| Previous changeset 3:4c2e97f928d7 (2013-03-04) Next changeset 5:97f1c89cd831 (2013-03-04) |
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Commit message:
Uploaded |
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modified:
peptide_prophet_wrapper.rb repository_dependencies.xml |
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added:
pepxml_to_table.xml |
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| diff -r 4c2e97f928d7 -r a67a5d30bb80 peptide_prophet_wrapper.rb --- a/peptide_prophet_wrapper.rb Mon Mar 04 18:41:22 2013 -0500 +++ b/peptide_prophet_wrapper.rb Mon Mar 04 19:04:16 2013 -0500 |
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| @@ -33,4 +33,4 @@ cmd << ";ruby -pi -e \"gsub('#{actual_input_path_string}', '#{original_input_file}')\" peptide_prophet_output.pep.xml" cmd << ";ruby -pi -e \"gsub('#{full_tmp_output_path_string}', '#{actual_output_path_string}')\" peptide_prophet_output.pep.xml" -%x[#{cmd}] +p %x[#{cmd}] |
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| diff -r 4c2e97f928d7 -r a67a5d30bb80 pepxml_to_table.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pepxml_to_table.xml Mon Mar 04 19:04:16 2013 -0500 |
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| @@ -0,0 +1,29 @@ +<tool id="pepxml_to_table_1" name="PepXML to Table" version="1.0.0"> + + <requirements> + <requirement type="package" version="1.1.9">galaxy_protk</requirement> + </requirements> + + + + <description>Converts a pepXML file to a tab delimited text file</description> + + +<!-- 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 $output</command> + + +<inputs> + + <param name="input_file" type="data" format="pepxml,peptideprophet_pepxml,interprophet_pepxml" multiple="false" label="Input File" help="A pepXML file"/> + +</inputs> +<outputs> + <data format="csv" name="output" metadata_source="input_file" label="${input_file.display_name}.csv" /> +</outputs> + +<help> + Convert a pepXML file to Tab delimited text +</help> + +</tool> |
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| diff -r 4c2e97f928d7 -r a67a5d30bb80 repository_dependencies.xml --- a/repository_dependencies.xml Mon Mar 04 18:41:22 2013 -0500 +++ b/repository_dependencies.xml Mon Mar 04 19:04:16 2013 -0500 |
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| @@ -1,7 +1,7 @@ <?xml version="1.0"?> <repositories description="Proteomics datatypes and 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"/> |