Mercurial > repos > iracooke > tpp_prophets
changeset 15:0746a2ae9e04 draft
planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
| author | iracooke |
|---|---|
| date | Tue, 20 Oct 2015 20:45:24 -0400 |
| parents | d90c8bc10a9c |
| children | 1b86e378de37 |
| files | interprophet.xml peptide_prophet.xml pepxml_to_table.xml protein_prophet.xml protxml_to_table.xml repository_dependencies.xml tool_dependencies.xml |
| diffstat | 7 files changed, 252 insertions(+), 277 deletions(-) [+] |
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--- a/interprophet.xml Thu Mar 26 19:55:19 2015 -0400 +++ b/interprophet.xml Tue Oct 20 20:45:24 2015 -0400 @@ -1,59 +1,71 @@ -<tool id="proteomics_search_interprophet_1" name="InterProphet" version="1.1.0"> - - <requirements> - <container type="docker">iracooke/protk-1.4.1</container> - <requirement type="package" version="1.4">protk</requirement> - <requirement type="package" version="4.8.0">trans_proteomic_pipeline</requirement> - </requirements> - - - <description>Combine Peptide Prophet results from multiple search engines</description> - - <command>interprophet.rb --galaxy +<tool id="proteomics_search_interprophet_1" name="InterProphet" version="1.1.1"> + <description>Combine Peptide Prophet results from multiple search engines</description> + <requirements> + <container type="docker">iracooke/protk-1.4.3</container> + <requirement type="package" version="1.4.3">protk</requirement> + <requirement type="package" version="4.8.0">trans_proteomic_pipeline</requirement> + </requirements> + <command> +<![CDATA[ + interprophet.rb --galaxy + #if str( $input_type.type ) == "files": + #for $pepxml_file in $input_type.pepxml_files: + ${pepxml_file} + #end for + #else + #for $list_item in $input_type.pepxml_list: + ${list_item} + #end for + #for $extra_list_holder in $input_type.extra_pepxml_lists: + #for $list_item in $extra_list_holder.extra_list: + ${list_item} + #end for + #end for + #end if - -o interprophet_output.pep.xml - - $use_nss - - $use_nrs - - $use_nse - - $use_nsi - - $use_nsm - - --p-thresh $p_thresh + -o interprophet_output.pep.xml + $use_nss + $use_nrs + $use_nse + $use_nsi + $use_nsm + --p-thresh $p_thresh + --threads "\${GALAXY_SLOTS:-12}" - --threads $threads - -#for $pepxml_file in $pepxml_files: - ${pepxml_file} -#end for - - </command> - - - <inputs> - - <param name="pepxml_files" multiple="true" type="data" format="peptideprophet_pepxml" label="Peptide Prophet Results" help="These files will typically be outputs from search tools that have subsequently been run through peptide prophet"/> +]]> + </command> + <inputs> - <param name="use_nss" checked="true" type="boolean" label="Include NSS in Model" help="Include NSS (Number of Sibling Searches) in Statistical Model" truevalue="" falsevalue="--no-nss"/> - <param name="use_nrs" checked="true" type="boolean" label="Include NRS in Model" help="Include NRS (Number of Replicate Spectra) in Statistical Model" truevalue="" falsevalue="--no-nrs"/> - <param name="use_nse" checked="true" type="boolean" label="Include NSE in Model" help="Include NSE (Number of Sibling Experiments) in Statistical Model" truevalue="" falsevalue="--no-nse"/> - <param name="use_nsi" checked="true" type="boolean" label="Include NSI in Model" help="Include NSI (Number of Sibling Ions) in Statistical Model" truevalue="" falsevalue="--no-nsi"/> - <param name="use_nsm" checked="true" type="boolean" label="Include NSM in Model" help="Include NSM (Number of Sibling Modifications) in Statistical Model" truevalue="" falsevalue="--no-nsm"/> - - <param name="p_thresh" help="Peptides scoring less than this value are discarded" type="float" value="0.05" min="0" max="1" label="Probability Threshold"/> + <conditional name="input_type"> + <param name="type" type="select" label="Input Type"> + <option value="files" selected="true">Datasets</option> + <option value="collections">Collections</option> + </param> + <when value="files"> + <param name="pepxml_files" multiple="true" type="data" format="peptideprophet_pepxml" label="Peptide Prophet Results" help="These files will typically be outputs from search tools