| Previous changeset 3:155b6449fdf3 (2013-03-05) Next changeset 5:a9c27818f417 (2014-06-14) |
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Commit message:
Update |
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modified:
omssa.xml repository_dependencies.xml tool_dependencies.xml |
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| diff -r 155b6449fdf3 -r 54b870eaca8d omssa.xml --- a/omssa.xml Tue Mar 05 00:25:34 2013 -0500 +++ b/omssa.xml Sun Jun 09 08:18:30 2013 -0500 |
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| @@ -1,17 +1,20 @@ <tool id="proteomics_search_omssa_1" name="OMSSA MSMS Search" version="1.0.1"> <requirements> - <requirement type="package" version="1.2.0">galaxy_protk</requirement> - <requirement type="package" version="2.1.8">omssa</requirement> + <requirement type="package" version="1.2.2">galaxy_protk</requirement> + <requirement type="package" version="2.1.9">omssa</requirement> <requirement type="package" version="2.2.27">blast</requirement> </requirements> <description>Run an OMSSA MS/MS Search</description> - <command>#if $database.source_select=="built_in": - rvm 1.9.3@protk-1.2.0 do omssa_search.rb -d $database.dbkey - #else #rvm 1.9.3@protk-1.2.0 do omssa_search.rb -d $database.fasta_file + <command>rvm 1.9.3@protk-1.2.2 do omssa_search.rb + + #if $database.source_select=="built_in": + -d $database.dbkey + #else + -d $database.fasta_file #end if --var-mods=' @@ -26,7 +29,28 @@ $searched_ions ' - $input_file -o $output -r --enzyme=$enzyme --precursor-ion-tol-units=$precursor_tolu -v $missed_cleavages -f $fragment_ion_tol -p $precursor_ion_tol --num-peaks-for-multi-isotope-search $multi_isotope $use_average_mass $respect_precursor_charges --max-hit-expect $max_hit_expect --intensity-cut-off $intensity_cut_off + $input_file + -o $output + -r + + --enzyme=$enzyme + + --precursor-ion-tol-units=$precursor_tolu + + -v $missed_cleavages + + -f $fragment_ion_tol + + -p $precursor_ion_tol + + --num-peaks-for-multi-isotope-search $multi_isotope + + $use_average_mass + $respect_precursor_charges + + --max-hit-expect $max_hit_expect + + --intensity-cut-off $intensity_cut_off </command> |
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| diff -r 155b6449fdf3 -r 54b870eaca8d repository_dependencies.xml --- a/repository_dependencies.xml Tue Mar 05 00:25:34 2013 -0500 +++ b/repository_dependencies.xml Sun Jun 09 08:18:30 2013 -0500 |
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| @@ -1,18 +1,12 @@ <?xml version="1.0"?> -<!-- <repositories description="Requires Proteomics Datatypes"> - <repository toolshed="http://10.211.55.28:9009" name="proteomics_datatypes" owner="iracooke" changeset_revision="699a890a9d99"/> - </repositories> - --> +<repositories description="Proteomics datatypes, omssa and blast executables"> + + <repository toolshed="http://toolshed.g2.bx.psu.edu" name="proteomics_datatypes" owner="iracooke" changeset_revision="09b89b345de2"/> - - <repositories description="Proteomics datatypes, omssa and blast executables"> - <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="galaxy_protk" owner="iracooke" changeset_revision="c25df71f7b68" prior_installation_required="True"/> - <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="protk_blast" owner="iracooke" changeset_revision="e34365cd29fa"/> - <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_blast" owner="iracooke" changeset_revision="0d86d29aaed6" /> + <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_omssa" owner="iracooke" changeset_revision="8f3813e7b0a6"/> - <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_omssa" owner="iracooke" changeset_revision="f77532db59b6" /> - - -</repositories> \ No newline at end of file +</repositories> |
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| diff -r 155b6449fdf3 -r 54b870eaca8d tool_dependencies.xml --- a/tool_dependencies.xml Tue Mar 05 00:25:34 2013 -0500 +++ b/tool_dependencies.xml Sun Jun 09 08:18:30 2013 -0500 |
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| @@ -1,29 +1,18 @@ <?xml version="1.0"?> <tool_dependency> - <!-- <package name="galaxy_protk" version="1.2.0"> - <repository toolshed="http://10.211.55.28:9009" name="galaxy_protk" owner="iracooke" changeset_revision="5610168f3b53"/> + + <package name="galaxy_protk" version="1.2.2"> + <repository toolshed="http://toolshed.g2.bx.psu.edu" name="galaxy_protk" owner="iracooke" changeset_revision="c25df71f7b68" prior_installation_required="True"/> </package> <package name="blast" version="2.2.27"> - <repository toolshed="http://10.211.55.28:9009" name="protk_blast" owner="iracooke" changeset_revision="0f3b7bbdfdd4" /> + <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_blast" owner="iracooke" changeset_revision="e34365cd29fa"/> </package> - <package name="omssa" version="2.1.8"> - <repository toolshed="http://10.211.55.28:9009" name="protk_omssa" owner="iracooke" changeset_revision="117faa58df2a" /> - </package> --> - -<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="blast" version="2.2.27"> - <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_blast" owner="iracooke" changeset_revision="0d86d29aaed6" /> - </package> - - <package name="omssa" version="2.1.8"> - <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_omssa" owner="iracooke" changeset_revision="f77532db59b6" /> + <package name="omssa" version="2.1.9"> + <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_omssa" owner="iracooke" changeset_revision="8f3813e7b0a6"/> </package> -</tool_dependency> \ No newline at end of file +</tool_dependency> |