Mercurial > repos > iracooke > xtandem
diff tandem.xml @ 15:0faaab4f192a draft
planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
| author | iracooke |
|---|---|
| date | Tue, 20 Oct 2015 20:47:05 -0400 |
| parents | 9d6e0ad4d600 |
| children | 63b15b77e56c |
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--- a/tandem.xml Thu Mar 26 19:53:53 2015 -0400 +++ b/tandem.xml Tue Oct 20 20:47:05 2015 -0400 @@ -1,206 +1,180 @@ -<tool id="proteomics_search_tandem_1" name="X!Tandem MSMS Search" version="1.1.0"> - +<tool id="proteomics_search_tandem_1" name="X!Tandem MSMS Search" version="1.1.1"> + <description>Run an X!Tandem Search</description> <requirements> - <container type="docker">iracooke/protk-1.4.1</container> - <requirement type="package" version="1.4">protk</requirement> - </requirements> - - <description>Run an X!Tandem Search</description> + <container type="docker">iracooke/protk-1.4.3</container> + <requirement type="package" version="1.4.3">protk</requirement> + </requirements> + <command> + #if $database.source_select=="built_in": + tandem_search.rb -d $database.dbkey + #else + tandem_search.rb -d $database.fasta_file + #end if - <command> - #if $database.source_select=="built_in": - tandem_search.rb -d $database.dbkey - #else - tandem_search.rb -d $database.fasta_file - #end if - - #if $tandem_params.source_select=="built_in": - -T $tandem_params.paramskey - #else - -T $tandem_params.params_file - #end if + #if $tandem_params.source_select=="built_in": + -T $tandem_params.paramskey + #else + -T $tandem_params.params_file + #end if - --var-mods=' - $variable_mods - #for $custom_variable_mod in $custom_variable_mods: - ,${custom_variable_mod.custom_mod} - #end for - ' + --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 + --fix-mods=' + $fixed_mods + #for $custom_fix_mod in $custom_fix_mods: + ,${custom_fix_mod.custom_mod} + #end for + ' - --precursor-ion-tol-units=$precursor_tolu - - -v $missed_cleavages + $input_file -o $output -r - -f $fragment_ion_tol - - -p $precursor_ion_tol - - $allow_multi_isotope_search + --enzyme=$enzyme - $acetyl_protein_nterm - - $cleavage_semi - - $keep_spectra - - --threads $threads - - </command> + --precursor-ion-tol-units=$precursor_tolu + -v $missed_cleavages + -f $fragment_ion_tol + -p $precursor_ion_tol + $allow_multi_isotope_search + $acetyl_protein_nterm + $cleavage_semi + $keep_spectra + --threads "\${GALAXY_SLOTS:-12}" - <inputs> - <conditional name="database"> - <param name="source_select" type="select" label="Database source"> - <option value="built_in">Built-In</option> - <option value="input_ref" selected="true">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> - - <conditional name="tandem_params"> - <param name="source_select" type="select" label="Baseline Parameters"> - <option value="built_in" selected="true">Built-In</option> - <option value="input_ref">Custom parameter file</option> - </param> - <when value="built_in"> - <param name="paramskey" type="select" format="text" > - <label>Paramset</label> - <option value="isb_kscore">ISB K-Score (Recommended for TPP)</option> - <option value="isb_native">ISB Native</option> - <option value="gpm">GPM</option> - </param> - </when> - <when value="input_ref"> - <param name="params_file" type="data" format="xml" label="Custom X!Tandem Parameters" /> - </when> - </conditional> + </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" selected="true">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> + <conditional name="tandem_params"> + <param name="source_select" type="select" label="Baseline Parameters"> + <option value="built_in" selected="true">Built-In</option> + <option value="input_ref">Custom parameter file</option> + </param> + <when value="built_in"> + <param name="paramskey" type="select" format="text" > + <label>Paramset</label> + <option value="isb_kscore">ISB K-Score (Recommended for TPP)</option> + <option value="isb_native">ISB Native</option> + <option value="gpm">GPM</option> + </param> + </when> + <when value="input_ref"> + <param name="params_file" type="data" format="xml" label="Custom X!Tandem Parameters" /> + </when> + </conditional> - <param name="input_file" type="data" format="mzml,mgf" multiple="false" label="MSMS File" help="A file with MS/MS data"/> + <param name="input_file" type="data" format="mzml,mgf" multiple="false" label="MSMS File" help="A 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> + <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_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="acetyl_protein_nterm" type="boolean" label="Allow N-terminal protein acetylation as a variable modification" truevalue="-y" falsevalue="" /> - + <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 selected="true" value="2">2</option> - </param> + <param name="acetyl_protein_nterm" type="boolean" label="Allow N-terminal protein acetylation as a variable modification" truevalue="-y" falsevalue="" /> + <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 selected="true" value="2">2</option> + </param> - <param name="cleavage_semi" type="boolean" label="Allow semi-cleaved peptides" help="This can increase search time dramatically" truevalue="--cleavage-semi" falsevalue=""/> - - <param name="keep_spectra" type="boolean" label="Keep Spectra" help="Include spectra in the output" truevalue="--output-spectra" falsevalue=""/> + <param name="cleavage_semi" type="boolean" label="Allow semi-cleaved peptides" help="This can increase search time dramatically" truevalue="--cleavage-semi" falsevalue=""/> + <param name="keep_spectra" type="boolean" label="Keep Spectra" help="Include spectra in the output" truevalue="--output-spectra" falsevalue=""/> - <param name="threads" type="integer" value="1" label="Threads" help="Number of threads to use for search. Maximum is 16"/> - - <param name="enzyme" type="select" format="text"> - <label>Enzyme</label> - <option value="[R]__pc__{P}">argc - [R]|{P}</option> - <option value="[X]__pc__[D]">aspn - [X]|[D]</option> - <option value="[FLMWY]__pc__{P}">chymotrypsin - [FLMWY]|{P}</option> - <option value="[R]__pc__[X]">clostripain - [R]|[X]</option> - <option value="[M]__pc__{X}">cnbr - [M]|{X}</option> - <option value="[AGILV]__pc__{P}">elastase - [AGILV]|{P}</option> - <option value="[D]__pc__{P}">formicacid - [D]|{P}</option> - <option value="[DE]__pc__{P}">gluc - [DE]|{P}</option> - <option value="[E]__pc__{P}">gluc_bicarb - [E]|{P}</option> - <option value="[W]__pc__[X]">iodosobenzoate - [W]|[X]</option> - <option value="[K]__pc__{P}">lysc - [K]|{P}</option> - <option value="[K]__pc__[X]">lysc-p - [K]|[X]</option> - <option value="[X]__pc__[K]">lysn - [X]|[K]</option> - <option value="[X]__pc__[AKRS]">lysn_promisc - [X]|[AKRS]</option> - <option value="[X]__pc__[X]">nonspecific - [X]|[X]</option> - <option value="[FL]__pc__[X]">pepsina - [FL]|[X]</option> - <option value="[P]__pc__[X]">protein_endopeptidase - [P]|[X]</option> - <option value="[E]__pc__[X]">staph_protease - [E]|[X]</option> - <option value="[FMWY]__pc__{P},[KR]__pc__{P},[X]__pc__[D]">tca - [FMWY]|{P},[KR]|{P},[X]|[D]</option> - <option value="[KR]__pc__{P}" selected="true">trypsin - [KR]|{P}</option> - <option value="[FKLMRWY]__pc__{P}">trypsin/chymotrypsin - [FKLMRWY]|{P}</option> - <option value="[KR]__pc__{P},[M]__pc__{P}">trypsin/cnbr - [KR]|{P},[M]|{P}</option> - <option value="[DEKR]__pc__{P}">trypsin_gluc - [DEKR]|{P}</option> - </param> + <param name="enzyme" type="select" format="text"> + <label>Enzyme</label> + <option value="[R]__pc__{P}">argc - [R]|{P}</option> + <option value="[X]__pc__[D]">aspn - [X]|[D]</option> + <option value="[FLWY]__pc__{P}">chymotrypsin - [FLWY]|{P}</option> + <option value="[R]__pc__[X]">clostripain - [R]|[X]</option> + <option