--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Tue Apr 21 17:41:18 2015 -0400
@@ -0,0 +1,70 @@
+<macros>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="1.2">samtools</requirement>
+            <yield/>
+        </requirements>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="bibtex">
+                @misc{SAM_def,
+                title={Definition of SAM/BAM format},
+                url = {https://samtools.github.io/hts-specs/SAMv1.pdf},}
+            </citation>
+            <citation type="doi">10.1093/bioinformatics/btp352</citation>
+            <citation type="doi">10.1093/bioinformatics/btr076</citation>
+            <citation type="doi">10.1093/bioinformatics/btr509</citation>
+            <citation type="bibtex">
+                @misc{Danecek_et_al,
+                Author={Danecek, P., Schiffels, S., Durbin, R.},
+                title={Multiallelic calling model in bcftools (-m)},
+                url = {http://samtools.github.io/bcftools/call-m.pdf},}
+            </citation>
+            <citation type="bibtex">
+                @misc{Durbin_VCQC,
+                Author={Durbin, R.},
+                title={Segregation based metric for variant call QC},
+                url = {http://samtools.github.io/bcftools/rd-SegBias.pdf},}
+            </citation>
+            <citation type="bibtex">
+                @misc{Li_SamMath,
+                Author={Li, H.},
+                title={Mathematical Notes on SAMtools Algorithms},
+                url = {http://www.broadinstitute.org/gatk/media/docs/Samtools.pdf},}
+            </citation>
+            <citation type="bibtex">
+                @misc{SamTools_github,
+                title={SAMTools GitHub page},
+                url = {https://github.com/samtools/samtools},}
+            </citation>
+        </citations>
+    </xml>
+    <xml name="version_command">
+        <version_command>samtools --version | head -n 1 | awk '{ print $2 }'</version_command>
+    </xml>
+    <xml name="stdio">
+        <stdio>
+            <exit_code range="1:" level="fatal" description="Error" />
+        </stdio>
+    </xml>
+    <token name="@no-chrom-options@">
+-----
+
+.. class:: warningmark
+
+**No options available? How to re-detect metadata**
+
+If you see a &quot;No options available&quot; within the &quot;**Select references (chromosomes and contigs) you would like to restrict bam to**&quot; drop down, you need to re-detect metadata for the dataset you are trying to process. To do this follow these steps:
+
+1. Click on the **pencil** icon adjacent to the dataset in the history
+2. A new menu will appear in the center pane of the interface
+3. Click **Datatype** tab
+4. Set **New Type** to **BAM**
+5. Click **Save**
+
+The medatada will be re-detected and you will be able to see the list of reference sequences in the &quot;**Select references (chromosomes and contigs) you would like to restrict bam to**&quot; drop-down.
+
+    </token>
+
+</macros>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/samtools_sort.xml	Tue Apr 21 17:41:18 2015 -0400
@@ -0,0 +1,40 @@
+<tool id="samtools_sort" name="Sort" version="2.0">
+    <description>BAM dataset</description>
+    <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements"></expand>
+    <expand macro="stdio"></expand>
+    <expand macro="version_command"></expand>
+    <command>samtools sort $sort_mode -@ \${GALAXY_SLOTS:-1} -o "${output1}" -O bam -T dataset "${input1}"</command>
+    <inputs>
+        <param name="input1" type="data" format="bam" label="BAM File" />
+        <param name="sort_mode" type="select" label="Sort by ">
+            <option value="" selected="True">Chromosomal coordinates</option>
+            <option value="-n">Read names (-n)</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="output1" format="bam" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input1" value="1.bam" ftype="bam" />
+            <output name="output1" file="1_sort.bam" ftype="bam" sort="True"/>
+        </test>
+        <test>
+            <param name="input1" value="1.bam" ftype="bam" />
+            <param name="sort_mode" value="-n"/>
+            <output name="output1" file="1_sort_read_names.bam" ftype="bam" sort="True"/>
+        </test>
+    </tests>
+    <help>
+
+**What it does**
+
+This tool uses ``samtools sort`` command to sort BAM datasets in coordinate or read name order.
+
+
+    </help>
+    <expand macro="citations"></expand>
+</tool>

Binary file test-data/1.bam has changed

Binary file test-data/1_sort.bam has changed

Binary file test-data/1_sort_read_names.bam has changed

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Tue Apr 21 17:41:18 2015 -0400
@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="samtools" version="1.2">
+        <repository changeset_revision="6eea04363026" name="package_samtools_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>