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changeset 19:a8eabd2838f6 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 542ddc9e98cee5cc2a9e4caae945dee4b2c747b8
author iuc
date Fri, 08 Dec 2017 03:26:42 -0500
parents 18aeac3cd1db
children df56e1b12d0c
files bedToBam.xml bedpeToBam.xml complementBed.xml coverageBed.xml fisherBed.xml flankBed.xml genomeCoverageBed.xml macros.xml makeWindowsBed.xml mapBed.xml maskFastaBed.xml multiIntersectBed.xml randomBed.xml reldist.xml shuffleBed.xml slopBed.xml test-data/reldistBed_result1.bed test-data/shuffleBed_result1.bed test-data/shuffleBed_result2.bed test-data/shuffleBed_result3.bed test-data/shuffleBed_result4.bed test-data/spacingBed_result1.bed unionBedGraphs.xml
diffstat 23 files changed, 36 insertions(+), 32 deletions(-) [+]
line wrap: on
line diff
--- a/bedToBam.xml	Sat Oct 21 07:57:53 2017 -0400
+++ b/bedToBam.xml	Fri Dec 08 03:26:42 2017 -0500
@@ -1,4 +1,4 @@
-<tool id="bedtools_bedtobam" name="BED to BAM" version="@WRAPPER_VERSION@.1">
+<tool id="bedtools_bedtobam" name="BED to BAM" version="@WRAPPER_VERSION@.0">
     <description>converter</description>
     <macros>
         <import>macros.xml</import>
--- a/bedpeToBam.xml	Sat Oct 21 07:57:53 2017 -0400
+++ b/bedpeToBam.xml	Fri Dec 08 03:26:42 2017 -0500
@@ -1,4 +1,4 @@
-<tool id="bedtools_bedpetobam" name="BEDPE to BAM" version="@WRAPPER_VERSION@.1">
+<tool id="bedtools_bedpetobam" name="BEDPE to BAM" version="@WRAPPER_VERSION@.0">
     <description>converter</description>
     <macros>
         <import>macros.xml</import>
--- a/complementBed.xml	Sat Oct 21 07:57:53 2017 -0400
+++ b/complementBed.xml	Fri Dec 08 03:26:42 2017 -0500
@@ -1,4 +1,4 @@
-<tool id="bedtools_complementbed" name="ComplementBed" version="@WRAPPER_VERSION@.1">
+<tool id="bedtools_complementbed" name="ComplementBed" version="@WRAPPER_VERSION@.0">
     <description>Extract intervals not represented by an interval file</description>
     <macros>
         <import>macros.xml</import>
--- a/coverageBed.xml	Sat Oct 21 07:57:53 2017 -0400
+++ b/coverageBed.xml	Fri Dec 08 03:26:42 2017 -0500
@@ -1,4 +1,4 @@
-<tool id="bedtools_coveragebed" name="Compute both the depth and breadth of coverage" version="@WRAPPER_VERSION@.1">
+<tool id="bedtools_coveragebed" name="Compute both the depth and breadth of coverage" version="@WRAPPER_VERSION@.0">
     <description>of features in file B on the features in file A (bedtools coverage)</description>
     <macros>
         <import>macros.xml</import>
--- a/fisherBed.xml	Sat Oct 21 07:57:53 2017 -0400
+++ b/fisherBed.xml	Fri Dec 08 03:26:42 2017 -0500
@@ -1,4 +1,4 @@
-<tool id="bedtools_fisher" name="FisherBed" version="@WRAPPER_VERSION@.1">
+<tool id="bedtools_fisher" name="FisherBed" version="@WRAPPER_VERSION@.0">
     <description>calculate Fisher statistic between two feature files</description>
     <macros>
         <import>macros.xml</import>
--- a/flankBed.xml	Sat Oct 21 07:57:53 2017 -0400
+++ b/flankBed.xml	Fri Dec 08 03:26:42 2017 -0500
@@ -1,4 +1,4 @@
-<tool id="bedtools_flankbed" name="FlankBed" version="@WRAPPER_VERSION@.1">
+<tool id="bedtools_flankbed" name="FlankBed" version="@WRAPPER_VERSION@.0">
     <description>create new intervals from the flanks of existing intervals</description>
     <macros>
         <import>macros.xml</import>
--- a/genomeCoverageBed.xml	Sat Oct 21 07:57:53 2017 -0400
