| Previous changeset 7:b3f2bd49029c (2013-03-05) Next changeset 9:e0a1e8a0500a (2014-06-13) |
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Commit message:
Update |
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modified:
README msgfplus_search.xml repository_dependencies.xml tool_dependencies.xml |
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| diff -r b3f2bd49029c -r 4f6cbe948065 README --- a/README Tue Mar 05 00:20:42 2013 -0500 +++ b/README Sun Jun 09 08:17:57 2013 -0500 |
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| @@ -1,7 +1,7 @@ This package is a galaxy wrapper for the MSGF+ search tool. Requirements: -This package depends on the galaxy_protk and protk_msgfplus and protk_proteowizard packages +This package depends on the galaxy_protk, protk_msgfplus, protk_proteowizard packages Please see instructions for those packages before installing In addition to basic requirements you must also have unzip and java 6 runtime (or greater) installed |
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| diff -r b3f2bd49029c -r 4f6cbe948065 msgfplus_search.xml --- a/msgfplus_search.xml Tue Mar 05 00:20:42 2013 -0500 +++ b/msgfplus_search.xml Sun Jun 09 08:17:57 2013 -0500 |
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| @@ -1,7 +1,7 @@ <tool id="proteomics_search_msgfplus_1" name="MSGF+ 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="20130227">msgfplus</requirement> <requirement type="package" version="3_0_4388">proteowizard</requirement> </requirements> @@ -10,9 +10,11 @@ <description>Run an MSGF+ Search</description> <command> + rvm 1.9.3@protk-1.2.2 do msgfplus_search.rb #if $database.source_select=="built_in": - rvm 1.9.3@protk-1.2.0 do msgfplus_search.rb --galaxy -d $database.dbkey - #else #rvm 1.9.3@protk-1.2.0 do msgfplus_search.rb --galaxy -d $database.fasta_file + --galaxy -d $database.dbkey + #else + --galaxy -d $database.fasta_file #end if --var-mods=' @@ -29,10 +31,44 @@ #end for ' - $input_file -o $output -r --enzyme=$enzyme --precursor-ion-tol-units=$precursor_tolu -v $missed_cleavages -f $fragment_ion_tol -p $precursor_ion_tol --instrument=$instrument + $input_file + + -o $output + + -r + + --enzyme=$enzyme + + --precursor-ion-tol-units=$precursor_tolu + + -v $missed_cleavages + + -f $fragment_ion_tol + + -p $precursor_ion_tol + + --instrument=$instrument - - + --isotope-error-range=$isotope_error_range + + --fragment-method=$fragment_method + + --protocol=$protocol + + --min-pep-len=$min_pep_len + --max-pep-len=$max_pep_len + --max-pep-charge=$max_pep_charge + --min-pep-charge=$min_pep_charge + --num-reported-matches=$num_reported_matches + + --java-mem=$java_mem + + #if $pepxml_output_use + + #else + --no-pepxml + #end if + </command> <inputs> @@ -58,8 +94,7 @@ <param name="input_file" type="data" format="mzml" multiple="false" label="MSMS File" help="An mzML file with MS/MS data"/> - <param name="variable_mods" format="text" type="select" multiple="true" label="Variable Modifications" help="Hold the appropriate key while - clicking to select multiple items"> + <param name="variable_mods" format="text" type="select" multiple="true" label="Variable Modifications" help="Multiple Selection Allowed"> <options from_file="msgfplus_mods.loc"> <column name="name" index="0" /> <column name="value" index="2" /> @@ -72,8 +107,7 @@ </repeat> - <param name="fixed_mods" format="text" type="select" multiple="true" label="Fixed Modifications" help="Hold the appropriate key while - clicking to select multiple items"> + <param name="fixed_mods" format="text" type="select" multiple="true" label="Fixed Modifications" help="Multiple Selection Allowed"> <options from_file="msgfplus_mods.loc"> <column name="name" index="0" /> <column name="value" index="2" /> @@ -96,7 +130,16 @@ <param name="enzyme" type="select" format="text"> <label>Enzyme</label> - <option value="Trypsin">Trypsin</option> + <option value="0">unspecific cleavage</option> + <option value="1">Trypsin</option> + <option value="2">Chymotrypsin</option> + <option value="3">Lys-C</option> + <option value="4">Lys-N</option> + <option value="5">glutamyl endopeptidase</option> + <option value="6">Arg-C</option> + <option value="7">Asp-N</option> + <option value="8">alphaLP</option> + <option value="9">no cleavage</option> </param> <param name="instrument" type="select" format="text"> @@ -106,6 +149,23 @@ <option value="1">High-res LTQ</option> </param> + <param name="fragment_method" type="select" format="text"> + <label>Fragmentation Method</label> + <option value="0">Respect Input File</option> + <option value="1">CID</option> + <option value="2">ETD</option> + <option value="3">HCD</option> + <option value="4">Merge spectra from same precursor</option> + </param> + + <param