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Initial commit.
author galaxyp
date Thu, 09 May 2013 17:14:17 -0400
parents
children 437a18ccbdc2
files LICENSE README.md README_GALAXYP.md README_REPO.md iquant.xml repository_dependencies.xml tool_dependencies.xml update.sh
diffstat 8 files changed, 363 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/LICENSE	Thu May 09 17:14:17 2013 -0400
@@ -0,0 +1,202 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md	Thu May 09 17:14:17 2013 -0400
@@ -0,0 +1,23 @@
+TODO: Document this tool repository.
+# 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.
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README_GALAXYP.md	Thu May 09 17:14:17 2013 -0400
@@ -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.
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README_REPO.md	Thu May 09 17:14:17 2013 -0400
@@ -0,0 +1,1 @@
+TODO: Document this tool repository.
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/iquant.xml	Thu May 09 17:14:17 2013 -0400
@@ -0,0 +1,69 @@
+<tool id="iquant" name="iQuant" version="0.2.0">
+  <description>Perform quantitation on data labeled with isobaric tags.</description>
+  <command>
+    LTQ-iQuant-cli --report_type ${peptide_report.report_type} --group_type ${group_type} --report ${peptide_report.report} --type ${quant_type} --output $output
+    #for $input in $inputs:
+    "${input}"
+    #end for
+  </command>
+  <inputs>
+    <conditional name="peptide_report">
+      <param name="report_type" type="select" label="Identification Report Type">
+        <option value="PEPXML">PepXML</option>
+        <option value="SCAFFOLD">Scaffold Spectrum Report</option>
+        <option value="PROTEIN_PILOT">ProteinPilot Peptide Report</option>
+        <option value="MAX_QUANT">MaxQuant MSMS Export</option>
+      </param>
+      <when value="PEPXML">
+        <param format="pepxml" name="report" type="data" label="Input PepXML"/>
+      </when>
+      <when value="SCAFFOLD">
+        <param format="text" name="report" type="data" label="Input Scaffold Report"/>
+      </when>
+      <when value="PROTEIN_PILOT">
+        <param format="text" name="report" type="data" label="Input ProteinPilot Peptide Report"/>
+      </when>
+      <when value="MAX_QUANT">
+        <param format="text" name="report" type="data" label="Input MaxQuant MSMS Export"/>
+      </when>
+    </conditional>
+    <param name="inputs" multiple="true" type="data" format="mzxml,mzml" label="Peaklist(s)" help=""/>
+    <param name="quant_type" type="select" label="Quantification type">
+      <option value="FOUR_PLEX">iTRAQ 4-plex</option>
+      <option value="EIGHT_PLEX">iTRAQ 8-plex</option>
+      <option value="TMT_TWO_PLEX">TMT 2-plex</option>
+      <option value="TMT_SIX_PLEX">TMT 6-plex</option>
+    </param>
+    <param name="group_type" type="select" label="Quantify based on grouping of">
+      <option value="PROTEIN">Proteins</option>
+      <option value="PEPTIDE">Peptides</option>
+      <option value="PEPTIDE_WITH_MODIFICATIONS">Peptides with modifications</option>
+      <option value="PEPTIDE_WITH_UNIQUE_MODIFICATION">Peptide with an identified modification</option>
+    </param>
+  </inputs>
+
+  <outputs>
+    <data format="tabular" name="output" />
+  </outputs>
+
+  <requirements>
+    <requirement type="package" version="1.19.19">tint_proteomics_scripts</requirement><!-- Version 1.19.19 or higher -->
+  </requirements>
+
+  <help>
+**What it does**
+
+iQuant is a tool that performs tag based isobaric quantification by implementing a technique assigning collective reporter ion intensity-based weights to each peptide abundance ratio and calculating a protein's weighted average abundance ratio and p-value. 
+
+iQuant requires identification results from an upstream identification pipeline along with XML peak lists for the data (mzXML is well supported and an mzML option has been provided for testing). 
+
+------
+
+**Citation**
+
+For the underlying tool, please cite ``Onsongo G, Stone MD, Van Riper SK, Chilton J, Wu B, Higgins L, Lund TC, Carlis JV, Griffin TJ, 2010. LTQ-iQuant: A freely available software pipeline for automated and accurate protein quantification of isobaric tagged peptide data from LTQ instruments. Proteomics. 10(19).  doi: 10.1002/pmic.201000189.``
+
+If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-iquant
+
+  </help>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/repository_dependencies.xml	Thu May 09 17:14:17 2013 -0400
@@ -0,0 +1,5 @@
+<?xml version="1.0"?>
+<repositories description="Required proteomics dependencies.">
+  <repository toolshed="http://toolshed.g2.bx.psu.edu" name="tint" owner="galaxyp" changeset_revision="ab43b5ba7a4e"/>
+  <repository toolshed="http://toolshed.g2.bx.psu.edu" name="proteomics_datatypes" owner="iracooke" changeset_revision="f74290b136fc" />
+</repositories>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Thu May 09 17:14:17 2013 -0400
@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<tool_dependency>
+  <package name="tint_proteomics_scripts" version="1.19.19">
+    <repository toolshed="http://toolshed.g2.bx.psu.edu" name="tint" owner="galaxyp" changeset_revision="ab43b5ba7a4e"/>
+  </package>
+</tool_dependency>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/update.sh	Thu May 09 17:14:17 2013 -0400
@@ -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