# HG changeset patch
# User bgruening
# Date 1389374291 18000
# Node ID 07390b1a7bdc39e97b671083be3aa1d35d21e1bc
# Parent  662c1741c22d4667189ff76c23d489e9951def61
Uploaded

diff -r 662c1741c22d -r 07390b1a7bdc bamToBed.xml
--- a/bamToBed.xml	Fri Jan 10 11:51:13 2014 -0500
+++ b/bamToBed.xml	Fri Jan 10 12:18:11 2014 -0500
@@ -1,36 +1,31 @@
-<tool id="bedtools_bamtobed" name="Convert from BAM to BED" version="0.2.0">
-
-    <description>
-    </description>
-
+<tool id="bedtools_bamtobed" name="BAM to BED" version="2.18.2.0">
+    <description>converter</description>
     <requirements>
-        <requirement type="package" version="2.17.0_5e4507c54355a4a38c6d3e7497a2836a123c6655">bedtools</requirement>
+        <requirement type="package" version="2.18.2">bedtools2</requirement>
     </requirements>
-
-<command>
-    bamToBed $option $ed_score -i '$input' &gt; '$output' 
-    #if str($tag):
-      -tag      $tag
-    #end if
-</command>
+    <version_command>bedtools --version</version_command>
+    <command>
+        bamToBed $option $ed_score -i '$input' &gt; '$output' 
+        #if str($tag):
+          -tag      $tag
+        #end if
+    </command>
+    <inputs>
+        <param format="bam" name="input" type="data" label="Convert the following BAM file to BED"/>
+        <param name="option" type="select" label="What type of BED output would you like">
+            <option value="">Create a 6-column BED file.</option>
+            <option value="-bed12">Create a full, 12-column "blocked" BED file.</option>
+            <option value="-bedpe">Create a paired-end, BEDPE format.</option>
+        </param>
+        <param name="split" type="boolean" label="Report spliced BAM alignments as separate BED entries" truevalue="-split" falsevalue="" checked="false"/>
+        <param name="ed_score" type="boolean" label="Use alignment's edit-distance for BED score" truevalue="-ed" falsevalue="" checked="false"/>
+        <param name="tag" type="text" optional="true" label="Use other NUMERIC BAM alignment tag as the BED score"/>
+    </inputs>
 
-<inputs>
-    <param format="bam" name="input" type="data" label="Convert the following BAM file to BED"/>
-    <param name="option" type="select" label="What type of BED output would you like">
-        <option value="">Create a 6-column BED file.</option>
-        <option value="-bed12">Create a full, 12-column "blocked" BED file.</option>
-        <option value="-bedpe">Create a paired-end, BEDPE format.</option>
-    </param>
-    <param name="split" type="boolean" label="Report spliced BAM alignments as separate BED entries" truevalue="-split" falsevalue="" checked="false"/>
-    <param name="ed_score" type="boolean" label="Use alignment's edit-distance for BED score" truevalue="-ed" falsevalue="" checked="false"/>
-    <param name="tag" type="text" optional="true" label="Use other NUMERIC BAM alignment tag as the BED score"/>
-</inputs>
-
-<outputs>
-    <data format="bed" name="output" metadata_source="input" label="${input.name} (as BED)"/>
-</outputs>
-
-<help>
+    <outputs>
+        <data format="bed" name="output" metadata_source="input" label="${input.name} (as BED)"/>
+    </outputs>
+    <help>
 
 **What it does**
 
@@ -60,7 +55,5 @@
     .. __: http://cphg.virginia.edu/quinlan/
     .. __: http://bioinformatics.oxfordjournals.org/content/26/6/841.short
 