+++ b/genomeCoverageBed.xml	Fri Dec 08 03:26:42 2017 -0500
@@ -1,4 +1,4 @@
-<tool id="bedtools_genomecoveragebed" name="Genome Coverage" version="@WRAPPER_VERSION@.1">
+<tool id="bedtools_genomecoveragebed" name="Genome Coverage" version="@WRAPPER_VERSION@.0">
     <description>compute the coverage over an entire genome</description>
     <macros>
         <import>macros.xml</import>
--- a/macros.xml	Sat Oct 21 07:57:53 2017 -0400
+++ b/macros.xml	Fri Dec 08 03:26:42 2017 -0500
@@ -1,11 +1,11 @@
 <macros>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="2.26.0gx">bedtools</requirement>
+            <requirement type="package" version="2.27.0">bedtools</requirement>
             <yield/>
         </requirements>
     </xml>
-    <token name="@WRAPPER_VERSION@">2.26.0</token>
+    <token name="@WRAPPER_VERSION@">2.27.0</token>
     <xml name="stdio">
         <stdio>
             <!-- Anything other than zero is an error -->
--- a/makeWindowsBed.xml	Sat Oct 21 07:57:53 2017 -0400
+++ b/makeWindowsBed.xml	Fri Dec 08 03:26:42 2017 -0500
@@ -1,4 +1,4 @@
-<tool id="bedtools_makewindowsbed" name="MakeWindowsBed" version="@WRAPPER_VERSION@.1">
+<tool id="bedtools_makewindowsbed" name="MakeWindowsBed" version="@WRAPPER_VERSION@.0">
     <description>make interval windows across a genome</description>
     <macros>
         <import>macros.xml</import>
--- a/mapBed.xml	Sat Oct 21 07:57:53 2017 -0400
+++ b/mapBed.xml	Fri Dec 08 03:26:42 2017 -0500
@@ -1,4 +1,4 @@
-<tool id="bedtools_map" name="MapBed" version="@WRAPPER_VERSION@.1">
+<tool id="bedtools_map" name="MapBed" version="@WRAPPER_VERSION@.0">
     <description>apply a function to a column for each overlapping interval</description>
     <macros>
         <import>macros.xml</import>
--- a/maskFastaBed.xml	Sat Oct 21 07:57:53 2017 -0400
+++ b/maskFastaBed.xml	Fri Dec 08 03:26:42 2017 -0500
@@ -9,10 +9,11 @@
 <![CDATA[
         bedtools maskfasta
             $soft
-            -mc "${mc}"
-            -fi "${fasta}"
-            -bed "${input}"
-            -fo "${output}"
+            -mc '${mc}'
+            -fi '${fasta}'
+            -bed '${input}'
+            -fo '${output}'
+            $fullheader
 ]]>
     </command>
     <inputs>
@@ -24,6 +25,9 @@
         <param name="mc" type="text"  value="N"
             label="Replace masking character"
             help="That is, instead of masking with Ns, use another character. (-mc)" />
+        <param argument="-fullheader" type="boolean" truevalue="-fullheader" falsevalue=""
+            label="Use full fasta header." 
+            help="By default, only the word before the first space or tab is used"/>
     </inputs>
     <outputs>
         <data format="fasta" name="output" />
--- a/multiIntersectBed.xml	Sat Oct 21 07:57:53 2017 -0400
+++ b/multiIntersectBed.xml	Fri Dec 08 03:26:42 2017 -0500
@@ -1,4 +1,4 @@
-<tool id="bedtools_multiintersectbed" name="Multiple Intersect" version="@WRAPPER_VERSION@.1">
+<tool id="bedtools_multiintersectbed" name="Multiple Intersect" version="@WRAPPER_VERSION@.0">
     <description>identifies common intervals among multiple interval files</description>
     <macros>
         <import>macros.xml</import>
--- a/randomBed.xml	Sat Oct 21 07:57:53 2017 -0400
+++ b/randomBed.xml	Fri Dec 08 03:26:42 2017 -0500
@@ -1,4 +1,4 @@
-<tool id="bedtools_randombed" name="RandomBed" version="@WRAPPER_VERSION@.1">
