| Next changeset 1:49d15d40117d (2013-03-04) |
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Commit message:
Uploaded |
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added:
tandem.xml tool-data/pepxml_databases.loc.sample tool-data/tandem_mods.loc.sample |
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| diff -r 000000000000 -r ac11abcfc621 tandem.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tandem.xml Sun Jan 06 19:18:09 2013 -0500 |
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| @@ -0,0 +1,128 @@ +<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> |
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| diff -r 000000000000 -r ac11abcfc621 tool-data/pepxml_databases.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/pepxml_databases.loc.sample Sun Jan 06 19:18:09 2013 -0500 |
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| @@ -0,0 +1,13 @@ +#This file lists the names of protein databases installed locally in protk. +# These are used by omssa and x!tandem as well as the "mascot to pepxml" tool +# In order to combine search results with Interprophet searches must be run against an identical database +# +# Entries should follow the be structured as follows +# Display_name omssa_tandem_dbname dbkey +# +# +Swissprot spall_ spall spall_ +Combined PlasmboDB (falciparum) and Swissprot Human plasmodb_pfalciparum_sphuman_ plasmodb_pfalciparum_sphuman plasmodb_pfalciparum_sphuman_ +Swissprot Human sphuman_ sphuman sphuman_ +Combined Swissprot/TRembl Human sptrhuman_ sptrhuman sptrhuman_ +Swissprot Mouse spmouse_ spmouse spmouse_ |
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| diff -r 000000000000 -r ac11abcfc621 tool-data/tandem_mods.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/tandem_mods.loc.sample Sun Jan 06 19:18:09 2013 -0500 |
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| @@ -0,0 +1,6 @@ +#This file lists the names of inbuilt chemical modifications accepted by X!Tandem +# +# +Carbamidomethyl C carbamidomethyl_c_ 57.021464@C carbamidomethyl_c_ +Glycocapture-N glycocapture_n_ 0.998@N!{P}[ST] glycocapture_n_ +Oxidation M oxidation_m_ 15.994915@M oxidation_m_ \ No newline at end of file |