that have subsequently been run through peptide prophet"/> + </when> + <when value="collections"> + <param name="pepxml_list" type="data_collection" multiple="true" collection_type="list" format="peptideprophet_pepxml" label="Peptide Prophet Results" help="These files will typically be outputs from search tools that have subsequently been run through peptide prophet"/> + <repeat name="extra_pepxml_lists" title="Additional PepXML Collections" > + <param name="extra_list" type="data_collection" multiple="true" collection_type="list" format="peptideprophet_pepxml" label="Peptide Prophet Results" help="These files will typically be outputs from search tools that have subsequently been run through peptide prophet"/> + </repeat> + </when> + </conditional> - <param name="threads" type="integer" value="1" min="0" label="Threads" help="Number of threads to use"/> - - </inputs> - <outputs> - <data format="interprophet_pepxml" name="output" label="interprophet.${pepxml_files[0].display_name}" from_work_dir="interprophet_output.pep.xml"/> - </outputs> + <!-- <param name="pepxml_files" multiple="true" type="data" format="peptideprophet_pepxml" label="Peptide Prophet Results" help="These files will typically be outputs from search tools that have subsequently been run through peptide prophet"/> --> - <help> + <param name="use_nss" checked="true" type="boolean" label="Include NSS in Model" help="Include NSS (Number of Sibling Searches) in Statistical Model" truevalue="" falsevalue="--no-nss"/> + <param name="use_nrs" checked="true" type="boolean" label="Include NRS in Model" help="Include NRS (Number of Replicate Spectra) in Statistical Model" truevalue="" falsevalue="--no-nrs"/> + <param name="use_nse" checked="true" type="boolean" label="Include NSE in Model" help="Include NSE (Number of Sibling Experiments) in Statistical Model" truevalue="" falsevalue="--no-nse"/> + <param name="use_nsi" checked="true" type="boolean" label="Include NSI in Model" help="Include NSI (Number of Sibling Ions) in Statistical Model" truevalue="" falsevalue="--no-nsi"/> + <param name="use_nsm" checked="true" type="boolean" label="Include NSM in Model" help="Include NSM (Number of Sibling Modifications) in Statistical Model" truevalue="" falsevalue="--no-nsm"/> + <param name="p_thresh" help="Peptides scoring less than this value are discarded" type="float" value="0.05" min="0" max="1" label="Probability Threshold"/> + + </inputs> + <outputs> + <data format="interprophet_pepxml" name="output" from_work_dir="interprophet_output.pep.xml"/> + </outputs> + <help> **What it does** @@ -67,6 +79,5 @@ Shteynberg D, et al. “iProphet: Improved statistical validation of peptide identifications in shotgun proteomics.” *Molecular and Cellular Proteomics* 10, M111.007690 (2011). - </help> - + </help> </tool>
--- a/peptide_prophet.xml Thu Mar 26 19:55:19 2015 -0400 +++ b/peptide_prophet.xml Tue Oct 20 20:45:24 2015 -0400 @@ -1,73 +1,66 @@ -<tool id="proteomics_search_peptide_prophet_1" name="Peptide Prophet" version="1.1.0"> +<tool id="proteomics_search_peptide_prophet_1" name="Peptide Prophet" version="1.1.1"> + <description>Calculate Peptide Prophet statistics on search results</description> <requirements> - <container type="docker">iracooke/protk-1.4.1</container> - <requirement type="package" version="1.4">protk</requirement> + <container type="docker">iracooke/protk-1.4.3</container> + <requirement type="package" version="1.4.3">protk</requirement> <requirement type="package" version="4.8.0">trans_proteomic_pipeline</requirement> - </requirements> - - <description>Calculate Peptide Prophet statistics on search results</description> - - <command> - peptide_prophet.rb --galaxy $input_file -o peptide_prophet_output.pep.xml - - -r - $glyco - $useicat - $phospho - $usepi - $usert - $accurate_mass - $no_ntt - $no_nmc - $use_gamma - $use_only_expect - $force_fit - $allow_alt_instruments - $maldi - $usedecoys - --decoy-prefix $decoy_prefix_string - -#if $experiment_label - --experiment-label $experiment_label -#end if + </requirements> + <command> + peptide_prophet.rb + --galaxy $input_file + -o peptide_prophet_output.pep.xml + -r + $glyco + $useicat + $phospho + $usepi + $usert + $accurate_mass + $no_ntt + $no_nmc + $use_gamma + $use_only_expect + $force_fit + $allow_alt_instruments + $maldi + $usedecoys + --decoy-prefix $decoy_prefix_string - --p-thresh $p_thresh - - --threads $threads - - </command> - - <inputs> - - <param name="input_file" type="data" format="raw_pepxml" multiple="false" label="Raw Search Results" help="These files will typically be outputs from omssa or xtandem search tools"/> + #if $experiment_label + --experiment-label $experiment_label + #end if - <param name="glyco" type="boolean" label="Expect true positives to have a glycocapture motif" truevalue="--glyco" falsevalue=""/> - <param name="useicat" type="boolean" label="Use icat information" truevalue="--useicat" falsevalue=""/> - <param name="phospho" type="boolean" label="Use phospho information" truevalue="--phospho" falsevalue=""/> - <param name="usepi" type="boolean" label="Use pI information" truevalue="--usepi" falsevalue=""/> - <param name="usert" type="boolean" label="Use hydrophobicity / RT information" truevalue="--usert" falsevalue=""/> - <param name="accurate_mass" type="boolean" label="Use accurate mass binning" truevalue="--accurate-mass" falsevalue=""/> - <param name="no_ntt" type="boolean" label="Don't use NTT model" truevalue="--no-ntt" falsevalue=""/> - <param name="no_nmc" type="boolean" label="Don't use NMC model" truevalue="--no-nmc" falsevalue=""/> - <param name="use_gamma" type="boolean" label="Use Gamma distribution to model the negatives" help="Applies only to X!Tandem results" truevalue="--usegamma" falsevalue=""/> - <param name="use_only_expect" type="boolean" label="Only use Expect Score as the discriminant" help="Applies only to X!Tandem results. - Helpful for data with homologous top hits e.g. phospho or glyco" truevalue="--use-only-expect" falsevalue=""/> - <param name="force_fit" type="boolean" label="Force fitting" help="Bypasses automatic mixture model checks and forces fitting of a mixture model" truevalue="--force-fit" falsevalue=""/> - <param name="allow_alt_instruments" type="boolean" label="Allow multiple instrument types" help="Warning instead of exit with error if instrument types between runs is different" truevalue="--allow-alt-instruments" falsevalue=""/> - <param name="maldi" type="boolean" label="Maldi data" truevalue="-l" falsevalue=""/> - <param name="usedecoys" type="boolean" label="Use decoys to pin down the negative distribution" truevalue="" falsevalue="--no-decoy"/> - <param name="decoy_prefix_string" help="Prefix string for decoy ids" type="text" value="decoy_" label="Decoy Prefix String" size="20"/> - <param name="experiment_label" help="Used to commonly label all spectra from one experiment" type="text" value="" label="Experiment Label" size="20"/> - <param name="p_thresh" help="Peptides scoring less than this value are discarded" type="float" value="0.05" min="0" max="1" label="Probability Threshold"/> - <param name="threads" type="integer" value="1" min="0" label="Threads" help="Number of threads to use"/> - - </inputs> - <outputs> - <data format="peptideprophet_pepxml" name="output" metadata_source="input_file" label="peptide_prophet.${input_file.display_name}.pep.xml" from_work_dir="peptide_prophet_output.pep.xml"/> - </outputs> + --p-thresh $p_thresh + --threads "\${GALAXY_SLOTS:-12}" -<help> + </command> + <inputs> + <param name="input_file" type="data" format="pepxml,raw_pepxml" multiple="false" label="Raw Search Results" help="These files will typically be outputs from omssa or xtandem search tools"/> + + <param name="glyco" type="boolean" label="Expect true positives to have a glycocapture motif" truevalue="--glyco" falsevalue=""/> + <param name="useicat" type="boolean" label="Use icat information" truevalue="--useicat" falsevalue=""/> + <param name="phospho" type="boolean" label="Use phospho information" truevalue="--phospho" falsevalue=""/> + <param name="usepi" type="boolean" label="Use pI information" truevalue="--usepi" falsevalue=""/> + <param name="usert" type="boolean" label="Use hydrophobicity / RT information" truevalue="--usert" falsevalue=""/> + <param