# HG changeset patch
# User aaronquinlan
# Date 1323282533 18000
# Node ID f2270e47bda180c6757af9a4e0ca1d1f514aa065
# Parent  52830b3f342a8f59628f268615449d88a81e4972
Uploaded

diff -r 52830b3f342a -r f2270e47bda1 bedtools-galaxy/bedtools-galaxy/bamToBed.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bedtools-galaxy/bedtools-galaxy/bamToBed.xml	Wed Dec 07 13:28:53 2011 -0500
@@ -0,0 +1,75 @@
+<tool id="bedtools_bamtobed" name="Convert from BAM to BED." version="2.14.4">
+<description></description>
+
+<requirements>
+    <requirement type="binary">bamToBed</requirement>
+</requirements>
+
+<command>
+    bamToBed $option $ed_score -i '$input' &gt; '$output' 
+    #if str($tag):
+      -tag      $tag
+    #end if
+</command>
+
+<inputs>
+    <param format="bam" name="input" type="data" label="Input BAM file"/>
+    <param name="option" type="select" label="Output formatting options">
+        <option value="">Create a 6-column BED file.</option>
+        <option value="-bed12">Create a full, 12-column "blocked" BED file.</option>
+        <option value="-bedpe">Create a paired-end, BEDPE format.</option>
+    </param>
+    <param name="split" type="boolean" label="Report spliced BAM alignments as separate BED entries." truevalue="-split" falsevalue="" checked="false"/>
+    <param name="ed_score" type="boolean" label="Use alignment's edit-distance for BED score" truevalue="-ed" falsevalue="" checked="false"/>
+    <param name="tag" type="text" optional="true" label="Use other NUMERIC BAM alignment tag as the BED score"/>
+</inputs>
+
+<outputs>
+    <data format="bed" name="output" metadata_source="input" label="${input.name} (as BED)"/>
+</outputs>
+
+<help>
+
+**What it does**
+
+This tool converts a BAM file to a BED file. The end coordinate is computed
+by inspecting the CIGAR string. The QNAME for the alignment is used as the 
+BED name field and, by default, the MAPQ is used as the BED score.
+
+-------
+
+**Options**::
+    
+    -bedpe  Write BEDPE format.
+            - Requires BAM to be grouped or sorted by query.
+    
+    -bed12  Write "blocked" BED format (aka "BED12").
+            http://genome-test.cse.ucsc.edu/FAQ/FAQformat#format1
+    
+    -split  Report "split" BAM alignments as separate BED entries.
+    
+    -ed     Use BAM edit distance (NM tag) for BED score.
+              * Default for BED is to use mapping quality.
+              * Default for BEDPE is to use the minimum of the two mapping qualities for the pair.
+              * When -ed is used with -bedpe, the total edit distance from the two mates is reported.
+    
+    -tag    Use other NUMERIC BAM alignment tag for BED score.
+              * Default for BED is to use mapping quality.
+              * Disallowed with BEDPE output.
+<!--    
+    -color  An R,G,B string for the color used with BED12 format.
+            Default is (255,0,0).
+    
+    -cigar  Add the CIGAR string to the BED entry as a 7th column.
+-->
+
+------
+
+
+This tool is part of the `BEDTools package`__ from the `Quinlan laboratory`__.
+
+.. __: http://code.google.com/p/bedtools/
+.. __: http://cphg.virginia.edu/quinlan/
+
+</help>
+</tool>
diff -r 52830b3f342a -r f2270e47bda1 bedtools-galaxy/galaxy_configs/tool_conf.xml
--- a/bedtools-galaxy/galaxy_configs/tool_conf.xml	Sat Nov 19 16:22:54 2011 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,10 +0,0 @@
-<?xml version="1.0"?>
-<toolbox>
-	
-  <label text="BEDTools 2.14.1" id="bedtools" />
-
-  <section name="Genome Arithmetic Tools" id="bedtools_ga">
-    <tool file="bedtools/galaxy_configs/tools/bamToBed.xml"/>
-  </section>
-
-</toolbox>
\ No newline at end of file
diff -r 52830b3f342a -r f2270e47bda1 bedtools-galaxy/galaxy_configs/tools/bamToBed.xml
--- a/bedtools-galaxy/galaxy_configs/tools/bamToBed.xml	Sat Nov 19 16:22:54 2011 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,71 +0,0 @@
-<tool id="bedtools_bamtobed" name="Convert from BAM to BED." version="2.14.4">
-<description></description>
-
-<command>
-    bamToBed $option $ed_score -i '$input' &gt; '$output' 
-    #if str($tag):
-      -tag      $tag
-    #end if
-</command>
-
-<inputs>
-    <param format="bam" name="input" type="data" label="Input BAM file"/>
-    <param name="option" type="select" label="Output formatting options">
-        <option value="">Create a 6-column BED file.</option>
-        <option value="-bed12">Create a full, 12-column "blocked" BED file.</option>
-        <option value="-bedpe">Create a paired-end, BEDPE format.</option>
-    </param>
-    <param name="split" type="boolean" label="Report spliced BAM alignments as separate BED entries." truevalue="-split" falsevalue="" checked="false"/>
-    <param name="ed_score" type="boolean" label="Use alignment's edit-distance for BED score" truevalue="-ed" falsevalue="" checked="false"/>
-    <param name="tag" type="text" optional="true" label="Use other NUMERIC BAM alignment tag as the BED score"/>
-</inputs>
-
-<outputs>
-    <data format="bed" name="output" metadata_source="input" label="${input.name} (as BED)"/>
-</outputs>
-
-<help>
-
-**What it does**
-
-This tool converts a BAM file to a BED file. The end coordinate is computed
-by inspecting the CIGAR string. The QNAME for the alignment is used as the 
-BED name field and, by default, the MAPQ is used as the BED score.
-
--------
-
-**Options**::
-    
-    -bedpe  Write BEDPE format.
-            - Requires BAM to be grouped or sorted by query.
-    
-    -bed12  Write "blocked" BED format (aka "BED12").
-            http://genome-test.cse.ucsc.edu/FAQ/FAQformat#format1
-    
-    -split  Report "split" BAM alignments as separate BED entries.
-    
-    -ed     Use BAM edit distance (NM tag) for BED score.
-              * Default for BED is to use mapping quality.
-              * Default for BEDPE is to use the minimum of the two mapping qualities for the pair.
-              * When -ed is used with -bedpe, the total edit distance from the two mates is reported.
-    
-    -tag    Use other NUMERIC BAM alignment tag for BED score.
-              * Default for BED is to use mapping quality.
-              * Disallowed with BEDPE output.
-<!--    
-    -color  An R,G,B string for the color used with BED12 format.
-            Default is (255,0,0).
-    
-    -cigar  Add the CIGAR string to the BED entry as a 7th column.
--->
-
-------
-
-
-This tool is part of the `BEDTools package`__ from the `Quinlan laboratory`__.
-
-.. __: http://code.google.com/p/bedtools/
-.. __: http://cphg.virginia.edu/quinlan/
-
-</help>
-</tool>
diff -r 52830b3f342a -r f2270e47bda1 bedtools-galaxy/suite_config.xml
--- a/bedtools-galaxy/suite_config.xml	Sat Nov 19 16:22:54 2011 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,11 +0,0 @@
-<suite id="bedtools_suite" name="bedtools" version="2.14.4">
-
-	<description>
-		bedtools: A flexible toolset for genome arithmetic and analysis.
-	</description>
-
-	<tool id="bedtools_bamtobed" name="Upload File" version="1.1.2">
-	    <description>from your computer</description>
-	</tool>
-
-</suite>
\ No newline at end of file