Mercurial > repos > bgruening > peptideshaker
changeset 11:e5bdaa2ac9c7 draft
Improved help text
| author | iracooke |
|---|---|
| date | Wed, 07 May 2014 00:47:14 -0400 |
| parents | 5a74b76d48fc |
| children | b9f2cedab007 |
| files | peptide_shaker.xml |
| diffstat | 1 files changed, 149 insertions(+), 140 deletions(-) [+] |
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--- a/peptide_shaker.xml Tue May 06 15:45:35 2014 -0400 +++ b/peptide_shaker.xml Wed May 07 00:47:14 2014 -0400 @@ -1,6 +1,6 @@ <tool id="peptide_shaker" name="Peptide Shaker" version="1.18.3.0"> <description> - Peform protein identification combining X! Tandem and OMSSA (using SearchGUI) and PeptideShaker pipeline. + Perform protein identification using various search engines (using SearchGUI) and combine results with PeptideShaker. </description> <requirements> <requirement type="package" version="0.28.0">peptide_shaker</requirement> @@ -244,9 +244,9 @@ </command> <inputs> <param format="fasta" name="input_database" type="data" label="Protein Database" - help="Select FASTA database from history. Typically, a target-decoy database is incorporated into the Scaffold engine for FDR analysis"/> + help="Select FASTA database from history"/> - <param name="create_decoy" label="Create a concatenated target/decoy database before running PeptideShaker." type="boolean" truevalue="True" falsevalue="False" checked="true" /> + <param name="create_decoy" label="Create a concatenated target/decoy database before running PeptideShaker." type="boolean" truevalue="True" falsevalue="False" checked="true" help="Selecting this option will help PeptideShaker calculate FDR values" /> <param format="mgf" name="peak_lists" type="data" multiple="true" label="Input Peak Lists (mgf)" help="Select appropriate MGF dataset(s) from history" /> @@ -288,21 +288,21 @@ <option value="Semi-Glu-C">Semi-Glu-C</option> </param> - <param name="correct_titles" type="select" label="Correct for duplicate spectrum titles" - help="(-correct_titles)"> + <param name="correct_titles" type="select" label="How should PeptideShaker deal with duplicate spectra?" + help="Unless you suspect some input files to be genuine duplicates then rename spectra is the safest option"> <option value="0">no correction</option> <option value="1" selected="True">rename spectra</option> <option value="2">delete spectra</option> </param> <param name="mgf_splitting" type="integer" value="1000" label="The maximum mgf file size in MB before splitting the mgf" - help="(-mgf_splitting)"/> + help="Choose a smaller value if you are running on a machine with limited memory"/> <param name="mgf_spectrum_count" type="integer" value="25000" label="The maximum number of spectra per mgf file when splitting" - help="(-mgf_spectrum_count)"/> + help="Choose a smaller value if you are running on a machine with limited memory"/> <conditional name="species_type"> <param name="species_type_selector" type="select" optional="true" label="The species type to use for the gene annotation" - help="(-species_type)"> + help="(Optional) If your species is supported under one of the groups, selecting it will allow GO annotations and other information to be included in the results"> <option value="Fungi">Fungi</option> <option value="Plants">Plants</option> <option value="Metazoa">Metazoa</option> @@ -312,7 +312,7 @@ </param> <when value="Protists"> <param name="species" type="select" label="The species to use for the gene annotation" - help="(-species)"> + help=""> <option value="Albugo laibachii">Albugo laibachii</option> <option value="Dictyostelium discoideum">Dictyostelium discoideum</option> <option value="Entamoeba histolytica">Entamoeba histolytica</option> @@ -338,7 +338,7 @@ </when> <when value="Plants"> <param name="species" type="select" label="The species to use for the gene annotation" - help="(-species)"> + help=""> <option value="Arabidopsis lyrata">Arabidopsis lyrata</option> <option value="Arabidopsis thaliana">Arabidopsis thaliana</option> <option value="Brachypodium distachyon">Brachypodium distachyon</option> @@ -366,7 +366,7 @@ </when> <when value="Metazoa"> <param name="species" type="select" label="The species to use for the gene annotation" - help="(-species)"> + help=""> <option value="Acyrthosiphon pisum">Acyrthosiphon pisum</option> <option value="Aedes aegypti">Aedes aegypti</option> <option value="Amphimedon queenslandica">Amphimedon queenslandica</option> @@ -414,7 +414,7 @@ </when> <when value="Fungi"> <param name="species" type="select" label="The species to use for the gene annotation" - help="(-species)"> + help=""> <option value="Ashbya gossypii">Ashbya gossypii</option> <option value="Aspergillus clavatus">Aspergillus clavatus</option> <option value="Aspergillus flavus">Aspergillus flavus</option> @@ -458,7 +458,7 @@ </when> <when value="Vertebrates"> <param name="species" type="select" label="The species to use for the gene annotation" - help="(-species)"> + help=""> <option value="Ailuropoda melanoleuca">Ailuropoda melanoleuca</option> <option value="Anolis carolinensis">Anolis carolinensis</option> <option value="Bos taurus">Bos taurus</option> @@ -524,7 +524,7 @@ </conditional> <param name="missed_cleavages" type="integer" value="2" label="Maximum Missed Cleavages" - help="Allow peptides to contain up to this many missed enzyme cleavage sites. 