+<tool id="bedtools_randombed" name="RandomBed" version="@WRAPPER_VERSION@.0">
     <description>generate random intervals in a genome</description>
     <macros>
         <import>macros.xml</import>
--- a/reldist.xml	Sat Oct 21 07:57:53 2017 -0400
+++ b/reldist.xml	Fri Dec 08 03:26:42 2017 -0500
@@ -25,8 +25,8 @@
     </outputs>
     <tests>
         <test>
-            <param name="inputA" value="windowBed_result1.bed" ftype="bed" />
-            <param name="inputB" value="windowBed_result1.bed" ftype="bed" />
+            <param name="inputA" value="a.bed" ftype="bed" />
+            <param name="inputB" value="a.bed" ftype="bed" />
             <output name="output" file="reldistBed_result1.bed" ftype="bed" />
         </test>
     </tests>
--- a/shuffleBed.xml	Sat Oct 21 07:57:53 2017 -0400
+++ b/shuffleBed.xml	Fri Dec 08 03:26:42 2017 -0500
@@ -1,4 +1,4 @@
-<tool id="bedtools_shufflebed" name="ShuffleBed" version="@WRAPPER_VERSION@.1">
+<tool id="bedtools_shufflebed" name="ShuffleBed" version="@WRAPPER_VERSION@.0">
     <description>randomly redistrubute intervals in a genome</description>
     <macros>
         <import>macros.xml</import>
--- a/slopBed.xml	Sat Oct 21 07:57:53 2017 -0400
+++ b/slopBed.xml	Fri Dec 08 03:26:42 2017 -0500
@@ -1,4 +1,4 @@
-<tool id="bedtools_slopbed" name="SlopBed" version="@WRAPPER_VERSION@.1">
+<tool id="bedtools_slopbed" name="SlopBed" version="@WRAPPER_VERSION@.0">
     <description>adjust the size of intervals</description>
     <macros>
         <import>macros.xml</import>
--- a/test-data/reldistBed_result1.bed	Sat Oct 21 07:57:53 2017 -0400
+++ b/test-data/reldistBed_result1.bed	Fri Dec 08 03:26:42 2017 -0500
@@ -1,2 +1,2 @@
 reldist	count	total	fraction
-0.00	1	1	1.000
+0.00	4	4	1.000
--- a/test-data/shuffleBed_result1.bed	Sat Oct 21 07:57:53 2017 -0400
+++ b/test-data/shuffleBed_result1.bed	Fri Dec 08 03:26:42 2017 -0500
@@ -1,2 +1,2 @@
-chr2	5070	5170	a1	1	+
-chr1	2199	3199	a2	2	-
+chr2	51	151	a1	1	+
+chr2	720	1720	a2	2	-
--- a/test-data/shuffleBed_result2.bed	Sat Oct 21 07:57:53 2017 -0400
+++ b/test-data/shuffleBed_result2.bed	Fri Dec 08 03:26:42 2017 -0500
@@ -1,2 +1,2 @@
-chr1	9383	9483	a1	1	+
-chr1	886	1886	a2	2	-
+chr1	5845	5945	a1	1	+
+chr1	6139	7139	a2	2	-
--- a/test-data/shuffleBed_result3.bed	Sat Oct 21 07:57:53 2017 -0400
+++ b/test-data/shuffleBed_result3.bed	Fri Dec 08 03:26:42 2017 -0500
@@ -1,2 +1,2 @@
-chr2	5070	5170	a1	1	+
-chr1	2199	3199	a2	2	-
+chr2	51	151	a1	1	+
+chr2	720	1720	a2	2	-
--- a/test-data/shuffleBed_result4.bed	Sat Oct 21 07:57:53 2017 -0400
+++ b/test-data/shuffleBed_result4.bed	Fri Dec 08 03:26:42 2017 -0500
@@ -1,2 +1,2 @@
-chr2	5070	5170	a1	1	+
-chr3	4411	5000	a2	2	-
+chr2	51	151	a1	1	+
+chr2	720	1720	a2	2	-
--- a/test-data/spacingBed_result1.bed	Sat Oct 21 07:57:53 2017 -0400
+++ b/test-data/spacingBed_result1.bed	Fri Dec 08 03:26:42 2017 -0500
@@ -1,4 +1,4 @@
 chr1	100	200	.
-chr1	180	250	0
+chr1	180	250	-1
 chr1	250	500	0
 chr1	501	1000	1
--- a/unionBedGraphs.xml	Sat Oct 21 07:57:53 2017 -0400
+++ b/unionBedGraphs.xml	Fri Dec 08 03:26:42 2017 -0500
@@ -1,4 +1,4 @@
-<tool id="bedtools_unionbedgraph" name="Merge BedGraph files" version="@WRAPPER_VERSION@.1">
+<tool id="bedtools_unionbedgraph" name="Merge BedGraph files" version="@WRAPPER_VERSION@.0">
     <description>combines coverage intervals from multiple BEDGRAPH files</description>
     <macros>
         <import>macros.xml</import>