# HG changeset patch
# User iuc
# Date 1444771234 14400
# Node ID 5efc48568d8dcdde1462087f1d9af8cffd78b254
# Parent  a2d4c30ba2f9c07ba9e55e44d085c2f9082d566e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5a5ad091c621348dc6ce2df861475ebc54a380e

diff -r a2d4c30ba2f9 -r 5efc48568d8d annotateBed.xml
--- a/annotateBed.xml	Sun Jun 21 22:49:46 2015 -0400
+++ b/annotateBed.xml	Tue Oct 13 17:20:34 2015 -0400
@@ -1,4 +1,4 @@
-<tool id="bedtools_annotatebed" name="AnnotateBed" version="@WRAPPER_VERSION@.0">
+<tool id="bedtools_annotatebed" name="AnnotateBed" version="@WRAPPER_VERSION@.1">
     <description>annotate coverage of features from multiple files</description>
     <macros>
         <import>macros.xml</import>
@@ -7,6 +7,7 @@
     <expand macro="stdio" />
     <command>
 <![CDATA[
+
         bedtools annotate
         -i "${inputA}"
         #if $names.names_select == 'yes':
@@ -22,6 +23,8 @@
         #else:
             #set files = '" "'.join( [ str( $file ) for $file in $names.beds ] )
             -files "${files}"
+            #set names = '" "'.join( [ str( $name.display_name ) for $name in $names.beds ] )
+            -names "${names}"
         #end if
         $strand
         $counts
diff -r a2d4c30ba2f9 -r 5efc48568d8d bamToBed.xml
--- a/bamToBed.xml	Sun Jun 21 22:49:46 2015 -0400
+++ b/bamToBed.xml	Tue Oct 13 17:20:34 2015 -0400
@@ -3,10 +3,19 @@
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements" />
+    <expand macro="requirements">
+        <requirement type="package" version="1.2">samtools</requirement>
+    </expand>
     <expand macro="stdio" />
     <command>
 <![CDATA[
+
+        #if $input.extension == 'bam' and $option == "-bedpe":
+            samtools sort -n "${input}" ./input &&
+        #else
+            ln -s "${input}" ./input.bam &&
+        #end if
+
         bedtools bamtobed
         $option
         $ed_score
@@ -14,20 +23,20 @@
         #if $tag and str($tag).strip():
           -tag "${tag}"
         #end if
-        -i "${input}"
+        -i ./input.bam
         > "${output}"
 ]]>
     </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>
+            <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>
         <expand macro="split" />
         <param name="ed_score" type="boolean" truevalue="-ed" falsevalue="" checked="false"
-            label="Use alignment's edit-distance for BED score" />
+            label="Use alignment's edit-distance for BED score" help="(-ed)" />
         <param name="tag" type="text" optional="true" label="Use other NUMERIC BAM alignment tag as the BED score"
             help="(-tag)"/>
     </inputs>
@@ -56,16 +65,16 @@
 
 .. class:: infomark
 
-The "Report spliced BAM alignment..." option breaks BAM alignments with the "N" (splice) operator into distinct BED entries.  For example, using this option on a CIGAR such as 50M1000N50M would, by default, produce a single BED record that spans 1100bp.  However, using this option, it would create two separate BED records that are each 50bp in size and are separated by 1000bp (the size of the N operation).  This is important for RNA-seq and structural variation experiments.
+The "Report spliced BAM alignment..." option breaks BAM alignments with the "N" (splice) operator into distinct BED entries.
+For example, using this option on a CIGAR such as 50M1000N50M would, by default, produce a single BED record that spans 1100bp.
+However, using this option, it would create two separate BED records that are each 50bp in size and are separated by 1000bp (the size of the N operation).
+This is important for RNA-seq and structural variation experiments.
 
 
 .. class:: warningmark
 
-If using a custom BAM alignment TAG as  the BED score, note that this must be a numeric tag (e.g., type "i" as in NM:i:0).
+If using a custom BAM alignment TAG as the BED score, note that this must be a numeric tag (e.g., type "i" as in NM:i:0).
 
-.. class:: warningmark
-
-If creating a BEDPE output (see output formatting options), the BAM file should be sorted by query name.
 
