Mercurial > repos > galaxyp > ms2preproc
changeset 0:59e5d8c53c81 draft
Uploaded
| author | galaxyp |
|---|---|
| date | Wed, 19 Dec 2012 00:27:24 -0500 |
| parents | |
| children | 5fcf7b8a1e80 |
| files | LICENSE README.md README_GALAXYP.md README_REPO.md ms2preproc.xml update.sh |
| diffstat | 6 files changed, 379 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Wed Dec 19 00:27:24 2012 -0500 @@ -0,0 +1,44 @@ +# ms2preproc + +This repository contains a tool wrapper for ms2preproc. + +http://hci.iwr.uni-heidelberg.de/MIP/Software/ms2preproc.php + +This tool requires Galaxy to be equipped with common proteomic +datatypes. These can be obtained by installing Ira Cooke's ProtK via +the tool shed or merging the changesets from the following repository +into your Galaxy instance: + + https://bitbucket.org/galaxyp/galaxy-dist-proteomics + +# Installing + +This tool wrapper requires ms2preproc to be installed. + +For Galaxy-P we are installing this tool via CloudBioLinux +(https://github.com/jmchilton/cloudbiolinux/blob/proteomics/cloudbio/custom/bio_proteomics.py). While +this fabric script may not be exactly appropriate for your environment +it may serve as a template for how to install this software. + +# 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 Wed Dec 19 00:27:24 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.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README_REPO.md Wed Dec 19 00:27:24 2012 -0500 @@ -0,0 +1,22 @@ +# ms2preproc + +This repository contains a tool wrapper for ms2preproc. + +http://hci.iwr.uni-heidelberg.de/MIP/Software/ms2preproc.php + +This tool requires Galaxy to be equipped with common proteomic +datatypes. These can be obtained by installing Ira Cooke's ProtK via +the tool shed or merging the changesets from the following repository +into your Galaxy instance: + + https://bitbucket.org/galaxyp/galaxy-dist-proteomics + +# Installing + +This tool wrapper requires ms2preproc to be installed. + +For Galaxy-P we are installing this tool via CloudBioLinux +(https://github.com/jmchilton/cloudbiolinux/blob/proteomics/cloudbio/custom/bio_proteomics.py). While +this fabric script may not be exactly appropriate for your environment +it may serve as a template for how to install this software. +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ms2preproc.xml Wed Dec 19 00:27:24 2012 -0500 @@ -0,0 +1,54 @@ +<tool id="ms2preproc" name="ms2preproc" version="0.1.0"> + <description>preprocess and filter MS/MS spectra</description> + + <command> + #if $window: + #set $window_arg = "-Z %s" % $window + #else + #set $window_arg = "" + #end if + ms2preproc --infile ${input} --outfile ${output} --informat mgf --top ${top} ${window_arg}; sed -i -e 's/,SCAN\(.*\)$/\nSCANS=\1/' ${output} + </command> + + <inputs> + <param format="mgf" name="input" type="data" label="Input MGF" /> + <param name="top" type="integer" label="Number of top peaks to keep" value="200" help="" /> + <param name="window" type="float" label="m/z Window" value="" optional="true" help="m/z Windows (+/-Z) around high-intensity peaks in which the number specified above are selected. (Optional)" /> + </inputs> + <outputs> + <data format="mgf" name="output" label="ms2preproc on ${on_string}"/> + </outputs> + + <requirements> + <requirement type="package">ms2preproc</requirement> + </requirements> + + <help> +**What it does** + +ms2preproc is a software tool to preprocess MS/MS spectra, please see the citation below for more information. + +**Inputs and Parameters** + +ms2preproc is very specific about the formatting of the MGF file it parses. Therefore it is recommended that the MGF Formatter tool is used to create a MGF file specifically for ms2preproc prior to the use of this tool. + +The authors of this software recommend running ms2preproc with the following settings: + + Mascot: + Select top 200 peaks globally. + + Sequest: + Select top 6 peaks in windows of size 30 m/z. + + ProteinPilot: + Select top 6 peaks in windows of size 30 m/z. + +------ + +**Citation** + +For the underlying tool, please cite `Renard BY, Kirchner M, Monigatti F, Invanov AR, Rappsilber J, Winter D, Steen JAJ, Hamprecht FA, Steen H. When Less Can Yield More - Computational Preprocessing of MS/MS Spectra for Peptide Identification, Proteomics (2009).` + +If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-ms2preproc + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/update.sh Wed Dec 19 00:27:24 2012 -0500 @@ -0,0 +1,35 @@ +#!/bin/bash + +LICENSE_FILE=LICENSE +# Ensure repository contains license file. +if [ ! -e "$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