| Previous changeset 6:7005346b534d (2013-03-04) Next changeset 8:d19a95abf2e4 (2013-06-09) |
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Commit message:
Uploaded |
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modified:
interprophet.xml interprophet_wrapper.rb peptide_prophet.xml peptide_prophet_wrapper.rb pepxml_to_table.xml protein_prophet.xml protein_prophet_wrapper.rb repository_dependencies.xml tool_dependencies.xml |
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README |
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| diff -r 7005346b534d -r 3f0cb90824f1 README --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README Tue Mar 05 00:28:22 2013 -0500 |
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| @@ -0,0 +1,5 @@ +This package installs wrapper scripts for Peptide Prophet, iProphet and Protein Prophet + +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 7005346b534d -r 3f0cb90824f1 interprophet.xml --- a/interprophet.xml Mon Mar 04 19:20:05 2013 -0500 +++ b/interprophet.xml Tue Mar 05 00:28:22 2013 -0500 |
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| @@ -1,7 +1,7 @@ -<tool id="proteomics_search_interprophet_1" name="InterProphet" version="1.0.0"> +<tool id="proteomics_search_interprophet_1" name="InterProphet" 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> |
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| diff -r 7005346b534d -r 3f0cb90824f1 interprophet_wrapper.rb --- a/interprophet_wrapper.rb Mon Mar 04 19:20:05 2013 -0500 +++ b/interprophet_wrapper.rb Tue Mar 05 00:28:22 2013 -0500 |
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| @@ -34,7 +34,7 @@ actual_input_path_string end -cmd << "rvm 1.9.3@protk-1.1.9 do interprophet.rb" +cmd << "rvm 1.9.3@protk-1.2.0 do interprophet.rb" cmd << " --no-nss" unless use_nss=="blank" cmd << " --no-nrs" unless use_nrs=="blank" |
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| diff -r 7005346b534d -r 3f0cb90824f1 peptide_prophet.xml --- a/peptide_prophet.xml Mon Mar 04 19:20:05 2013 -0500 +++ b/peptide_prophet.xml Tue Mar 05 00:28:22 2013 -0500 |
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| @@ -1,6 +1,6 @@ -<tool id="proteomics_search_peptide_prophet_1" name="Peptide Prophet" version="1.0.0"> +<tool id="proteomics_search_peptide_prophet_1" name="Peptide Prophet" 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> |
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| diff -r 7005346b534d -r 3f0cb90824f1 peptide_prophet_wrapper.rb --- a/peptide_prophet_wrapper.rb Mon Mar 04 19:20:05 2013 -0500 +++ b/peptide_prophet_wrapper.rb Tue Mar 05 00:28:22 2013 -0500 |
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| @@ -18,7 +18,7 @@ cmd = "ln -s #{original_input_file} #{actual_input_path_string};" -cmd << "rvm 1.9.3@protk-1.1.9 do peptide_prophet.rb" +cmd << "rvm 1.9.3@protk-1.2.0 do peptide_prophet.rb" ARGV[0]="#{actual_input_path_string}" |
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| diff -r 7005346b534d -r 3f0cb90824f1 pepxml_to_table.xml --- a/pepxml_to_table.xml Mon Mar 04 19:20:05 2013 -0500 +++ b/pepxml_to_table.xml Tue Mar 05 00:28:22 2013 -0500 |
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| @@ -1,7 +1,7 @@ -<tool id="pepxml_to_table_1" name="PepXML to Table" version="1.0.0"> +<tool id="pepxml_to_table_1" name="PepXML to Table" 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> @@ -10,7 +10,7 @@ <!-- Note .. the input file is assumed to be the first argument --> -<command>rvm 1.9.3@protk-1.1.9 do pepxml_to_table.rb $input_file -o $output</command> +<command>rvm 1.9.3@protk-1.2.0 do pepxml_to_table.rb $input_file -o $output</command> <inputs> |
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| diff -r 7005346b534d -r 3f0cb90824f1 protein_prophet.xml --- a/protein_prophet.xml Mon Mar 04 19:20:05 2013 -0500 +++ b/protein_prophet.xml Tue Mar 05 00:28:22 2013 -0500 |
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| @@ -1,6 +1,6 @@ -<tool id="proteomics_search_protein_prophet_1" name="Protein Prophet" version="1.0.0"> +<tool id="proteomics_search_protein_prophet_1" name="Protein Prophet" 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> |
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| diff -r 7005346b534d -r 3f0cb90824f1 protein_prophet_wrapper.rb --- a/protein_prophet_wrapper.rb Mon Mar 04 19:20:05 2013 -0500 +++ b/protein_prophet_wrapper.rb Tue Mar 05 00:28:22 2013 -0500 |
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| @@ -17,7 +17,7 @@ cmd = "ln -s #{original_input_file} #{actual_input_path_string};" -cmd << "rvm 1.9.3@protk-1.1.9 do protein_prophet.rb" +cmd << "rvm 1.9.3@protk-1.2.0 do protein_prophet.rb" ARGV[0]="#{actual_input_path_string}" |
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| diff -r 7005346b534d -r 3f0cb90824f1 repository_dependencies.xml --- a/repository_dependencies.xml Mon Mar 04 19:20:05 2013 -0500 +++ b/repository_dependencies.xml Tue Mar 05 00:28:22 2013 -0500 |
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| @@ -3,8 +3,8 @@ <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 7005346b534d -r 3f0cb90824f1 tool_dependencies.xml --- a/tool_dependencies.xml Mon Mar 04 19:20:05 2013 -0500 +++ b/tool_dependencies.xml Tue Mar 05 00:28:22 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 |