 @REFERENCES@
 ]]>
diff -r a2d4c30ba2f9 -r 5efc48568d8d bamToFastq.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bamToFastq.xml	Tue Oct 13 17:20:34 2015 -0400
@@ -0,0 +1,39 @@
+<tool id="bedtools_bamtofastq" name="Convert from BAM to FastQ" version="@WRAPPER_VERSION@.0">
+    <description></description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <command>
+        bedtools bamtofastq
+        $tags
+        -i '$input'
+        -fq '$output'
+        #if $fq2:
+           -fq2 '$output2'
+        #end if
+    </command>
+    <inputs>
+        <param format="bam" name="input" type="data" label="Convert the following BAM file to FASTQ"/>
+        <param name="tags" type="boolean" truevalue="-tags" falsevalue="" selected="False" label="Create FASTQ based on the mate info in the BAM R2 and Q2 tags."/>
+        <param name="fq2" type="boolean" truevalue="-fq2" falsevalue="" selected="False" label="FASTQ for second end.
+            Used if BAM contains paired-end data. BAM should be sorted by query name if creating paired FASTQ with this option."/>
+    </inputs>
+    <outputs>
+        <data format="fastq" name="output" metadata_source="input" label="${input.name} (as FASTQ)"/>
+        <data format="fastq2" name="output2" metadata_source="input" label="${input.name} (as FASTQ)">
+            <filter>fq2 is True</filter>
+        </data>
+    </outputs>
+<help>
+
+**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>
diff -r a2d4c30ba2f9 -r 5efc48568d8d flankBed.xml
--- a/flankBed.xml	Sun Jun 21 22:49:46 2015 -0400
+++ b/flankBed.xml	Tue Oct 13 17:20:34 2015 -0400
@@ -27,10 +27,10 @@
         <expand macro="genome" />
         <param name="pct" type="boolean" checked="false" truevalue="-pct" falsevalue=""
             label="Define -l and -r as a fraction of the feature’s length"
-            help="E.g. if used on a 1000bp feature, -l 0.50, will add 500 bp “upstream”" />
+            help="E.g. if used on a 1000bp feature, -l 0.50, will add 500 bp “upstream”. (-pct)" />
         <param name="strand" type="boolean" checked="false" truevalue="-s" falsevalue=""
             label="Define -l and -r based on strand"
-            help="For example. if used, -l 500 for a negative-stranded feature, it will add 500 bp to the end coordinate" />
+            help="For example. if used, -l 500 for a negative-stranded feature, it will add 500 bp to the end coordinate. (-s)" />
         <expand macro="addition" />
     </inputs>
     <outputs>
diff -r a2d4c30ba2f9 -r 5efc48568d8d intersectBed.xml
--- a/intersectBed.xml	Sun Jun 21 22:49:46 2015 -0400
+++ b/intersectBed.xml	Tue Oct 13 17:20:34 2015 -0400
@@ -28,6 +28,7 @@
             $once
             $header
             $modes
+            $count
             > "${output}"
 ]]>
     </command>
diff -r a2d4c30ba2f9 -r 5efc48568d8d test-data/annotateBed_result.bed
--- a/test-data/annotateBed_result.bed	Sun Jun 21 22:49:46 2015 -0400
+++ b/test-data/annotateBed_result.bed	Tue Oct 13 17:20:34 2015 -0400
@@ -1,3 +1,4 @@
+#					annotateBed2.bed	annotateBed3.bed	annotateBed4.bed	
 chr1	100	200	nasty	1	-	0.500000	1.000000	0.300000
 chr2	500	1000	ugly	2	+	0.000000	0.600000	1.000000
 chr3	1000	5000	big	3	-	1.000000	0.250000	0.000000
diff -r a2d4c30ba2f9 -r 5efc48568d8d tool_dependencies.xml
--- a/tool_dependencies.xml	Sun Jun 21 22:49:46 2015 -0400
+++ b/tool_dependencies.xml	Tue Oct 13 17:20:34 2015 -0400
@@ -1,6 +1,9 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="bedtools" version="2.23">
-        <repository changeset_revision="c472a4f6a603" name="package_bedtools_2_23" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    <package name="bedtools" version="2.24">
+        <repository changeset_revision="e6f4a7398a47" name="package_bedtools_2_24" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="samtools" version="1.2">
+        <repository changeset_revision="192f00129358" name="package_samtools_1_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>