name="accurate_mass" type="boolean" label="Use accurate mass binning" truevalue="--accurate-mass" falsevalue=""/> + <param name="no_ntt" type="boolean" label="Don't use NTT model" truevalue="--no-ntt" falsevalue=""/> + <param name="no_nmc" type="boolean" label="Don't use NMC model" truevalue="--no-nmc" falsevalue=""/> + <param name="use_gamma" type="boolean" label="Use Gamma distribution to model the negatives" help="Applies only to X!Tandem results" truevalue="--usegamma" falsevalue=""/> + <param name="use_only_expect" type="boolean" label="Only use Expect Score as the discriminant" help="Applies only to X!Tandem results. + Helpful for data with homologous top hits e.g. phospho or glyco" truevalue="--use-only-expect" falsevalue=""/> + <param name="force_fit" type="boolean" label="Force fitting" help="Bypasses automatic mixture model checks and forces fitting of a mixture model" truevalue="--force-fit" falsevalue=""/> + <param name="allow_alt_instruments" type="boolean" label="Allow multiple instrument types" help="Warning instead of exit with error if instrument types between runs is different" truevalue="--allow-alt-instruments" falsevalue=""/> + <param name="maldi" type="boolean" label="Maldi data" truevalue="-l" falsevalue=""/> + <param name="usedecoys" type="boolean" label="Use decoys to pin down the negative distribution" truevalue="" falsevalue="--no-decoy"/> + <param name="decoy_prefix_string" help="Prefix string for decoy ids" type="text" value="decoy_" label="Decoy Prefix String" size="20"/> + <param name="experiment_label" help="Used to commonly label all spectra from one experiment" type="text" value="" label="Experiment Label" size="20"/> + <param name="p_thresh" help="Peptides scoring less than this value are discarded" type="float" value="0.05" min="0" max="1" label="Probability Threshold"/> + </inputs> + <outputs> + <data format="peptideprophet_pepxml" name="output" metadata_source="input_file" label="peptide_prophet.${input_file.display_name}.pep.xml" from_work_dir="peptide_prophet_output.pep.xml"/> + </outputs> + <help> **What it does** @@ -82,7 +75,7 @@ Keller A., et al. “Empirical Statistical Model to Estimate the Accuracy of Peptide Identifications Made by MS/MS and Database Search” *Anal. Chem.* 74, 5383-5392 (2002). -</help> + </help> <!--PeptideProphet options [following the 'O']:
--- a/pepxml_to_table.xml Thu Mar 26 19:55:19 2015 -0400 +++ b/pepxml_to_table.xml Tue Oct 20 20:45:24 2015 -0400 @@ -1,45 +1,30 @@ -<tool id="pepxml_to_table_1" name="PepXML to Table" version="1.1.0"> - - <requirements> - <container type="docker">iracooke/protk-1.4.1</container> - <requirement type="package" version="1.4">protk</requirement> - </requirements> - - - - <description>Converts a pepXML file to a tab delimited text file</description> - - -<!-- Note .. the input file is assumed to be the first argument --> -<command>pepxml_to_table.rb $input_file -o $output $invert_probs</command> - - -<inputs> - - <param name="input_file" type="data" format="pepxml,raw_pepxml,peptideprophet_pepxml,interprophet_pepxml" multiple="false" label="Input File" help="A pepXML file"/> - <param name="invert_probs" type="boolean" label="Print inverted probabilities (ie 1-p instead of p)" truevalue="--invert-probabilities" falsevalue=""/> - -</inputs> -<outputs> - <data format="csv" name="output" metadata_source="input_file" label="${input_file.display_name}.csv" /> -</outputs> - - - <tests> - <!-- Just test that the tool runs and produces vaguely correct output --> - <test> - <param name="input_file" value="mr176-BSA100fmole_BA3_01_8168.d_tandem.pep.xml" format="raw_pepxml"/> - <output name="output" format="csv"> - <assert_contents> - <has_text text="ANTNNYAPKSSR" /> - </assert_contents> - </output> - </test> - </tests> - - +<tool id="pepxml_to_table_1" name="PepXML to Table" version="1.1.1"> + <description>Converts a pepXML file to a tab delimited text file</description> + <requirements> + <container type="docker">iracooke/protk-1.4.3</container> + <requirement type="package" version="1.4.3">protk</requirement> + </requirements> + <!