value="[M]__pc__{X}">cnbr - [M]|{X}</option> + <option value="[AGILV]__pc__{P}">elastase - [AGILV]|{P}</option> + <option value="[D]__pc__{P}">formicacid - [D]|{P}</option> + <option value="[DE]__pc__{P}">gluc - [DE]|{P}</option> + <option value="[E]__pc__{P}">gluc_bicarb - [E]|{P}</option> + <option value="[W]__pc__[X]">iodosobenzoate - [W]|[X]</option> + <option value="[K]__pc__{P}">lysc - [K]|{P}</option> + <option value="[K]__pc__[X]">lysc-p - [K]|[X]</option> + <option value="[X]__pc__[K]">lysn - [X]|[K]</option> + <option value="[X]__pc__[AKRS]">lysn_promisc - [X]|[AKRS]</option> + <option value="[X]__pc__[X]">nonspecific - [X]|[X]</option> + <option value="[FL]__pc__[X]">pepsina - [FL]|[X]</option> + <option value="[P]__pc__[X]">protein_endopeptidase - [P]|[X]</option> + <option value="[E]__pc__[X]">staph_protease - [E]|[X]</option> + <option value="[FMWY]__pc__{P},[KR]__pc__{P},[X]__pc__[D]">tca - [FMWY]|{P},[KR]|{P},[X]|[D]</option> + <option value="[KR]__pc__{P}" selected="true">trypsin - [KR]|{P}</option> + <option value="[FKLMRWY]__pc__{P}">trypsin/chymotrypsin - [FKLMRWY]|{P}</option> + <option value="[KR]__pc__{P},[M]__pc__{P}">trypsin/cnbr - [KR]|{P},[M]|{P}</option> + <option value="[DEKR]__pc__{P}">trypsin_gluc - [DEKR]|{P}</option> + </param> - - <param name="fragment_ion_tol" help="Fragment Ion Tolerance in Daltons" type="float" value="0.5" min="0" max="10000" label="Fragment ion tolerance"/> - - <param name="precursor_ion_tol" help="Precursor Ion Tolerance (Da or ppm)" type="float" value="10" 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="--multi-isotope-search" falsevalue=""/> - - </inputs> - - - <outputs> - <data format="tandem" 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}.${input_file.display_name}.tandem"/> - </outputs> - - <tests> - <!-- Just test that the tool runs and produces vaguely correct output --> - <test> - <param name="source_select" value="input_ref"/> - <param name="fasta_file" value="testdb.fasta" format="fasta"/> - <param name="input_file" value="tiny.mzML" format="mzml"/> - <output name="output" format="tandem"> - <assert_contents> - <has_text text="tandem-style" /> - </assert_contents> - </output> - </test> - </tests> + <param name="fragment_ion_tol" help="Fragment Ion Tolerance in Daltons" type="float" value="0.5" min="0" max="10000" label="Fragment ion tolerance"/> + <param name="precursor_ion_tol" help="Precursor Ion Tolerance (Da or ppm)" type="float" value="10" min="0" max="10000" label="Precursor ion tolerance"/> + <param name="precursor_tolu" type="select" format="text"> + <label>Precursor Ion Tolerance Units</label> + <option value="ppm">ppm</option> + <option value="Da">Da</option> + </param> + <param name="allow_multi_isotope_search" type="boolean" label="Allow multi-isotope search" help="This allows peptide candidates in windows around -1 Da and -2 Da from the acquired mass to be considered. Only applicable when the minus/plus window above is set to less than 0.5 Da. Good for accurate-mass instruments for which the reported precursor mass is not corrected to the monoisotopic mass." truevalue="--multi-isotope-search" falsevalue=""/> + </inputs> + <outputs> + <data format="tandem" name="output" metadata_source="input_file" label="X!Tandem_vs_${database.dbkey if $database.has_key('dbkey') else $database.fasta_file.display_name}.${input_file.display_name}.${input_file.display_name}.tandem"/> + </outputs> + <tests> + <!-- Just test that the tool runs and produces vaguely correct output --> + <test> + <param name="source_select" value="input_ref"/> + <param name="fasta_file" value="testdb.fasta" format="fasta"/> + <param name="input_file" value="tiny.mzML" format="mzml"/> + <output name="output" format="tandem"> + <assert_contents> + <has_text text="tandem-style" /> + </assert_contents> + </output> + </test> + </tests> <help> **What it does**