# HG changeset patch
# User brenninc
# Date 1458825972 14400
# Node ID 6a2c228f93e3ce36afcf252aa37fdac18cbccdab

Uploaded upload

diff -r 000000000000 -r 6a2c228f93e3 pairedbamtobed.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pairedbamtobed.xml	Thu Mar 24 09:26:12 2016 -0400
@@ -0,0 +1,49 @@
+<tool id="pairedbamtobed12" name="Paired bam to bed12" version="0.1">
+    <description>Paired Bam to Bed. With samtools sorting by name beforehand and back to required order for galaxy afterwards.</description>
+    <requirements>
+        <requirement type="package" version="1.0">pairedbamtobed12</requirement>
+        <requirement type="package" version="1.2">samtools</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range="1:" level="fatal" description="Error" />
+    </stdio>
+    <command>
+    <![CDATA[
+        samtools sort -n -O bam -T by_name        -o sorted_by_name.bam  "${input}" ;
+        pairedBamToBed12 -i sorted_by_name.bam > "${output}"
+    ]]>
+    </command>
+    <inputs>
+        <param name="input" format="bam" label="Select BAM dataset to convert to bed" type="data" />
+    </inputs>
+    <outputs>
+        <data format="bed" name="output" label="Bed12 version of ${on_string}" />
+    </outputs>
+    <tests>
+        <!-- test data too large for toolshed 
+             See: https://github.com/Christian-B/galaxy_shedtools/tree/master/pairedBamToBed12 -->
+        <!--test>
+            <param ftype="bam" name="input" value="filtered.bam" />
+            <output file="paired.bed" ftype="bed" name="output" />
+        </test-->
+    </tests>
+    <help>
+<![CDATA[
+This tools runs pairedbamtobed12 to convert a paired bam file to a bed file.
+
+As pairedbamtobed12 requires a bam file sorted by name, while galaxy only allows ones sorted by alignment this tool first uses Samtools to reorder the bam file.
+
+
+]]>
+    </help>
+    <citations>
+        <citation type="bibtex">
+            @misc{
+                pairedBamToBed12,
+                author = {Nicolas Bertin, Mickaël Mendez, Charles Plessy},
+                title = {pairedBamToBed12 on GitHub},
+                url = {https://github.com/Population-Transcriptomics/pairedBamToBed12}
+            }
+        </citation>
+    </citations>
+</tool>
diff -r 000000000000 -r 6a2c228f93e3 tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Thu Mar 24 09:26:12 2016 -0400
@@ -0,0 +1,9 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="samtools" version="1.2">
+        <repository changeset_revision="5b7172f9b230" name="package_samtools_1_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="pairedbamtobed12" version="1.0">
+        <repository changeset_revision="664d90d44e82" name="package_pairedbamtobed12" owner="brenninc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>