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Commit message:
planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty |
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modified:
interprophet.xml peptide_prophet.xml pepxml_to_table.xml protein_prophet.xml protxml_to_table.xml |
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added:
tool_dependencies.xml |
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removed:
repository_dependencies.xml |
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| diff -r d90c8bc10a9c -r 0746a2ae9e04 interprophet.xml --- a/interprophet.xml Thu Mar 26 19:55:19 2015 -0400 +++ b/interprophet.xml Tue Oct 20 20:45:24 2015 -0400 |
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| @@ -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> |
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| diff -r d90c8bc10a9c -r 0746a2ae9e04 peptide_prophet.xml --- a/peptide_prophet.xml Thu Mar 26 19:55:19 2015 -0400 +++ b/peptide_prophet.xml Tue Oct 20 20:45:24 2015 -0400 |
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| b'@@ -1,73 +1,66 @@\n-<tool id="proteomics_search_peptide_prophet_1" name="Peptide Prophet" version="1.1.0">\n+<tool id="proteomics_search_peptide_prophet_1" name="Peptide Prophet" version="1.1.1">\n+ <description>Calculate Peptide Prophet statistics on search results</description>\n <requirements>\n- <container type="docker">iracooke/protk-1.4.1</container>\n- <requirement type="package" version="1.4">protk</requirement>\n+ <container type="docker">iracooke/protk-1.4.3</container>\n+ <requirement type="package" version="1.4.3">protk</requirement>\n <requirement type="package" version="4.8.0">trans_proteomic_pipeline</requirement>\n- </requirements>\n- \n-\t<description>Calculate Peptide Prophet statistics on search results</description>\n-\n-\t<command>\n- peptide_prophet.rb --galaxy $input_file -o peptide_prophet_output.pep.xml\n-\n- -r \n- $glyco \n- $useicat \n- $phospho \n- $usepi \n- $usert \n- $accurate_mass \n- $no_ntt \n- $no_nmc \n- $use_gamma \n- $use_only_expect \n- $force_fit \n- $allow_alt_instruments \n- $maldi\n- $usedecoys\n- --decoy-prefix $decoy_prefix_string\n-\n-#if $experiment_label\n- --experiment-label $experiment_label\n-#end if\n+ </requirements>\n+ <command>\n+ peptide_prophet.rb\n+ --galaxy $input_file\n+ -o peptide_prophet_output.pep.xml\n+ -r \n+ $glyco \n+ $useicat \n+ $phospho \n+ $usepi\n+ $usert\n+ $accurate_mass\n+ $no_ntt\n+ $no_nmc\n+ $use_gamma\n+ $use_only_expect\n+ $force_fit\n+ $allow_alt_instruments\n+ $maldi\n+ $usedecoys\n+ --decoy-prefix $decoy_prefix_string\n \n- --p-thresh $p_thresh\n-\n- --threads $threads\n-\n-\t</command>\n-\n-\t<inputs>\n-\t\n- <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"/>\n+ #if $experiment_label\n+ --experiment-label $experiment_label\n+ #end if\n \n-\t<param name="glyco" type="boolean" label="Expect true positives to have a glycocapture motif" truevalue="--glyco" falsevalue=""/>\n-\t<param name="useicat" type="boolean" label="Use icat information" truevalue="--useicat" falsevalue=""/>\n-\t<param name="phospho" type="boolean" label="Use phospho information" truevalue="--phospho" falsevalue=""/>\n-\t<param name="usepi" type="boolean" label="Use pI information" truevalue="--usepi" falsevalue=""/>\n-\t<param name="usert" type="boolean" label="Use hydrophobicity / RT information" truevalue="--usert" falsevalue=""/>\n-\t<param name="accurate_mass" type="boolean" label="Use accurate mass binning" truevalue="--accurate-mass" falsevalue=""/>\n-\t<param name="no_ntt" type="boolean" label="Don\'t use NTT model" truevalue="--no-ntt" falsevalue=""/>\n-\t<param name="no_nmc" type="boolean" label="Don\'t use NMC model" truevalue="--no-nmc" falsevalue=""/>\n-\t<param name="use_gamma" type="boolean" label="Use Gamma distribution to model the negatives" help="Applies only to X!Tandem