name="protocol" type="select" format="text"> + <label>Protocol</label> + <option value="0">NoProtocol</option> + <option value="1">Phosphorylation</option> + <option value="2">iTRAQ</option> + <option value="3">iTRAQPhospho</option> + </param> + <param name="fragment_ion_tol" help="Fragment Ion Tolerance in Daltons" type="float" value="0.65" min="0" max="10000" label="Fragment ion tolerance"/> <param name="precursor_ion_tol" help="Precursor Ion Tolerance (Da or ppm)" type="float" value="100" min="0" max="10000" label="Precursor ion tolerance"/> @@ -115,12 +175,42 @@ <option value="Da">Da</option> </param> + <param name="isotope_error_range" help="Takes into account of the error introduced by chooosing a non-monoisotopic peak for fragmentation." type="text" size="80" value="0,1" label="Isotope Error Range"/> + + <param name="min_pep_len" help="" type="integer" value="6" label="Minimum Peptide Length"/> + <param name="max_pep_len" help="" type="integer" value="40" label="Maximum Peptide Length"/> + <param name="min_pep_charge" help="" type="integer" value="2" label="Minimum Peptide Charge"/> + <param name="max_pep_charge" help="" type="integer" value="3" label="Maximum Peptide Charge"/> + <param name="num_reported_matches" help="Number of matches per spectrum to be reported" type="integer" value="1" label="Num reported matches"/> + <param name="java_mem" help="Increase this value if you get out of memory errors" type="text" size="80" value="3500M" label="Java Memory Limit"/> + + + <param name="pepxml_output_use" type="boolean" label="Convert results to pepXML" help="" truevalue="true" falsevalue="false" /> + </inputs> - <outputs> +<!-- <outputs> <data format="raw_pepxml" name="output" metadata_source="input_file" label="MSGF+_vs_${database.dbkey if $database.has_key('dbkey') else $database.fasta_file.display_name}.${input_file.display_name}.${input_file.display_name}.pepXML"/> </outputs> + --> + <outputs> + <data format="mzid" name="output" metadata_source="input_file" label="MSGF+_vs_${database.dbkey if $database.has_key('dbkey') else $database.fasta_file.display_name}.${input_file.display_name}.${input_file.display_name}"> + <change_format> + <when input="pepxml_output_use" value="true" format="raw_pepxml" metadata_source="input_file" label="MSGF+_vs_${database.dbkey if $database.has_key('dbkey') else $database.fasta_file.display_name}.${input_file.display_name}.${input_file.display_name}"/> + </change_format> + </data> + </outputs> + + + <tests> + <test> + <param name="source_select" value="input_ref"/> + <param name="fasta_file" value="bsa.fasta"/> + <param name="input_file" value="bsa.mzML"/> + <output name="output" file="bsa.mzid" compare="sim_size" delta="600" /> + </test> + </tests> <help> |
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| diff -r b3f2bd49029c -r 4f6cbe948065 repository_dependencies.xml --- a/repository_dependencies.xml Tue Mar 05 00:20:42 2013 -0500 +++ b/repository_dependencies.xml Sun Jun 09 08:17:57 2013 -0500 |
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| @@ -1,12 +1,6 @@ <?xml version="1.0"?> <repositories description="Proteomics datatypes, MSGF+ and Protk"> - - <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="dac478a72c1d"/> - - <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_msgfplus" owner="iracooke" changeset_revision="21c7f6a61d61"/> - - <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_proteowizard" owner="iracooke" changeset_revision="dd22a794a86b"/> + + <repository toolshed="http://toolshed.g2.bx.psu.edu" name="proteomics_datatypes" owner="iracooke" changeset_revision="09b89b345de2"/> </repositories> |
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| diff -r b3f2bd49029c -r 4f6cbe948065 tool_dependencies.xml --- a/tool_dependencies.xml Tue Mar 05 00:20:42 2013 -0500 +++ b/tool_dependencies.xml Sun Jun 09 08:17:57 2013 -0500 |
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| @@ -1,17 +1,18 @@ <?xml version="1.0"?> <tool_dependency> - <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 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="proteowizard" version="3_0_4388"> - <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_proteowizard" owner="iracooke" changeset_revision="dd22a794a86b"/> + <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_proteowizard" owner="iracooke" changeset_revision="863462ea0187"/> </package> <package name="msgfplus" version="20130227"> - <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_msgfplus" owner="iracooke" changeset_revision="21c7f6a61d61"/> + <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_msgfplus" owner="iracooke" changeset_revision="75a2edcb6d0c"/> </package> -</tool_dependency> \ No newline at end of file +</tool_dependency> |