2 is the recommended value"/> + help="Allow peptides to contain up to this many missed enzyme cleavage sites."/> <param name="fixed_modifications" type="select" label="Fixed Modifications" multiple="true" help="Occurs in known places on peptide sequence. Hold the appropriate key while clicking to select multiple items"> <options from_file="searchgui_mods.loc"> @@ -616,7 +616,7 @@ <param name="peptide_fdr" label="FDR at the peptide level" help="In percent (default 1% FDR: '1')" value="1" type="float" /> <param name="psm_fdr" label="FDR at the PSM level" help="In percent (default 1% FDR: '1')" value="1" type="float" /> <param name="protein_fraction_mw_confidence" label="Minimum confidence required for a protein in the fraction MW plot" value="" type="float" - help="default 95%: '95.0' (-protein_fraction_mw_confidence)" /> + help="default 95%: '95.0'" /> <conditional name="ptm_score"> <param name="ptm_score_selector" type="select" label="The PTM probabilistic score to use for PTM localization"> <option value="0" selected="True">A-score</option> @@ -626,7 +626,7 @@ <when value="1"> <param name="score_neutral_losses" label="Include Neutral Losses in A Score" type="boolean" truevalue="1" falsevalue="0" /> <param name="ptm_threshold" label="The threshold to use for the PTM scores" value="" type="float" - help="Automatic mode will be used if not set." /> + help="Automatic mode will be used if not set" /> </when> </conditional> <!-- SKIPPING -protein_fraction_mw_confidence ${processing_options.protein_fraction_mw_confidence} --> @@ -642,14 +642,14 @@ <when value="yes"> <param name="min_peptide_length" label="Minimum Peptide Length" value="6" type="integer" /> <param name="max_peptide_length" label="Maximum Peptide Length" value="30" type="integer" /> - <param name="max_precursor_error" label="Maximum Precursor Error" value="10" type="float" help="Next option specifies units (Da or ppm)." /> + <param name="max_precursor_error" label="Maximum Precursor Error" value="10" type="float" help="Next option specifies units (Da or ppm)" /> <param name="max_precursor_error_type" label="Maximum Precursor Error Type" type="select"> <option value="0">ppm</option> <option value="1">Daltons</option> </param> <param name="max_xtandem_e" label="Maximum X! Tandem e-value" value="100" type="float" help="" /> <param name="max_omssa_e" label="Maximum OMSSA e-value" value="100" type="float" help="" /> - <param name="max_mascot_e" label="Maximum Mascot e-value filter" value="100" type="float" help="(-max_mascot_e)" /> + <param name="max_mascot_e" label="Maximum Mascot e-value filter" value="100" type="float" help="" /> <param name="exclude_unknown_ptms" label="Exclude Unknown PTMs" type="boolean" truevalue="1" falsevalue="0" checked="true" /> </when> </conditional> @@ -661,7 +661,7 @@ <option value="0">Certificate of Analysis</option> <option value="1">Hierarchical Report</option> <option value="cps">CPS file</option> - <validator type="no_options" message="Please select at least one output file." /> + <validator type="no_options" message="Please select at least one output file" /> </param> </inputs> <outputs> @@ -708,139 +708,148 @@ Runs multiple search engines (X! Tandem and OMSSA) on any number of MGF peak lists using the SearchGUI application and combines the results. https://code.google.com/p/peptide-shaker/ + https://code.google.com/p/searchgui/ -**Reports** - -*PSM Report* +---- -Protein(s) Protein(s) to which the peptide can be attached. -Sequence Sequence of the peptide. -Variable Modifications The variable modifications. -D-score D-score for variable PTM localization. -probabilistic PTM score The probabilistic score (e.g. A-score or PhosphoRS) used for variable PTM localization. -Localization Confidence The confidence in variable PTM localization. -Fixed Modifications The fixed modifications. -Spectrum File The spectrum file. -Spectrum Title The title of the spectrum. -Spectrum Scan Number The spectrum scan number. -RT Retention time -m/z Measured m/z -Measured Charge The charge as given in the spectrum file. -Identification Charge The charge as inferred by the search engine. -Theoretical Mass The theoretical mass of the peptide. -Isotope Number The isotope number targetted by the instrument. -Precursor m/z Error The precursor m/z matching error. -Score Score of the retained peptide as a combination of the algorithm scores (used to rank PSMs). -Confidence Confidence in percent associated to the retained PSM. -Decoy Indicates whether the peptide is a decoy (1: yes, 0: no). -Validation Indicates the validation level of the protein group. +Reports +======= -*Protein Report* +PSM Report +---------- -Main Accession Main accession of the protein group. -Description Description of the protein designed by the main accession. -Gene Name The gene names of the Ensembl gene ID associated to the main accession. -Chromosome The chromosome of the Ensembl gene ID associated to the main accession. -PI Protein Inference status of the protein group. -Secondary Accessions Other accessions in the protein group (alphabetical order). -Protein Group The complete protein group (alphabetical order). -#Peptides Total number of peptides. -#Validated Peptides Number of validated peptides. -#Unique Total number of peptides unique to this protein group. -#PSMs Number of PSMs -#Validated PSMs Number of validated PSMs -Coverage (%) Sequence coverage in percent of the protein designed by the main accession. -Possible Coverage (%) Possible sequence coverage in percent of the protein designed by the main accession according to the search settings. -MW (kDa) Molecular Weight. -Spectrum Counting NSAF Normalized Spectrum Abundance Factor (NSAF) -Spectrum Counting emPAI exponentially modified Protein Abundance Index (emPAI) -Confident Modification Sites, # Confident Modification Sites List of the sites where a variable modification was confidently localized. -Other Modification Sites, # Other Modification Sites List of the non-confident sites where a variable modification was localized. -Score Score of the protein group. -Confidence Confidence in percent associated to the protein group. -Decoy Indicates whether the protein group is a decoy (1: yes, 0: no). -Validation Indicates the validation level of the protein group. +* Protein(s): Protein(s) to which the peptide can be attached +* Sequence: Sequence of the peptide +* Variable Modifications: The variable modifications +* D-score: D-score for variable PTM localization +* probabilistic PTM score: The probabilistic score (e.g. A-score or PhosphoRS) used for variable PTM localization. +* Localization Confidence: The confidence in variable PTM localization. +* Fixed Modifications: The fixed modifications. +* Spectrum File: The spectrum file. +* Spectrum Title: The title of the spectrum. +* Spectrum Scan Number: The spectrum scan number. +* RT: Retention time +* m/z: Measured m/z +* Measured Charge: The charge as given in the spectrum file. +* Identification Charge: The charge as inferred by the search engine. +* Theoretical Mass: The theoretical mass of the peptide. +* Isotope Number: The isotope number targetted by the instrument. +* Precursor m/z Error: The precursor m/z matching error. +* Score: Score of the retained peptide as a combination of the algorithm scores (used to rank PSMs). +* Confidence: Confidence in percent associated to the retained PSM. +* Decoy: Indicates whether the peptide is a decoy (1: yes, 0: no). +* Validation: Indicates the validation level of the protein group. -*Peptide Report* +Protein Report +-------------- + +* Main Accession: Main accession of the protein group. +* Description: Description of the protein designed by the main accession. +* Gene Name: The gene names of the Ensembl gene ID associated to the main accession. +* Chromosome: The chromosome of the Ensembl gene ID associated to the main accession. +* PI: Protein Inference status of the protein group. +* Secondary Accessions: Other accessions in the protein group (alphabetical order). +* Protein Group: The complete protein group (alphabetical order). +* #Peptides: Total number of peptides. +* #Validated Peptides: Number of validated peptides. +* #Unique: Total number of peptides unique to this protein group. +* #PSMs: Number of PSMs +* #Validated PSMs: Number of validated PSMs +* Coverage (%): Sequence coverage in percent of the protein designed by the main accession. +* Possible Coverage (%): Possible sequence coverage in percent of the protein designed by the main accession according to the search settings. +* MW (kDa): Molecular Weight. +* Spectrum Counting NSAF: Normalized Spectrum Abundance Factor (NSAF) +* Spectrum Counting emPAI: exponentially modified Protein Abundance Index (emPAI) +* Confident Modification Sites: Number of Confident Modification Sites List of the sites where a variable modification was confidently localized. +* Other Modification Sites: Number of other Modification Sites List of the non*confident sites where a variable modification was localized. +* Score: Score of the protein group. +* Confidence: Confidence in percent associated to the protein group. +* Decoy: Indicates whether the protein group is a decoy (1: yes, 0: no). +* Validation: Indicates the validation level of the protein group. + + +Peptide Report +-------------- -Protein(s) Protein(s) to which this peptide can be attached. -AAs Before The amino-acids before the sequence. -Sequence Sequence of the peptide. -AAs After The amino-acids after the sequence. -Modified Sequence The peptide sequence annotated with variable modifications. -Variable Modifications The variable modifications. -Localization Confidence The confidence in PTMs localization. -Fixed Modifications The fixed modifications. -#Validated PSMs Number of validated PSMs. -#PSMs Number of PSMs. -Score Score of the peptide. -Confidence Confidence in percent associated to the peptide. -Decoy Indicates whether the peptide is a decoy (1: yes, 0: no). -Validation Indicates the validation level of the protein group. +* Protein(s): Protein(s) to which this peptide can be attached. +* AAs Before: The amino-acids before the sequence. +* Sequence: Sequence of the peptide. +* AAs After: The amino-acids after the sequence. +* Modified Sequence: The peptide sequence annotated with variable modifications. +* Variable Modifications: The variable modifications. +* Localization Confidence: The confidence in PTMs localization. +* Fixed Modifications: The fixed modifications. +* #Validated PSMs: Number of validated PSMs. +* #PSMs: Number of PSMs. +* Score: Score of the peptide. +* Confidence: Confidence in percent associated to the peptide. +* Decoy: Indicates whether the peptide is a decoy (1: yes, 0: no). +* Validation: Indicates the validation level of the protein group. -*Hirachical Report* +Hierachical Report +------------------ -Main Accession Main accession of the protein group. -Description Description of the protein designed by the main accession. -PI Protein Inference status of the protein group. -Secondary Accessions Other accessions in the protein group (alphabetical order). -Protein Group The complete protein group (alphabetical order). -#Peptides Total number of peptides. -#Validated Peptides Number of validated peptides. -#Unique Total number of peptides unique to this protein group. -#PSMs Number of PSMs -#Validated PSMs Number of validated PSMs -Coverage (%) Sequence coverage in percent of the protein designed by the main accession. -Possible Coverage (%) Possible sequence coverage in percent of the protein designed by the main accession according to the search settings. -MW (kDa) Molecular Weight. -Spectrum Counting NSAF Normalized Spectrum Abundance Factor (NSAF) -Spectrum Counting emPAI exponentially modified Protein Abundance Index (emPAI) -Confident Modification Sites, # Confident Modification Sites List of the sites where a variable modification was confidently localized. -Other Modification Sites, # Other Modification Sites List of the non-confident sites where a variable modification was localized. -Score Score of the protein group. -Confidence Confidence in percent associated to the protein group. -Decoy Indicates whether the protein group is a decoy (1: yes, 0: no). -Validation Indicates the validation level of the protein group. -Protein(s) Protein(s) to which this peptide can be attached. -AAs Before The amino-acids before the sequence. -Sequence Sequence of the peptide. -AAs After The amino-acids after the sequence. -Variable Modifications The variable modifications. -Localization Confidence The confidence in PTMs localization. -Fixed Modifications The fixed modifications. -#Validated PSMs Number of validated PSMs. -#PSMs Number of PSMs. -Score Score of the peptide. -Confidence Confidence in percent associated to the peptide. -Decoy Indicates whether the peptide is a decoy (1: yes, 0: no). -Validation Indicates the validation level of the protein group. -Protein(s) Protein(s) to which the peptide can be attached. -Sequence Sequence of the peptide. -Modified Sequence The peptide sequence annotated with variable modifications. -Variable Modifications The variable modifications. -D-score D-score for variable PTM localization. -probabilistic PTM score The probabilistic score (e.g. A-score or PhosphoRS) used for variable PTM localization. -Localization Confidence The confidence in variable PTM