectbed" name="bedtools Multiple Intersect" version="@TOOL_VERSION@">
     <description>identifies common intervals among multiple interval files</description>
     <macros>
         <import>macros.xml</import>
--- a/tagBed.xml	Mon Apr 29 05:55:48 2019 -0400
+++ b/tagBed.xml	Fri Sep 06 14:29:59 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="bedtools_tagbed" name="bedtools TagBed" version="@TOOL_VERSION@+galaxy1">
+<tool id="bedtools_tagbed" name="bedtools TagBed" version="@TOOL_VERSION@">
     <description>tag BAM alignments based on overlaps with interval files</description>
     <macros>
         <import>macros.xml</import>
--- a/test-data/bamToFastq_result1.fastq	Mon Apr 29 05:55:48 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,32 +0,0 @@
-@GA5:3:2:1710:1301#0
-GAACTCCTGACCTCAGGTGATCTGCCCGCCTTGGCCTCCCAAAGTGCTGGAATTACAGGCATGAGCCACCGTGCCC
-+
-6->;B==?B?AAA??9B<AA?@A==AA9A?<A?<&:A?=<9<?>19;?A=9:?999;=4=6A9/8;4==;1';;3=
-@GA5:3:24:462:583#0
-TAAAAAAAGGACAGTGACGCACCTTGTATAGCGATGTGTCATCTAAAACATCTATTCAAAGAACAGAAGACTCACC
-+
-BBABBBB@BBBBBA?BBBBBBAA@AB?BBBA@B=>@?@;@?@?A>=1=?>??><???;;>?;;;?>8999;;9;;<
-@GA5:3:29:1241:1653#0
-TCATGCACACACAGACAGCTGTCGGGGGATGCATGCCAACCAGAGGGGCCACACATATACCGTGTTGATGGGACAG
-+
-BBBBBBACBCBBBBBBBBBBBABBABBB@AA>@?@?@>=????<???:?915399<=5=<==5=559545432353
-@GA5:3:33:1591:303#0
-CTCGCCTGGGCCCGGTAAAGCCCCCACGTAGCCCCAGCCAGCCTGGAACATGCTTCCTGAGCTCCCAGCTCTTGGT
-+
-BBBBBBBBBBB@BBB?BBBA@A>B@B?AABB?@>?BA?>AB;??A?6;=AAAAA=>3=9;@;===6,=?;;5==;6
-@GA5:3:31:677:1537#0
-CTTCCGCCACTGGCCGGTGTCGGGGTCTGGGACACCCTGAGACCCTAAGCTCTCCTGGCTGCTCTCTCAAACCCTC
-+
-BBBBBBBBBBBBBBBBA=B?AA?AA4A>??A>?AA??>>8>?>>????>?9=9==9>###################
-@GA5:3:49:1480:1116#0
-TTTCCAGAGAGTTGGTGTGTAGGGGGCAGGGGAGGGAGGTGATGGCTGTGGGTCCCTGAAGTCCTGGCCTCCTCCC
-+
-BBBAAABAA?A?ABA;A=A=??==>?=>???=;==449=4:44#################################
-@GA5:3:61:213:1812#0
-TCCTGGCTTCAGTTTTTCAATTCGTAAAAAGAGCAAACAAAGCCCAACAGCTGGTCCAGTCCGACCCCGCCGGACC
-+
-BCBBBBBBBB;B4B@ABA9AAABB>BBBB>5>=BAB@@A8C=BA@@;;=6:78:7;;1,),4=584=8495,18=/
-@GA5:3:116:1581:552#0
-AAGGCTCTGCCTTAGAAGCAGAGATGGGTACCTCACCAGACACCAAACCTGCTGGCACCCTGACCTTAGGCTTTCT
-+
-B?BBCBBABBBBB@B???BBBAB@=@AB6AB@@A?B?@@>AA=<@@@89??@8?=<;@8<8<89;=3,92478884
--- a/test-data/jaccardBed_result1.bed	Mon Apr 29 05:55:48 2019 -0400
+++ b/test-data/jaccardBed_result1.bed	Fri Sep 06 14:29:59 2019 -0400
@@ -1,2 +1,2 @@
-intersection	union-intersection	jaccard	n_intersections
+intersection	union	jaccard	n_intersections
 5	20	0.25	1
--- a/test-data/jaccardBed_result2.bed	Mon Apr 29 05:55:48 2019 -0400
+++ b/test-data/jaccardBed_result2.bed	Fri Sep 06 14:29:59 2019 -0400
@@ -1,2 +1,2 @@
-intersection	union-intersection	jaccard	n_intersections
+intersection	union	jaccard	n_intersections
 5	20	0.25	1
Binary file test-data/srma_in3.bam has changed