| Previous changeset 3:1747d568a7c8 (2013-03-04) Next changeset 5:327b2d99d4c5 (2013-06-09) |
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Commit message:
Uploaded |
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modified:
mascot.xml mascot_to_pepxml.xml repository_dependencies.xml tool_dependencies.xml |
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added:
README |
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| diff -r 1747d568a7c8 -r d9564913a944 README --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README Tue Mar 05 00:18:41 2013 -0500 |
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| @@ -0,0 +1,8 @@ +This package installs wrapper scripts for running Mascot MS/MS searches + +Running this tool requires a working installation of Mascot (commercial software). +Mascot is available from http://www.matrixscience.com/ + +Requirements: +This package depends on the galaxy_protk and protk_trans_proteomic_pipeline packages +Please see instructions for those packages before installing |
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| diff -r 1747d568a7c8 -r d9564913a944 mascot.xml --- a/mascot.xml Mon Mar 04 18:40:40 2013 -0500 +++ b/mascot.xml Tue Mar 05 00:18:41 2013 -0500 |
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| @@ -1,14 +1,14 @@ -<tool id="proteomics_search_mascot_1" name="Mascot MSMS Search" version="1.0.0"> +<tool id="proteomics_search_mascot_1" name="Mascot MSMS Search" version="1.0.1"> <requirements> - <requirement type="package" version="1.1.9">galaxy_protk</requirement> + <requirement type="package" version="1.2.0">galaxy_protk</requirement> </requirements> - <description>Run a Mascot Search on a File</description> + <description>Mascot MS/MS Search</description> - <command>rvm 1.9.3@protk-1.1.9 do mascot_search.rb -d $database -f $fragment_ion_tol -S $server $input_file -o $output -r + <command>rvm 1.9.3@protk-1.2.0 do mascot_search.rb -d $database -f $fragment_ion_tol -S $server $input_file -o $output -r ## Variable Mods --var-mods=' |
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| diff -r 1747d568a7c8 -r d9564913a944 mascot_to_pepxml.xml --- a/mascot_to_pepxml.xml Mon Mar 04 18:40:40 2013 -0500 +++ b/mascot_to_pepxml.xml Tue Mar 05 00:18:41 2013 -0500 |
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| @@ -1,12 +1,12 @@ -<tool id="mascot_to_pepxml_1" name="Mascot to pepXML" version="1.0.0"> +<tool id="mascot_to_pepxml_1" name="Mascot to pepXML" version="1.0.1"> <requirements> - <requirement type="package" version="1.1.9">galaxy_protk</requirement> + <requirement type="package" version="1.2.0">galaxy_protk</requirement> <requirement type="package" version="4.6.1">trans_proteomic_pipeline</requirement> </requirements> <description>Converts a mascot results file to pepXML</description> -<command>rvm 1.9.3@protk-1.1.9 do mascot_to_pepxml.rb $input_file -o $output -d $database</command> +<command>rvm 1.9.3@protk-1.2.0 do mascot_to_pepxml.rb $input_file -o $output -d $database</command> <inputs> <param name="input_file" type="data" format="mascotdat" multiple="false" label="Input File" help="Mascot results file"/> |
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| diff -r 1747d568a7c8 -r d9564913a944 repository_dependencies.xml --- a/repository_dependencies.xml Mon Mar 04 18:40:40 2013 -0500 +++ b/repository_dependencies.xml Tue Mar 05 00:18:41 2013 -0500 |
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| @@ -1,10 +1,10 @@ <?xml version="1.0"?> <repositories description="Proteomics datatypes and mascot2xml from the TPP"> - <repository toolshed="http://toolshed.g2.bx.psu.edu" name="proteomics_datatypes" owner="iracooke" changeset_revision="f74290b136fc"/> + <repository toolshed="http://toolshed.g2.bx.psu.edu" name="proteomics_datatypes" owner="iracooke" changeset_revision="463328a6967f"/> - <repository toolshed="http://toolshed.g2.bx.psu.edu" name="galaxy_protk" owner="iracooke" changeset_revision="51f7c347c955"/> + <repository toolshed="http://toolshed.g2.bx.psu.edu" name="galaxy_protk" owner="iracooke" changeset_revision="dac478a72c1d"/> - <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_trans_proteomic_pipeline" owner="iracooke" changeset_revision="f302406a0297"/> + <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_trans_proteomic_pipeline" owner="iracooke" changeset_revision="cedd5e884349"/> </repositories> |
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| diff -r 1747d568a7c8 -r d9564913a944 tool_dependencies.xml --- a/tool_dependencies.xml Mon Mar 04 18:40:40 2013 -0500 +++ b/tool_dependencies.xml Tue Mar 05 00:18:41 2013 -0500 |
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| @@ -1,12 +1,12 @@ <?xml version="1.0"?> <tool_dependency> - <package name="galaxy_protk" version="1.1.9"> - <repository toolshed="http://toolshed.g2.bx.psu.edu" name="galaxy_protk" owner="iracooke" changeset_revision="51f7c347c955"/> + <package name="galaxy_protk" version="1.2.0"> + <repository toolshed="http://toolshed.g2.bx.psu.edu" name="galaxy_protk" owner="iracooke" changeset_revision="dac478a72c1d"/> </package> <package name="trans_proteomic_pipeline" version="4.6.1"> - <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_trans_proteomic_pipeline" owner="iracooke" changeset_revision="f302406a0297" /> + <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_trans_proteomic_pipeline" owner="iracooke" changeset_revision="cedd5e884349" /> </package> </tool_dependency> \ No newline at end of file |