-
-
-</help>
+    </help>
 </tool>
diff -r 662c1741c22d -r 07390b1a7bdc coverageBed_counts.xml
--- a/coverageBed_counts.xml	Fri Jan 10 11:51:13 2014 -0500
+++ b/coverageBed_counts.xml	Fri Jan 10 12:18:11 2014 -0500
@@ -1,7 +1,7 @@
 <tool id="bedtools_coveragebed_counts" name="Count intervals" version="2.18.2.0">
     <description>in one file overlapping intervals in another file</description>
     <requirements>
-        <requirement type="package" version="2.18.2">bedtools</requirement>
+        <requirement type="package" version="2.18.2">bedtools2</requirement>
     </requirements>
     <version_command>bedtools --version</version_command>
     <command>
diff -r 662c1741c22d -r 07390b1a7bdc genomeCoverageBed_bedgraph.xml
--- a/genomeCoverageBed_bedgraph.xml	Fri Jan 10 11:51:13 2014 -0500
+++ b/genomeCoverageBed_bedgraph.xml	Fri Jan 10 12:18:11 2014 -0500
@@ -1,7 +1,7 @@
 <tool id="bedtools_genomecoveragebed_bedgraph" name="Create a BedGraph" version="2.18.2.0">
     <description>of genome coverage</description>
     <requirements>
-        <requirement type="package" version="2.18.2">bedtools</requirement>
+        <requirement type="package" version="2.18.2">bedtools2</requirement>
     </requirements>
     <version_command>bedtools --version</version_command>
     <command>genomeCoverageBed
diff -r 662c1741c22d -r 07390b1a7bdc genomeCoverageBed_histogram.xml
--- a/genomeCoverageBed_histogram.xml	Fri Jan 10 11:51:13 2014 -0500
+++ b/genomeCoverageBed_histogram.xml	Fri Jan 10 12:18:11 2014 -0500
@@ -1,7 +1,7 @@
 <tool id="bedtools_genomecoveragebed_histogram" name="Create a histogram" version="2.18.2.0">
     <description>of genome coverage</description>
     <requirements>
-        <requirement type="package" version="2.18.2">bedtools</requirement>
+        <requirement type="package" version="2.18.2">bedtools2</requirement>
     </requirements>
     <version_command>bedtools --version</version_command>
     <command>genomeCoverageBed
diff -r 662c1741c22d -r 07390b1a7bdc intersectBed.xml
--- a/intersectBed.xml	Fri Jan 10 11:51:13 2014 -0500
+++ b/intersectBed.xml	Fri Jan 10 12:18:11 2014 -0500
@@ -2,7 +2,7 @@
     <description>
     </description>
     <requirements>
-        <requirement type="package" version="2.18.2">bedtools</requirement>
+        <requirement type="package" version="2.18.2">bedtools2</requirement>
     </requirements>
     <version_command>bedtools --version</version_command>
     <command>
diff -r 662c1741c22d -r 07390b1a7bdc multiIntersectBed.xml
--- a/multiIntersectBed.xml	Fri Jan 10 11:51:13 2014 -0500
+++ b/multiIntersectBed.xml	Fri Jan 10 12:18:11 2014 -0500
@@ -1,7 +1,7 @@
 <tool id="bedtools_multiintersectbed" name="Intersect" version="2.18.2.0">
     <description>multiple sorted BED files</description>
     <requirements>
-        <requirement type="package" version="2.18.2">bedtools</requirement>
+        <requirement type="package" version="2.18.2">bedtools2</requirement>
     </requirements>
     <version_command>bedtools --version</version_command>
     <command>multiIntersectBed
diff -r 662c1741c22d -r 07390b1a7bdc sortBed.xml
--- a/sortBed.xml	Fri Jan 10 11:51:13 2014 -0500
+++ b/sortBed.xml	Fri Jan 10 12:18:11 2014 -0500
@@ -1,7 +1,7 @@
 <tool id="bedtools_sortbed" name="Sort BED" version="2.18.2.0">
     <description>files</description>
     <requirements>
-        <requirement type="package" version="2.18.2">bedtools</requirement>
+        <requirement type="package" version="2.18.2">bedtools2</requirement>
     </requirements>
     <version_command>bedtools --version</version_command>
     <command>
diff -r 662c1741c22d -r 07390b1a7bdc tool_dependencies.xml
--- a/tool_dependencies.xml	Fri Jan 10 11:51:13 2014 -0500
+++ b/tool_dependencies.xml	Fri Jan 10 12:18:11 2014 -0500
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="bedtools" version="2.18.2">
-        <repository changeset_revision="044d68a0c07f" name="package_bedtools_2_18" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    <package name="bedtools2" version="2.18.2">
+        <repository changeset_revision="ea89a5911878" name="package_bedtools_2_18" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>
diff -r 662c1741c22d -r 07390b1a7bdc unionBedGraphs.xml
--- a/unionBedGraphs.xml	Fri Jan 10 11:51:13 2014 -0500
+++ b/unionBedGraphs.xml	Fri Jan 10 12:18:11 2014 -0500
@@ -1,7 +1,7 @@
 <tool id="bedtools_mergebedgraph" name="Merge BedGraph" version="2.18.2.0">
     <description>files</description>
     <requirements>
-        <requirement type="package" version="2.18.2">bedtools</requirement>
+        <requirement type="package" version="2.18.2">bedtools2</requirement>
     </requirements>
     <version_command>bedtools --version</version_command>
     <command>unionBedGraphs