| Previous changeset 0:18bf78e49e88 (2013-06-06) Next changeset 2:e79b95501048 (2013-09-26) |
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Commit message:
Fix |
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modified:
omssa.xml repository_dependencies.xml tool_dependencies.xml |
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| diff -r 18bf78e49e88 -r cd0d5e6b9a92 omssa.xml --- a/omssa.xml Thu Jun 06 01:33:45 2013 -0400 +++ b/omssa.xml Thu Jun 06 15:37:22 2013 +1000 |
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| @@ -1,7 +1,7 @@ <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="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> @@ -9,9 +9,12 @@ <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 18bf78e49e88 -r cd0d5e6b9a92 repository_dependencies.xml --- a/repository_dependencies.xml Thu Jun 06 01:33:45 2013 -0400 +++ b/repository_dependencies.xml Thu Jun 06 15:37:22 2013 +1000 |
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| @@ -1,12 +1,12 @@ <?xml version="1.0"?> <repositories description="Proteomics datatypes, omssa and blast executables"> - <repository toolshed="http://10.211.55.35:9009" name="proteomics_datatypes" owner="iracooke" changeset_revision="7049ac401bf6"/> + <repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="proteomics_datatypes" owner="iracooke" changeset_revision="7101f7e4b00b"/> - <repository toolshed="http://10.211.55.35:9009" name="galaxy_protk" owner="iracooke" changeset_revision="0a2b3dcc986c" prior_installation_required="True"/> + <repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="galaxy_protk" owner="iracooke" changeset_revision="32c643142290" prior_installation_required="True"/> - <repository toolshed="http://10.211.55.35:9009" name="protk_blast" owner="iracooke" changeset_revision="c685c193e5fe"/> + <repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="protk_blast" owner="iracooke" changeset_revision="a1b21b3844c8"/> - <repository toolshed="http://10.211.55.35:9009" name="protk_omssa" owner="iracooke" changeset_revision="5fefcc853388"/> + <repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="protk_omssa" owner="iracooke" changeset_revision="b386c6c95d0e"/> </repositories> |
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| diff -r 18bf78e49e88 -r cd0d5e6b9a92 tool_dependencies.xml --- a/tool_dependencies.xml Thu Jun 06 01:33:45 2013 -0400 +++ b/tool_dependencies.xml Thu Jun 06 15:37:22 2013 +1000 |
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| @@ -1,16 +1,16 @@ <?xml version="1.0"?> <tool_dependency> - <package name="galaxy_protk" version="1.2.0"> - <repository toolshed="http://10.211.55.35:9009" name="galaxy_protk" owner="iracooke" changeset_revision="0a2b3dcc986c" prior_installation_required="True"/> + <package name="galaxy_protk" version="1.2.2"> + <repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="galaxy_protk" owner="iracooke" changeset_revision="32c643142290" prior_installation_required="True"/> </package> <package name="blast" version="2.2.27"> - <repository toolshed="http://10.211.55.35:9009" name="protk_blast" owner="iracooke" changeset_revision="c685c193e5fe"/> + <repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="protk_blast" owner="iracooke" changeset_revision="a1b21b3844c8"/> </package> <package name="omssa" version="2.1.9"> - <repository toolshed="http://10.211.55.35:9009" name="protk_omssa" owner="iracooke" changeset_revision="5fefcc853388"/> + <repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="protk_omssa" owner="iracooke" changeset_revision="b386c6c95d0e"/> </package> |