results" truevalue="--usegamma" falsevalue=""/>\n-\t<param name="use_only_expect" type="boolean" label="Only use Expect Score as the discriminant" help="Applies only to X!Tandem results. \n- Helpful for data with homologous top hits e.g. phospho or glyco" truevalue="--use-only-expect" falsevalue=""/>\n-\t<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=""/>\n-\t<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=""/>\n-\t<param '..b'one experiment" type="text" value="" label="Experiment Label" size="20"/>\n- <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"/>\n- <param name="threads" type="integer" value="1" min="0" label="Threads" help="Number of threads to use"/>\n-\t\n- </inputs>\n- <outputs>\n- <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"/>\n- </outputs>\n+ --p-thresh $p_thresh\n+ --threads "\\${GALAXY_SLOTS:-12}"\n \n \n-<help>\n+ </command>\n+ <inputs>\n+ <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"/>\n+\n+ <param name="glyco" type="boolean" label="Expect true positives to have a glycocapture motif" truevalue="--glyco" falsevalue=""/>\n+ <param name="useicat" type="boolean" label="Use icat information" truevalue="--useicat" falsevalue=""/>\n+ <param name="phospho" type="boolean" label="Use phospho information" truevalue="--phospho" falsevalue=""/>\n+ <param name="usepi" type="boolean" label="Use pI information" truevalue="--usepi" falsevalue=""/>\n+ <param name="usert" type="boolean" label="Use hydrophobicity / RT information" truevalue="--usert" falsevalue=""/>\n+ <param name="accurate_mass" type="boolean" label="Use accurate mass binning" truevalue="--accurate-mass" falsevalue=""/>\n+ <param name="no_ntt" type="boolean" label="Don\'t use NTT model" truevalue="--no-ntt" falsevalue=""/>\n+ <param name="no_nmc" type="boolean" label="Don\'t use NMC model" truevalue="--no-nmc" falsevalue=""/>\n+ <param name="use_gamma" type="boolean" label="Use Gamma distribution to model the negatives" help="Applies only to X!Tandem results" truevalue="--usegamma" falsevalue=""/>\n+ <param name="use_only_expect" type="boolean" label="Only use Expect Score as the discriminant" help="Applies only to X!Tandem results. \n+ Helpful for data with homologous top hits e.g. phospho or glyco" truevalue="--use-only-expect" falsevalue=""/>\n+ <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=""/>\n+ <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=""/>\n+ <param name="maldi" type="boolean" label="Maldi data" truevalue="-l" falsevalue=""/>\n+ <param name="usedecoys" type="boolean" label="Use decoys to pin down the negative distribution" truevalue="" falsevalue="--no-decoy"/>\n+ <param name="decoy_prefix_string" help="Prefix string for decoy ids" type="text" value="decoy_" label="Decoy Prefix String" size="20"/> \n+ <param name="experiment_label" help="Used to commonly label all spectra from one experiment" type="text" value="" label="Experiment Label" size="20"/>\n+ <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"/>\n+ </inputs>\n+ <outputs>\n+ <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"/>\n+ </outputs>\n+ <help>\n \n **What it does**\n \n@@ -82,7 +75,7 @@\n Keller A., et al. \xe2\x80\x9cEmpirical Statistical Model to Estimate the Accuracy of Peptide Identifications Made by MS/MS and Database Search\xe2\x80\x9d *Anal. Chem.* 74, 5383-5392 (2002).\n \n \n-</help>\n+ </help>\n \n \n <!--PeptideProphet options [following the \'O\']:\n' |
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| diff -r d90c8bc10a9c -r 0746a2ae9e04 pepxml_to_table.xml --- 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 |
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| @@ -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> |
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| diff -r d90c8bc10a9c -r 0746a2ae9e04 protein_prophet.xml --- a/protein_prophet.xml Thu Mar 26 19:55:19 2015 -0400 +++ b/protein_prophet.xml Tue Oct 20 20:45:24 2015 -0400 |
