Binary file test-data/ex1.bam has changed

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ex1.depth.tabular	Wed May 13 10:29:23 2015 -0400
@@ -0,0 +1,3037 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
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+ref	46	1
+ref	47	1

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sam_spec_padded.sam	Wed May 13 10:29:23 2015 -0400
@@ -0,0 +1,10 @@
+@HD	VN:1.5	SO:coordinate
+@SQ	SN:ref	LN:47
+ref	516	ref	1	0	14M2D31M	*	0	0	AGCATGTTAGATAAGATAGCTGTGCTAGTAGGCAGTCAGCGCCAT	*
+r001	99	ref	7	30	14M1D3M	=	39	41	TTAGATAAAGGATACTG	*
+*	768	ref	8	30	1M	*	0	0	*	*	CT:Z:.;Warning;Note=Ref wrong?
+r002	0	ref	9	30	3S6M1D5M	*	0	0	AAAAGATAAGGATA	*	PT:Z:1;4;+;homopolymer
+r003	0	ref	9	30	5H6M	*	0	0	AGCTAA	*	NM:i:1
+r004	0	ref	18	30	6M14D5M	*	0	0	ATAGCTTCAGC	*
+r003	2064	ref	31	30	6H5M	*	0	0	TAGGC	*	NM:i:0
+r001	147	ref	39	30	9M	=	7	-41	CAGCGGCAT	*	NM:i:1

