# HG changeset patch
# User galaxyp
# Date 1355895014 18000
# Node ID e27d4f0f4b0103cd278ab7c5235bd7a81c33e9e4

Uploaded

diff -r 000000000000 -r e27d4f0f4b01 LICENSE
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+++ b/LICENSE	Wed Dec 19 00:30:14 2012 -0500
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+--2012-09-19 08:46:18--  http://www.apache.org/licenses/LICENSE-2.0.txt
+Resolving www.apache.org... 140.211.11.131, 192.87.106.229, 2001:610:1:80bc:192:87:106:229
+Connecting to www.apache.org|140.211.11.131|:80... connected.
+HTTP request sent, awaiting response... 200 OK
+Length: 11358 (11K) [text/plain]
+Saving to: “LICENSE-2.0.txt”
+
+     0K .......... .                                          100%  200K=0.06s
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+2012-09-19 08:46:18 (200 KB/s) - “LICENSE-2.0.txt” saved [11358/11358]
+
diff -r 000000000000 -r e27d4f0f4b01 README.md
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md	Wed Dec 19 00:30:14 2012 -0500
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+Tool wrapper for transproteomic pipeline application digestdb. 
+# Obtaining Tools
+
+Repositories for all Galaxy-P tools can be found at
+https:/bitbucket.org/galaxyp/.
+
+# Contact
+
+Please send suggestions for improvements and bug reports to
+jmchilton@gmail.com.
+
+# License
+
+All Galaxy-P tools are licensed under the Apache License Version 2.0
+unless otherwise documented.
+
+# Tool Versioning
+
+Galaxy-P tools will have versions of the form X.Y.Z. Versions
+differing only after the second decimal should be completely
+compatible with each other. Breaking changes should result in an
+increment of the number before and/or after the first decimal. All
+tools of version less than 1.0.0 should be considered beta.
diff -r 000000000000 -r e27d4f0f4b01 README_GALAXYP.md
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README_GALAXYP.md	Wed Dec 19 00:30:14 2012 -0500
@@ -0,0 +1,22 @@
+# Obtaining Tools
+
+Repositories for all Galaxy-P tools can be found at
+https:/bitbucket.org/galaxyp/.
+
+# Contact
+
+Please send suggestions for improvements and bug reports to
+jmchilton@gmail.com.
+
+# License
+
+All Galaxy-P tools are licensed under the Apache License Version 2.0
+unless otherwise documented.
+
+# Tool Versioning
+
+Galaxy-P tools will have versions of the form X.Y.Z. Versions
+differing only after the second decimal should be completely
+compatible with each other. Breaking changes should result in an
+increment of the number before and/or after the first decimal. All
+tools of version less than 1.0.0 should be considered beta.
diff -r 000000000000 -r e27d4f0f4b01 README_REPO.md
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README_REPO.md	Wed Dec 19 00:30:14 2012 -0500
@@ -0,0 +1,1 @@
+Tool wrapper for transproteomic pipeline application digestdb. 
diff -r 000000000000 -r e27d4f0f4b01 digestdb.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/digestdb.xml	Wed Dec 19 00:30:14 2012 -0500
@@ -0,0 +1,61 @@
+<tool id="digestdb" version="0.1.0" name="Digest Database">
+  <description>Perform a theoretical digest of a protein database.</description>
+  <requirements>
+    <requirement type="package">transproteomic_pipeline</requirement>    
+  </requirements>  
+  <command>
+    digestdb -m$missed_cleavages -l$min_mass -h$max_mass -r${str($enzyme).split(":")[0]} -n${str($enzyme).split(":")[1]} $sequences > $output
+  </command>
+  <inputs>
+    <param format="fasta" name="sequences" type="data" label="Input FASTA Database"/>
+    <param name="missed_cleavages" type="integer" label="Missed Cleavages" value="1"/>
+    <param name="min_mass" type="float" label="Minimum Peptide Mass" value="800.0"/>
+    <param name="max_mass" type="float" label="Maximum Peptide Mass" value="3000.0"/>
+    <param name="enzyme" type="select">
+      <option value="KR:P" selected="true">Trypsin</option>
+      <option value="KR:-">Trypsin/P</option>
+      <option value="FLWY:P">Chymotrypsin</option>
+      <option value="FLWY:-">Chymotrypsin/P</option>
+      <option value="EZ:P">V8_E</option>
+      <option value="EDBZ:P">V8_DE</option>
+      <option value="K:P">LysC</option>
+      <option value="K:-">LysC/P</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="tabular" name="output" label="Digest of database ${sequences.name}"/>
+  </outputs>
+  <help>
+**What it does**
+
+Produces a tabular description of peptides resulting from theoretical
+digest of a given protein database by the selected enzyme agent using
+the digestdb program distributed with the Transproteomic Pipeline.
+
+** Output **
+
+ Results are spit out to stdout in a tab-delimited format.
+
+ Asterisks (*) in sequence are treated as proper break points
+
+ Output columns:
+ - peptide length
+ - protein reference
+ - peptide mass
+ - previous amino acid before peptide
+ - peptide sequence
+ - next amino acid after peptide
+ - peptide start location
+ - peptide end location
+ - pI
+
+------
+
+**Citation**
+
+For the underlying tool, please cite `Proteomics. 2010 Mar;10(6):1150-9. A guided tour of the Trans-Proteomic Pipeline. Deutsch EW, Mendoza L, Shteynberg D, Farrah T, Lam H, Tasman N, Sun Z, Nilsson E, Pratt B, Prazen B, Eng JK, Martin DB, Nesvizhskii AI, Aebersold R. PMID 20101611`
+
+If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-digestdb
+
+  </help>
+</tool>
diff -r 000000000000 -r e27d4f0f4b01 update.sh
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/update.sh	Wed Dec 19 00:30:14 2012 -0500
@@ -0,0 +1,35 @@
+#!/bin/bash
+
+LICENSE_FILE=LICENSE
+# Ensure repository contains license file.
+if [ ! -e "$LICENSE_FILE" ];
+then
+    wget http://www.apache.org/licenses/LICENSE-2.0.txt -O "$LICENSE_FILE"
+fi
+
+# Run repository specific update actions.
+if [ -f update_repo.sh ];
+then
+    ./update_repo.sh
+fi
+
+wget https://raw.github.com/gist/3749747/README_GALAXYP.md -O README_GALAXYP.md
+
+# Create repository README
+if [ ! -e README_REPO.md ];
+then
+    echo "TODO: Document this tool repository." > README_REPO.md
+fi
+cat README_REPO.md README_GALAXYP.md > README.md
+
+
+# If version file exists, update all tools to this version
+VERSION_FILE=version
+if [ -e "$VERSION_FILE" ];
+then
+    VERSION=`cat $VERSION_FILE`
+    
+    # Replace tool version in each tool XML file   `
+    find -iname "*xml" -exec sed -i'' -e '0,/version="\(.\+\)"/s/version="\(.\+\)"/version="'$VERSION'"/1g' {} \;
+
+fi