-- Note .. the input file is assumed to be the first argument --> + <command>pepxml_to_table.rb $input_file -o $output $invert_probs</command> + <inputs> + <param name="input_file" type="data" format="pepxml,raw_pepxml,peptideprophet_pepxml,interprophet_pepxml" multiple="false" label="Input File" help="A pepXML file"/> + <param name="invert_probs" type="boolean" label="Print inverted probabilities (ie 1-p instead of p)" truevalue="--invert-probabilities" falsevalue=""/> + </inputs> + <outputs> + <data format="csv" name="output" metadata_source="input_file" label="${input_file.display_name}.csv" /> + </outputs> + <tests> + <!-- Just test that the tool runs and produces vaguely correct output --> + <test> + <param name="input_file" value="mr176-BSA100fmole_BA3_01_8168.d_tandem.pep.xml" format="raw_pepxml"/> + <output name="output" format="csv"> + <assert_contents> + <has_text text="ANTNNYAPKSSR" /> + </assert_contents> + </output> + </test> + </tests> <help> - Convert a pepXML file to Tab delimited text + Convert a pepXML file to Tab delimited text </help> - </tool>
--- a/protein_prophet.xml Thu Mar 26 19:55:19 2015 -0400 +++ b/protein_prophet.xml Tue Oct 20 20:45:24 2015 -0400 @@ -1,79 +1,73 @@ -<tool id="proteomics_search_protein_prophet_1" name="Protein Prophet" version="1.1.0"> - <requirements> - <container type="docker">iracooke/protk-1.4.1</container> - <requirement type="package" version="1.4">protk</requirement> - <requirement type="package" version="4.8.0">trans_proteomic_pipeline</requirement> - </requirements> - - <description>Calculate Protein Prophet statistics on search results</description> - +<tool id="proteomics_search_protein_prophet_1" name="Protein Prophet" version="1.1.1"> + <description>Calculate Protein Prophet statistics on search results</description> + <requirements> + <container type="docker">iracooke/protk-1.4.3</container> + <requirement type="package" version="1.4.3">protk</requirement> + <requirement type="package" version="4.8.0">trans_proteomic_pipeline</requirement> + </requirements> -<!-- Note .. the input file is assumed to be the first argument --> - <command> - protein_prophet.rb - - --galaxy $input_file - - -o protein_prophet_results.prot.xml - - -r + <command> + protein_prophet.rb + --galaxy + + #for $input_file in $input_files: + ${input_file} + #end for + + -o protein_prophet_results.prot.xml + -r - $iproph - $nooccam - $groupwts - $normprotlen - $logprobs - $confem - $allpeps - $unmapped - $instances - $delude - - --minprob=$minprob - --minindep=$minindep - </command> - <inputs> - - <param name="input_file" type="data" format="peptideprophet_pepxml,interprophet_pepxml" multiple="false" label="Peptide Prophet Results" help="These files will typically be outputs from peptide prophet or interprophet"/> + $iproph + $nooccam + $groupwts + $normprotlen + $logprobs + $confem + $allpeps + $unmapped + $instances + $delude + --minprob=$minprob + --minindep=$minindep + </command> + <inputs> + <param name="input_files" type="data" format="peptideprophet_pepxml,interprophet_pepxml" multiple="true" label="Peptide Prophet Results" help="These files will typically be outputs from peptide prophet or interprophet"/> - <param name="iproph" selected="true" type="boolean" label="Inputs are from iProphet" truevalue="--iprophet-input" falsevalue=""/> - <param name="nooccam" type="boolean" label="Don't apply Occam's razor" help="When selected no attempt will be made to derive the simplest protein list explaining observed peptides" truevalue="--no-occam" falsevalue=""/> - <param name="groupwts" type="boolean" label="Use group weights" help="Check peptide's total weight (rather than actual weight) in the Protein Group against the threshold" truevalue="--group-wts" falsevalue=""/> - <param name="normprotlen" type="boolean" label="Normalize NSP using Protein Length" truevalue="--norm-protlen" falsevalue=""/> - <param name="logprobs" type="boolean" label="Use the log of probability in the confidence calculations" truevalue="--log-prob" falsevalue=""/> - <param name="confem" type="boolean" label="Use the EM to compute probability given the confidenct" truevalue="--confem" falsevalue=""/> - <param