localization. -Fixed Modifications The fixed modifications. -Spectrum File The spectrum file. -Spectrum Title The title of the spectrum. -Spectrum Scan Number The spectrum scan number. -RT Retention time -m/z Measured m/z -Measured Charge The charge as given in the spectrum file. -Identification Charge The charge as inferred by the search engine. -Theoretical Mass The theoretical mass of the peptide. -Isotope Number The isotope number targetted by the instrument. -Precursor m/z Error The precursor m/z matching error. -Score Score of the retained peptide as a combination of the algorithm scores (used to rank PSMs). -Confidence Confidence in percent associated to the retained PSM. -Decoy Indicates whether the peptide is a decoy (1: yes, 0: no). -Validation Indicates the validation level of the protein group. +* Main Accession: Main accession of the protein group. +* Description: Description of the protein designed by the main accession. +* PI: Protein Inference status of the protein group. +* Secondary Accessions: Other accessions in the protein group (alphabetical order). +* Protein Group: The complete protein group (alphabetical order). +* #Peptides: Total number of peptides. +* #Validated Peptides: Number of validated peptides. +* #Unique: Total number of peptides unique to this protein group. +* #PSMs: Number of PSMs +* #Validated PSMs: Number of validated PSMs +* Coverage (%): Sequence coverage in percent of the protein designed by the main accession. +* Possible Coverage (%): Possible sequence coverage in percent of the protein designed by the main accession according to the search settings. +* MW (kDa): Molecular Weight. +* Spectrum Counting NSAF: Normalized Spectrum Abundance Factor (NSAF) +* Spectrum Counting emPAI: exponentially modified Protein Abundance Index (emPAI) +* Confident Modification Sites: # Confident Modification Sites List of the sites where a variable modification was confidently localized. +* Other Modification Sites: # Other Modification Sites List of the non-confident sites where a variable modification was localized. +* Score: Score of the protein group. +* Confidence: Confidence in percent associated to the protein group. +* Decoy: Indicates whether the protein group is a decoy (1: yes, 0: no). +* Validation: Indicates the validation level of the protein group. +* Protein(s): Protein(s) to which this peptide can be attached. +* AAs Before: The amino-acids before the sequence. +* Sequence: Sequence of the peptide. +* AAs After: The amino-acids after the sequence. +* Variable Modifications: The variable modifications. +* Localization Confidence: The confidence in PTMs localization. +* Fixed Modifications: The fixed modifications. +* #Validated PSMs: Number of validated PSMs. +* #PSMs: Number of PSMs. +* Score: Score of the peptide. +* Confidence: Confidence in percent associated to the peptide. +* Decoy: Indicates whether the peptide is a decoy (1: yes, 0: no). +* Validation: Indicates the validation level of the protein group. +* Protein(s): Protein(s) to which the peptide can be attached. +* Sequence: Sequence of the peptide. +* Modified Sequence: The peptide sequence annotated with variable modifications. +* Variable Modifications: The variable modifications. +* D-score: D-score for variable PTM localization. +* probabilistic PTM score: The probabilistic score (e.g. A-score or PhosphoRS) used for variable PTM localization. +* Localization Confidence: The confidence in variable PTM localization. +* Fixed Modifications: The fixed modifications. +* Spectrum File: The spectrum file. +* Spectrum Title: The title of the spectrum. +* Spectrum Scan Number: The spectrum scan number. +* RT: Retention time +* m/z: Measured m/z +* Measured Charge: The charge as given in the spectrum file. +* Identification Charge: The charge as inferred by the search engine. +* Theoretical Mass: The theoretical mass of the peptide. +* Isotope Number: The isotope number targetted by the instrument. +* Precursor m/z Error: The precursor m/z matching error. +* Score: Score of the retained peptide as a combination of the algorithm scores (used to rank PSMs). +* Confidence: Confidence in percent associated to the retained PSM. +* Decoy: Indicates whether the peptide is a decoy (1: yes, 0: no). +* Validation: Indicates the validation level of the protein group. @@ -849,7 +858,7 @@ **Citation** -For the underlying tool, please cite `TODO` +To cite the underlying tools (PeptideShaker and SearchGUI) please refer to the list of papers at http://peptide-shaker.googlecode.com If you use this tool in Galaxy, please cite Chilton J, Ira Cooke, Bjoern Gruening et al. https://bitbucket.org/galaxyp/peptideshaker </help>