# HG changeset patch
# User peterjc
# Date 1431527363 14400
# Node ID 3a70e3e49db888ec00172bce84aa726d1cade9ae
planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/samtools_depth commit 005b5833177c31dbcfcad35690f96c267581a7e1
diff -r 000000000000 -r 3a70e3e49db8 test-data/ex1.bam
Binary file test-data/ex1.bam has changed
diff -r 000000000000 -r 3a70e3e49db8 test-data/ex1.depth.tabular
--- /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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diff -r 000000000000 -r 3a70e3e49db8 test-data/sam_spec_padded.bam
Binary file test-data/sam_spec_padded.bam has changed
diff -r 000000000000 -r 3a70e3e49db8 test-data/sam_spec_padded.depth.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sam_spec_padded.depth.tabular Wed May 13 10:29:23 2015 -0400
@@ -0,0 +1,41 @@
+ref 7 1
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diff -r 000000000000 -r 3a70e3e49db8 test-data/sam_spec_padded.sam
--- /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
diff -r 000000000000 -r 3a70e3e49db8 tools/samtools_depth/README.rst
--- /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::
+
+
+
+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.
diff -r 000000000000 -r 3a70e3e49db8 tools/samtools_depth/samtools_depth.xml
--- /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 @@
+
+ samtools depth
+
+ samtools
+ samtools
+
+
+
+
+
+
+ samtools 2>&1 | grep -i "Version:"
+
+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# > "$out_depth"
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+**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
+
+
+ 10.1093/bioinformatics/btp352
+
+
diff -r 000000000000 -r 3a70e3e49db8 tools/samtools_depth/tool_dependencies.xml
--- /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 @@
+
+
+
+
+
+