name="allpeps" type="boolean" label="Consider all possible peptides in the database in the confidence model" truevalue="--allpeps" falsevalue=""/> - <param name="unmapped" type="boolean" label="Report results for unmapped proteins" truevalue="--unmapped" falsevalue=""/> - <param name="instances" type="boolean" label="Use Expected Number of Ion Instances to adjust the peptide probabilities prior to NSP adjustment" truevalue="--instances" falsevalue=""/> - <param name="delude" type="boolean" label="Do NOT use peptide degeneracy information when assessing proteins" truevalue="--delude" falsevalue=""/> + <param name="iproph" selected="true" type="boolean" label="Inputs are from iProphet" truevalue="--iprophet-input" falsevalue=""/> + <param name="nooccam" type="boolean" label="Don't apply Occam's razor" help="When selected no attempt will be made to derive the simplest protein list explaining observed peptides" truevalue="--no-occam" falsevalue=""/> + <param name="groupwts" type="boolean" label="Use group weights" help="Check peptide's total weight (rather than actual weight) in the Protein Group against the threshold" truevalue="--group-wts" falsevalue=""/> + <param name="normprotlen" type="boolean" label="Normalize NSP using Protein Length" truevalue="--norm-protlen" falsevalue=""/> + <param name="logprobs" type="boolean" label="Use the log of probability in the confidence calculations" truevalue="--log-prob" falsevalue=""/> + <param name="confem" type="boolean" label="Use the EM to compute probability given the confidenct" truevalue="--confem" falsevalue=""/> + <param name="allpeps" type="boolean" label="Consider all possible peptides in the database in the confidence model" truevalue="--allpeps" falsevalue=""/> + <param name="unmapped" type="boolean" label="Report results for unmapped proteins" truevalue="--unmapped" falsevalue=""/> + <param name="instances" type="boolean" label="Use Expected Number of Ion Instances to adjust the peptide probabilities prior to NSP adjustment" truevalue="--instances" falsevalue=""/> + <param name="delude" type="boolean" label="Do NOT use peptide degeneracy information when assessing proteins" truevalue="--delude" falsevalue=""/> - <param name="minprob" type="text" label="Minimum peptide prophet probability for peptides to be considered" value="0.05"/> - <param name="minindep" type="text" label="Minimum percentage of independent peptides required for a protein" value="0"/> - - </inputs> - <outputs> - <data format="protxml" name="output" metadata_source="input_file" label="protein_prophet.${input_file.display_name}.protXML" from_work_dir="protein_prophet_results.prot.xml"/> - </outputs> + <param name="minprob" type="text" label="Minimum peptide prophet probability for peptides to be considered" value="0.05"/> + <param name="minindep" type="text" label="Minimum percentage of independent peptides required for a protein" value="0"/> + </inputs> + <outputs> + <data format="protxml" name="output" from_work_dir="protein_prophet_results.prot.xml"/> + </outputs> <!--NOPLOT: do not generate plot png file - NOOCCAM: non-conservative maximum protein list - GROUPWTS: check peptide's total weight in the Protein Group against the threshold (default: check peptide's actual weight against threshold) - NORMPROTLEN: Normalize NSP using Protein Length - LOGPROBS: Use the log of the probabilities in the Confidence calculations - CONFEM: Use the EM to compute probability given the confidence - ALLPEPS: Consider all possible peptides in the database in the confidence model - UNMAPPED: Report results for UNMAPPED proteins - INSTANCES: Use Expected Number of Ion Instances to adjust the peptide probabilities prior to NSP adjustment - DELUDE: do NOT use peptide degeneracy information when assessing proteins - - MINPROB: peptideProphet probabilty threshold (default=0.05) - MININDEP: minimum percentage of independent peptides required for a protein (default=0) - - + NOOCCAM: non-conservative maximum protein list + GROUPWTS: check peptide's total weight in the Protein Group against the threshold (default: check peptide's actual weight against threshold) + NORMPROTLEN: Normalize NSP using Protein Length + LOGPROBS: Use the log of the probabilities in the Confidence calculations + CONFEM: Use the EM to compute probability given the confidence + ALLPEPS: Consider all possible peptides in the database in the confidence model + UNMAPPED: Report results for UNMAPPED proteins + INSTANCES: Use Expected Number of Ion Instances to adjust the peptide probabilities prior to NSP adjustment + DELUDE: do NOT use peptide degeneracy information when assessing proteins + + MINPROB: peptideProphet probabilty threshold (default=0.05) + MININDEP: minimum percentage of independent peptides required for a protein (default=0) --> - <help> + <help> **What it does** @@ -88,6 +82,5 @@ Nesvizhskii A., et al. “A Statistical Model for Identifying Proteins by Tandem Mass Spectrometry” *Anal. Chem.* 75, 4646-4658 (2003). - </help> - + </help> </tool>
--- a/protxml_to_table.xml Thu Mar 26 19:55:19 2015 -0400 +++ b/protxml_to_table.xml Tue Oct 20 20:45:24 2015 -0400 @@ -1,49 +1,37 @@ -<tool id="protxml_to_table_1" name="ProtXML to Table" version="1.1.0"> - <requirements> - <container type="docker">iracooke/protk-1.4.1</container> - <requirement type="package" version="1.4">protk</requirement> - </requirements> - - <description>Converts a ProtXML file to a table</description> - - <command> - protxml_to_table.rb - $invert_probs - - $input_file - -o $output - </command> - - <inputs> - - <param format="protxml" name="input_file" type="data" label="ProtXML File to Convert"/> - <param name="invert_probs" type="boolean" label="Print inverted probabilities (ie 1-p instead of p)" truevalue="--invert-probabilities" falsevalue=""/> - </inputs> - - - <outputs> - <data format="tabular" name="output" /> - </outputs> - - <tests> - <!-- Just test that the tool runs and produces vaguely correct output --> - <test> - <param name="input_file" value="mr176-BSA100fmole_BA3_01_8168.d_tandem_pproph_protproph.prot.xml" format="protxml"/> - <output name="output" format="tabular"> - <assert_contents> - <has_text text="AVQKYLTAHEQSK" /> - </assert_contents> - </output> - </test> - </tests> - - - <help> - +<tool id="protxml_to_table_1" name="ProtXML to Table" version="1.1.1"> + <description>Converts a ProtXML file to a table</description> + <requirements> + <container type="docker">iracooke/protk-1.4.3</container> + <requirement type="package" version="1.4.3">protk</requirement> + </requirements> + <command> + protxml_to_table.rb + $invert_probs + $input_file + -o $output + </command> + <inputs> + <param format="protxml" name="input_file" type="data" label="ProtXML File to Convert"/> + <param name="invert_probs" type="boolean" label="Print inverted probabilities (ie 1-p instead of p)" truevalue="--invert-probabilities" falsevalue=""/> + </inputs> + <outputs> + <data format="tabular" name="output" /> + </outputs> + <tests> + <!-- Just test that the tool runs and produces vaguely correct output --> + <test> + <param name="input_file" value="mr176-BSA100fmole_BA3_01_8168.d_tandem_pproph_protproph.prot.xml" format="protxml"/> + <output name="output" format="tabular"> + <assert_contents> + <has_text text="AVQKYLTAHEQSK" /> + </assert_contents> + </output> + </test> + </tests> + <help> **What it does** Converts a ProtXML file to a tab separated table - </help> - + </help> </tool>
--- a/repository_dependencies.xml Thu Mar 26 19:55:19 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -<?xml version="1.0"?> -<repositories description="Proteomics datatypes"> - <repository changeset_revision="ac51d9dbfb4d" name="proteomics_datatypes" owner="iracooke" toolshed="https://toolshed.g2.bx.psu.edu" /> - </repositories>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Tue Oct 20 20:45:24 2015 -0400 @@ -0,0 +1,9 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="protk" version="1.4.3"> + <repository changeset_revision="74bf855be117" name="package_protk_1_4_3" owner="iracooke" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="trans_proteomic_pipeline" version="4.8.0"> + <repository changeset_revision="a7273394d858" name="package_tpp_4_8_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency>