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Commit message:
Deleted selected files |
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removed:
tandem.xml |
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| diff -r b81d7a0466a6 -r cd2955b6646f tandem.xml --- a/tandem.xml Sun Jan 06 19:14:28 2013 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,128 +0,0 @@ -<tool id="proteomics_search_tandem_1" name="X!Tandem MSMS Search" version="1.0.0"> - <requirements><requirement type="package">protkgem</requirement></requirements> - <description>Run an X!Tandem Search</description> - - <command> - #if $database.source_select=="built_in": - tandem_search.rb -d $database.dbkey - #else #tandem_search.rb -d $database.fasta_file - #end if - - --var-mods=' - $variable_mods - #for $custom_variable_mod in $custom_variable_mods: - ,${custom_variable_mod.custom_mod} - #end for - ' - - --fix-mods=' - $fixed_mods - #for $custom_fix_mod in $custom_fix_mods: - ,${custom_fix_mod.custom_mod} - #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 $allow_multi_isotope_search --keep-params-files - - - - </command> - - <inputs> - <conditional name="database"> - <param name="source_select" type="select" label="Database source"> - <option value="built_in">Built-In</option> - <option value="input_ref">Your Upload File</option> - </param> - <when value="built_in"> - <param name="dbkey" type="select" format="text" > - <label>Database</label> - <options from_file="pepxml_databases.loc"> - <column name="name" index="0" /> - <column name="value" index="2" /> - </options> - </param> - </when> - <when value="input_ref"> - <param name="fasta_file" type="data" format="fasta" label="Uploaded FASTA file" /> - </when> - </conditional> - - <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"> - <options from_file="tandem_mods.loc"> - <column name="name" index="0" /> - <column name="value" index="2" /> - </options> - </param> - - <repeat name="custom_variable_mods" title="Custom Variable Modifications" help="You can specify a modification when present in a motif. For instance, 0.998@N!{P}[ST] is a deamidation modification on N only if it is present in an N[any but P][S or T] motif (N-glycosite)."> - <param name="custom_mod" type="text"> - </param> - </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"> - <options from_file="tandem_mods.loc"> - <column name="name" index="0" /> - <column name="value" index="2" /> - </options> - </param> - - <repeat name="custom_fix_mods" title="Custom Fixed Modifications" help="You can specify a modification when present in a motif. For instance, 0.998@N!{P}[ST] is a deamidation modification on N only if it is present in an N[any but P][S or T] motif (N-glycosite)."> - <param name="custom_mod" type="text"> - </param> - </repeat> - - - - <param name="missed_cleavages" type="select" format="text" help="Allow peptides to contain up to this many missed enzyme cleavage sites"> - <label>Missed Cleavages Allowed</label> - <option value="0">0</option> - <option value="1">1</option> - <option value="2">2</option> - </param> - - <param name="enzyme" type="select" format="text"> - <label>Enzyme</label> - <option value="Trypsin">Trypsin</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"/> - <param name="precursor_tolu" type="select" format="text"> - <label>Precursor Ion Tolerance Units</label> - <option value="ppm">ppm</option> - <option value="Da">Da</option> - </param> - - <param name="allow_multi_isotope_search" type="boolean" label="Allow multi-isotope search" help="This allows peptide candidates in windows around -1 Da and -2 Da from the acquired mass to be considered. Only applicable when the minus/plus window above is set to less than 0.5 Da. Good for accurate-mass instruments for which the reported precursor mass is not corrected to the monoisotopic mass." truevalue="" falsevalue="--strict-monoisotopic-mass"/> - - </inputs> - - - <outputs> - <data format="raw_pepxml" name="output" metadata_source="input_file" label="X!Tandem_vs_${database.dbkey if $database.has_key('dbkey') else $database.fasta_file.display_name}.${input_file.display_name}.${input_file.display_name}.pepXML"/> - </outputs> - - - <help> - -**What it does** - -Runs an MS/MS database search using the X!Tandem search engine. Output is in the form of a pepXML file containing identified peptides along with their raw search scores. - ----- - -**References** - -Please see http://www.thegpm.org/GPM/references.html for details of references describing the X!Tandem search engine. - - </help> - -</tool> |