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/samtools_depth/README.rst	Wed May 13 10:29:23 2015 -0400
@@ -0,0 +1,113 @@
+Galaxy wrapper for samtools depth
+=================================
+
+This wrapper is copyright 2013-2015 by Peter Cock, The James Hutton Institute
+(formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
+See the licence text below.
+
+This is a wrapper for part of the command line samtools suite.
+
+This wrapper is available from the Galaxy Tool Shed at:
+http://toolshed.g2.bx.psu.edu/view/peterjc/samtools_idxstats
+
+
+Automated Installation
+======================
+
+This should be straightforward, Galaxy should automatically download and install
+samtools 1.1 if required.
+
+
+Manual Installation
+===================
+
+This expects samtools to be on the $PATH, and was tested using v1.1
+
+To install the wrapper copy or move the following files under the Galaxy tools
+folder, e.g. in a ``tools/samtools_depth`` folder:
+
+* ``samtools_depth.xml`` (the Galaxy tool definition)
+* ``README.rst`` (this file)
+
+You will also need to modify the ``tools_conf.xml`` file to tell Galaxy to offer
+the tool. Just add the line, perhaps under the NGS tools section::
+
+  <tool file="samtools_depth/samtools_depth.xml" />
+
+If you wish to run the unit tests, also move/copy the ``test-data/`` files
+under Galaxy's ``test-data/`` folder. Then::
+
+    $ ./run_tests.sh -id samtools_depth
+
+That's it.
+
+
+History
+=======
+
+======= ======================================================================
+Version Changes
+------- ----------------------------------------------------------------------
+v0.0.1  - Initial public release
+v0.0.2  - Reorder XML elements (internal change only).
+        - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
+======= ======================================================================
+
+
+Developers
+==========
+
+Development is on this GitHub repository:
+https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth
+
+
+For pushing a release to the test or main "Galaxy Tool Shed", use the following
+Planemo commands (which requires you have set your Tool Shed access details in
+``~/.planemo.yml`` and that you have access rights on the Tool Shed)::
+
+    $ planemo shed_upload --shed_target testtoolshed --check_diff ~/repositories/pico_galaxy/tools/samtools_depth/
+    ...
+
+or::
+
+    $ planemo shed_upload --shed_target toolshed --check_diff ~/repositories/pico_galaxy/tools/samtools_depth/
+    ...
+
+To just build and check the tar ball, use::
+
+    $ planemo shed_upload --tar_only  ~/repositories/pico_galaxy/tools/samtools_depth/
+    ...
+    $ tar -tzf shed_upload.tar.gz 
+    test-data/ex1.bam
+    test-data/ex1.depth.tabular
+    test-data/sam_spec_padded.sam
+    test-data/sam_spec_padded.bam
+    test-data/sam_spec_padded.depth.tabular
+    tools/samtools_depth/README.rst
+    tools/samtools_depth/samtools_depth.xml
+    tools/samtools_depth/tool_dependencies.xml
+
+
+Licence (MIT)
+=============
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.
+
+NOTE: This is the licence for the Galaxy Wrapper only.
+samtools is available and licenced separately.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/samtools_depth/samtools_depth.xml	Wed May 13 10:29:23 2015 -0400
@@ -0,0 +1,90 @@
+<tool id="samtools_depth" name="SAM/BAM coverage depth" version="0.0.2">
+    <description>samtools depth</description>
+    <requirements>
+        <requirement type="binary">samtools</requirement>
+        <requirement type="package" version="1.1">samtools</requirement>
+    </requirements>
+    <stdio>
+        <!-- Assume anything other than zero is an error -->
+        <exit_code range="1:" />
+        <exit_code range=":-1" />
+    </stdio>
+    <version_command>samtools 2&gt;&amp;1 | grep -i "Version:"</version_command>
+    <command>
+samtools depth
+#if int($min_len)
+-l $min_len
+#end if
+#if int($base_quality_threshold)
+-q $base_quality_threshold
+#end if
+#if int($mapping_quality_threshold)
+-Q $mapping_quality_threshold
+#end if
+#for i in $input_bam#"${i}" #end for# &gt; "$out_depth"
+    </command>
+    <inputs>
+        <!-- Unlike samtools 0.1.x, samtools 1.1 will autodetect SAM vs BAM -->
+        <param name="input_bam" multiple="true" type="data" format="bam,sam" label="Input SAM/BAM file(s)" />
+        <param name="min_len" type="integer" value="0"
+	       label="Minimum mapped length (use zero for none)" />
+        <param name="base_quality_threshold" type="integer" value="0"
+	       label="Base quality threshold (use zero for none)" />
+        <param name="mapping_quality_threshold" type="integer" value="0"
+	       label="Mapping quality threshold (use zero for none)" />
+    </inputs>
+    <outputs>
+        <data name="out_depth" format="tabular" label="$on_string (depth)"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_bam" value="sam_spec_padded.sam" ftype="sam" />
+            <output name="out_depth" file="sam_spec_padded.depth.tabular" ftype="tabular" />
+        </test>
+        <test>
+            <param name="input_bam" value="sam_spec_padded.bam" ftype="bam" />
+            <output name="out_depth" file="sam_spec_padded.depth.tabular" ftype="tabular" />
+        </test>
+        <test>
+            <param name="input_bam" value="ex1.bam" ftype="bam" />
+            <output name="out_depth" file="ex1.depth.tabular" ftype="tabular" />
+        </test>
+    </tests>
+    <help>
+**What it does**
+
+This tool runs the ``samtools depth`` command in the SAMtools toolkit.
+
+The output is a tabular file, with one line for each base of each reference
+with any coverage (bases with no coverage may not appear).
+
+The first column is the reference name, the second column is the reference
+position, and then there is one column for each SAM/BAM file giving the
+coverage depth at that position.
+
+.. class:: warningmark
+
+**Note**. There is an internal hard limit of 8000 for the pileup routine in
+samtools, meaning the reported coverage from ``samtools depth`` will show
+maximum coverage depths *around* 8000.
+
+
+**Citation**
+
+If you use this Galaxy tool in work leading to a scientific publication please
+cite:
+
+Heng Li et al (2009). The Sequence Alignment/Map format and SAMtools.
+Bioinformatics 25(16), 2078-9.
+http://dx.doi.org/10.1093/bioinformatics/btp352
+
+Peter J.A. Cock (2014), Galaxy wrapper for the samtools depth command
+http://toolshed.g2.bx.psu.edu/view/peterjc/samtools_depth
+
+This wrapper is available to install into other Galaxy Instances via the Galaxy
+Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/samtools_depth
+    </help>
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/btp352</citation>
+    </citations>
+</tool>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/samtools_depth/tool_dependencies.xml	Wed May 13 10:29:23 2015 -0400
@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="samtools" version="1.1">
+        <repository changeset_revision="a287b1a43696" name="package_samtools_1_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>