| Next changeset 1:abbd37e8bd14 (2012-12-19) |
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LICENSE README.md README_GALAXYP.md README_REPO.md dbbuilder.xml update.sh |
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| diff -r 000000000000 -r 487f80fb99ae LICENSE --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/LICENSE Wed Dec 19 00:05:32 2012 -0500 |
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| b'@@ -0,0 +1,202 @@\n+\n+ Apache License\n+ Version 2.0, January 2004\n+ http://www.apache.org/licenses/\n+\n+ TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION\n+\n+ 1. Definitions.\n+\n+ "License" shall mean the terms and conditions for use, reproduction,\n+ and distribution as defined by Sections 1 through 9 of this document.\n+\n+ "Licensor" shall mean the copyright owner or entity authorized by\n+ the copyright owner that is granting the License.\n+\n+ "Legal Entity" shall mean the union of the acting entity and all\n+ other entities that control, are controlled by, or are under common\n+ control with that entity. 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| diff -r 000000000000 -r 487f80fb99ae README.md --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Wed Dec 19 00:05:32 2012 -0500 |
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| @@ -0,0 +1,26 @@ +# Protein Database Downloader + +This tool allows users to download protein databases from common +sources. This tool has no external dependencies beyond wget. +# 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. |
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| diff -r 000000000000 -r 487f80fb99ae README_GALAXYP.md --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README_GALAXYP.md Wed Dec 19 00:05:32 2012 -0500 |
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| @@ -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. |
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| diff -r 000000000000 -r 487f80fb99ae README_REPO.md --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README_REPO.md Wed Dec 19 00:05:32 2012 -0500 |
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| @@ -0,0 +1,4 @@ +# Protein Database Downloader + +This tool allows users to download protein databases from common +sources. This tool has no external dependencies beyond wget. |
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| diff -r 000000000000 -r 487f80fb99ae dbbuilder.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/dbbuilder.xml Wed Dec 19 00:05:32 2012 -0500 |
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| @@ -0,0 +1,46 @@ +<tool id="dbbuilder" version="0.1.0" name="Protein Database Downloader"> + <description> + </description> + <requirements> + <requirement type="binary">wget</requirement> + </requirements> + <stdio> + <exit_code range="1:" level="fatal" description="Error computing FDR" /> + </stdio> + <command> + #if $source.from == "uniprot" + #set $url = "http://www.uniprot.org/uniprot/?query=taxonomy%3a%22" + str($source.taxon) + "%22+keyword%3a1185&force=yes&format=fasta" + str($source.include_isoform) + #elif $source.from == "cRAP" + #set $url = "ftp://ftp.thegpm.org/fasta/cRAP/crap.fasta" + #end if + wget -nv '$url' -O '${output_database}' + </command> + <inputs> + <conditional name="source"> + <param name="from" type="select" label="Download from"> + <option value="uniprot">UniProtKB</option> + <option value="cRAP">cRAP (contaminants)</option> + </param> + <when value="uniprot"> + <param name="taxon" type="select" format="text" > + <label>Taxonomy</label> + <options from_file="uniprot_taxons.loc"> + <column name="name" index="0" /> + <column name="value" index="1" /> + </options> + </param> + <param name="include_isoform" type="boolean" truevalue="&include=yes" falsevalue="" label="Include isoform data" /> + </when> + </conditional> + </inputs> + <outputs> + <data format="fasta" name="output_database" label="Protein Database" /> + </outputs> + <help> +**Output** + +A FASTA file containing the specified protein sequences. + + </help> +</tool> + |
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| diff -r 000000000000 -r 487f80fb99ae update.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/update.sh Wed Dec 19 00:05:32 2012 -0500 |
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| @@ -0,0 +1,35 @@ +#!/bin/bash + +LICENSE_FILE=LICENSE +# Ensure repository contains license file. +if [ ! -e "$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 |