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| b'@@ -1,79 +1,73 @@\n-<tool id="proteomics_search_protein_prophet_1" name="Protein Prophet" version="1.1.0">\n-\t<requirements>\n- <container type="docker">iracooke/protk-1.4.1</container>\n-\t <requirement type="package" version="1.4">protk</requirement>\n-\t <requirement type="package" version="4.8.0">trans_proteomic_pipeline</requirement>\n- </requirements>\n-\n- <description>Calculate Protein Prophet statistics on search results</description>\n-\n+<tool id="proteomics_search_protein_prophet_1" name="Protein Prophet" version="1.1.1">\n+ <description>Calculate Protein Prophet statistics on search results</description>\n+ <requirements>\n+ <container type="docker">iracooke/protk-1.4.3</container>\n+ <requirement type="package" version="1.4.3">protk</requirement>\n+ <requirement type="package" version="4.8.0">trans_proteomic_pipeline</requirement>\n+ </requirements>\n \n-<!-- Note .. the input file is assumed to be the first argument -->\n- <command>\n- \tprotein_prophet.rb\n-\n- \t--galaxy $input_file \n-\n- \t-o protein_prophet_results.prot.xml\n-\n- \t-r\n+ <command>\n+ protein_prophet.rb\n+ --galaxy \n+ \n+ #for $input_file in $input_files:\n+ ${input_file}\n+ #end for\n+ \n+ -o protein_prophet_results.prot.xml\n+ -r\n \n- \t$iproph \n- \t$nooccam \n- \t$groupwts \n- \t$normprotlen \n- \t$logprobs \n- \t$confem \n- \t$allpeps \n- \t$unmapped \n- \t$instances \n- \t$delude\n- \t\n- \t--minprob=$minprob \n- \t--minindep=$minindep \n- </command>\n- <inputs>\n-\t\n- <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"/>\n+ $iproph\n+ $nooccam\n+ $groupwts\n+ $normprotlen\n+ $logprobs\n+ $confem\n+ $allpeps\n+ $unmapped\n+ $instances\n+ $delude\n+ --minprob=$minprob\n+ --minindep=$minindep\n+ </command>\n+ <inputs>\n+ <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"/>\n \n-\t<param name="iproph" selected="true" type="boolean" label="Inputs are from iProphet" truevalue="--iprophet-input" falsevalue=""/>\n-\t<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=""/>\n-\t<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=""/>\n-\t<param name="normprotlen" type="boolean" label="Normalize NSP using Protein Length" truevalue="--norm-protlen" falsevalue=""/>\n-\t<param name="logprobs" type="boolean" label="Use the log of probability in the confidence calculations" truevalue="--log-prob" falsevalue=""/>\n-\t<param name="confem" type="boolean" label="Use the EM to compute probability given the confidenct" truevalue="--confem" falsevalue=""/>\n-\t<param name="allpeps" type="boolean" label="Consider all possible peptides in the database in the confidence model" truevalue="--allpeps" falsevalue=""/>\n-\t<param name="unmapped" type="boolean" label="Report results for unmapped proteins" truevalue="--unmapped" falsevalue=""/>\n-\t<param name="instances" type="boolean" label="Use Expected Number of Ion Instances to adjust the peptide probabilities prior to NSP adjustment" truevalue="--instances" falsevalue=""/>\n-\t<param name="delude" type="boolean" label="Do NOT use peptide degeneracy information when assessing proteins" truevalue="--delude" falsevalue=""/>\n+ <param name="iproph" selected="true"'..b' Protein Length" truevalue="--norm-protlen" falsevalue=""/>\n+ <param name="logprobs" type="boolean" label="Use the log of probability in the confidence calculations" truevalue="--log-prob" falsevalue=""/>\n+ <param name="confem" type="boolean" label="Use the EM to compute probability given the confidenct" truevalue="--confem" falsevalue=""/>\n+ <param name="allpeps" type="boolean" label="Consider all possible peptides in the database in the confidence model" truevalue="--allpeps" falsevalue=""/>\n+ <param name="unmapped" type="boolean" label="Report results for unmapped proteins" truevalue="--unmapped" falsevalue=""/>\n+ <param name="instances" type="boolean" label="Use Expected Number of Ion Instances to adjust the peptide probabilities prior to NSP adjustment" truevalue="--instances" falsevalue=""/>\n+ <param name="delude" type="boolean" label="Do NOT use peptide degeneracy information when assessing proteins" truevalue="--delude" falsevalue=""/>\n \n-\t<param name="minprob" type="text" label="Minimum peptide prophet probability for peptides to be considered" value="0.05"/>\n-\t<param name="minindep" type="text" label="Minimum percentage of independent peptides required for a protein" value="0"/>\n-\t\n- </inputs>\n- <outputs>\n- <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"/>\n- </outputs>\n+ <param name="minprob" type="text" label="Minimum peptide prophet probability for peptides to be considered" value="0.05"/>\n+ <param name="minindep" type="text" label="Minimum percentage of independent peptides required for a protein" value="0"/>\n+ </inputs>\n+ <outputs>\n+ <data format="protxml" name="output" from_work_dir="protein_prophet_results.prot.xml"/>\n+ </outputs>\n \n \n <!--NOPLOT: do not generate plot png file\n-\t\tNOOCCAM: non-conservative maximum protein list\n-\t\tGROUPWTS: check peptide\'s total weight in the Protein Group against the threshold (default: check peptide\'s actual weight against threshold) \n-\t\tNORMPROTLEN: Normalize NSP using Protein Length\n-\t\tLOGPROBS: Use the log of the probabilities in the Confidence calculations\n-\t\tCONFEM: Use the EM to compute probability given the confidence \n-\t\tALLPEPS: Consider all possible peptides in the database in the confidence model\n-\t\tUNMAPPED: Report results for UNMAPPED proteins\n-\t\tINSTANCES: Use Expected Number of Ion Instances to adjust the peptide probabilities prior to NSP adjustment\n-\t\tDELUDE: do NOT use peptide degeneracy information when assessing proteins\n-\t\t\n-\t\tMINPROB: peptideProphet probabilty threshold (default=0.05) \n-\t\tMININDEP: minimum percentage of independent peptides required for a protein (default=0) \n-\t\t\n-\t\t\n+ NOOCCAM: non-conservative maximum protein list\n+ GROUPWTS: check peptide\'s total weight in the Protein Group against the threshold (default: check peptide\'s actual weight against threshold) \n+ NORMPROTLEN: Normalize NSP using Protein Length\n+ LOGPROBS: Use the log of the probabilities in the Confidence calculations\n+ CONFEM: Use the EM to compute probability given the confidence \n+ ALLPEPS: Consider all possible peptides in the database in the confidence model\n+ UNMAPPED: Report results for UNMAPPED proteins\n+ INSTANCES: Use Expected Number of Ion Instances to adjust the peptide probabilities prior to NSP adjustment\n+ DELUDE: do NOT use peptide degeneracy information when assessing proteins\n+ \n+ MINPROB: peptideProphet probabilty threshold (default=0.05) \n+ MININDEP: minimum percentage of independent peptides required for a protein (default=0) \n -->\n \n- <help>\n+ <help>\n \n **What it does**\n \n@@ -88,6 +82,5 @@\n Nesvizhskii A., et al. \xe2\x80\x9cA Statistical Model for Identifying Proteins by Tandem Mass Spectrometry\xe2\x80\x9d *Anal. Chem.* 75, 4646-4658 (2003).\n \n \n- </help>\n-\n+ </help>\n </tool>\n' |
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| diff -r d90c8bc10a9c -r 0746a2ae9e04 protxml_to_table.xml --- 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 |
| b |
| @@ -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> |
| b |
| diff -r d90c8bc10a9c -r 0746a2ae9e04 repository_dependencies.xml --- a/repository_dependencies.xml Thu Mar 26 19:55:19 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -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> |
| b |
| diff -r d90c8bc10a9c -r 0746a2ae9e04 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Tue Oct 20 20:45:24 2015 -0400 |
| b |
| @@ -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> |