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comparison protein_prophet.xml @ 15:0746a2ae9e04 draft

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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
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14:d90c8bc10a9c 15:0746a2ae9e04
1 <tool id="proteomics_search_protein_prophet_1" name="Protein Prophet" version="1.1.0"> 1 <tool id="proteomics_search_protein_prophet_1" name="Protein Prophet" version="1.1.1">
2 <requirements> 2 <description>Calculate Protein Prophet statistics on search results</description>
3 <container type="docker">iracooke/protk-1.4.1</container> 3 <requirements>
4 <requirement type="package" version="1.4">protk</requirement> 4 <container type="docker">iracooke/protk-1.4.3</container>
5 <requirement type="package" version="4.8.0">trans_proteomic_pipeline</requirement> 5 <requirement type="package" version="1.4.3">protk</requirement>
6 </requirements> 6 <requirement type="package" version="4.8.0">trans_proteomic_pipeline</requirement>
7 </requirements>
7 8
8 <description>Calculate Protein Prophet statistics on search results</description> 9 <command>
10 protein_prophet.rb
11 --galaxy
12
13 #for $input_file in $input_files:
14 ${input_file}
15 #end for
16
17 -o protein_prophet_results.prot.xml
18 -r
9 19
20 $iproph
21 $nooccam
22 $groupwts
23 $normprotlen
24 $logprobs
25 $confem
26 $allpeps
27 $unmapped
28 $instances
29 $delude
30 --minprob=$minprob
31 --minindep=$minindep
32 </command>
33 <inputs>
34 <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"/>
10 35
11 <!-- Note .. the input file is assumed to be the first argument --> 36 <param name="iproph" selected="true" type="boolean" label="Inputs are from iProphet" truevalue="--iprophet-input" falsevalue=""/>
12 <command> 37 <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=""/>
13 protein_prophet.rb 38 <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=""/>
39 <param name="normprotlen" type="boolean" label="Normalize NSP using Protein Length" truevalue="--norm-protlen" falsevalue=""/>
40 <param name="logprobs" type="boolean" label="Use the log of probability in the confidence calculations" truevalue="--log-prob" falsevalue=""/>
41 <param name="confem" type="boolean" label="Use the EM to compute probability given the confidenct" truevalue="--confem" falsevalue=""/>
42 <param name="allpeps" type="boolean" label="Consider all possible peptides in the database in the confidence model" truevalue="--allpeps" falsevalue=""/>
43 <param name="unmapped" type="boolean" label="Report results for unmapped proteins" truevalue="--unmapped" falsevalue=""/>
44 <param name="instances" type="boolean" label="Use Expected Number of Ion Instances to adjust the peptide probabilities prior to NSP adjustment" truevalue="--instances" falsevalue=""/>
45 <param name="delude" type="boolean" label="Do NOT use peptide degeneracy information when assessing proteins" truevalue="--delude" falsevalue=""/>
14 46
15 --galaxy $input_file 47 <param name="minprob" type="text" label="Minimum peptide prophet probability for peptides to be considered" value="0.05"/>
16 48 <param name="minindep" type="text" label="Minimum percentage of independent peptides required for a protein" value="0"/>
17 -o protein_prophet_results.prot.xml 49 </inputs>
18 50 <outputs>
19 -r 51 <data format="protxml" name="output" from_work_dir="protein_prophet_results.prot.xml"/>
20 52 </outputs>
21 $iproph
22 $nooccam
23 $groupwts
24 $normprotlen
25 $logprobs
26 $confem
27 $allpeps
28 $unmapped
29 $instances
30 $delude
31
32 --minprob=$minprob
33 --minindep=$minindep
34 </command>
35 <inputs>
36
37 <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"/>
38
39 <param name="iproph" selected="true" type="boolean" label="Inputs are from iProphet" truevalue="--iprophet-input" falsevalue=""/>
40 <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=""/>
41 <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=""/>
42 <param name="normprotlen" type="boolean" label="Normalize NSP using Protein Length" truevalue="--norm-protlen" falsevalue=""/>
43 <param name="logprobs" type="boolean" label="Use the log of probability in the confidence calculations" truevalue="--log-prob" falsevalue=""/>
44 <param name="confem" type="boolean" label="Use the EM to compute probability given the confidenct" truevalue="--confem" falsevalue=""/>
45 <param name="allpeps" type="boolean" label="Consider all possible peptides in the database in the confidence model" truevalue="--allpeps" falsevalue=""/>
46 <param name="unmapped" type="boolean" label="Report results for unmapped proteins" truevalue="--unmapped" falsevalue=""/>
47 <param name="instances" type="boolean" label="Use Expected Number of Ion Instances to adjust the peptide probabilities prior to NSP adjustment" truevalue="--instances" falsevalue=""/>
48 <param name="delude" type="boolean" label="Do NOT use peptide degeneracy information when assessing proteins" truevalue="--delude" falsevalue=""/>
49
50 <param name="minprob" type="text" label="Minimum peptide prophet probability for peptides to be considered" value="0.05"/>
51 <param name="minindep" type="text" label="Minimum percentage of independent peptides required for a protein" value="0"/>
52
53 </inputs>
54 <outputs>
55 <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"/>
56 </outputs>
57 53
58 54
59 <!--NOPLOT: do not generate plot png file 55 <!--NOPLOT: do not generate plot png file
60 NOOCCAM: non-conservative maximum protein list 56 NOOCCAM: non-conservative maximum protein list
61 GROUPWTS: check peptide's total weight in the Protein Group against the threshold (default: check peptide's actual weight against threshold) 57 GROUPWTS: check peptide's total weight in the Protein Group against the threshold (default: check peptide's actual weight against threshold)
62 NORMPROTLEN: Normalize NSP using Protein Length 58 NORMPROTLEN: Normalize NSP using Protein Length
63 LOGPROBS: Use the log of the probabilities in the Confidence calculations 59 LOGPROBS: Use the log of the probabilities in the Confidence calculations
64 CONFEM: Use the EM to compute probability given the confidence 60 CONFEM: Use the EM to compute probability given the confidence
65 ALLPEPS: Consider all possible peptides in the database in the confidence model 61 ALLPEPS: Consider all possible peptides in the database in the confidence model
66 UNMAPPED: Report results for UNMAPPED proteins 62 UNMAPPED: Report results for UNMAPPED proteins
67 INSTANCES: Use Expected Number of Ion Instances to adjust the peptide probabilities prior to NSP adjustment 63 INSTANCES: Use Expected Number of Ion Instances to adjust the peptide probabilities prior to NSP adjustment
68 DELUDE: do NOT use peptide degeneracy information when assessing proteins 64 DELUDE: do NOT use peptide degeneracy information when assessing proteins
69 65
70 MINPROB: peptideProphet probabilty threshold (default=0.05) 66 MINPROB: peptideProphet probabilty threshold (default=0.05)
71 MININDEP: minimum percentage of independent peptides required for a protein (default=0) 67 MININDEP: minimum percentage of independent peptides required for a protein (default=0)
72
73
74 --> 68 -->
75 69
76 <help> 70 <help>
77 71
78 **What it does** 72 **What it does**
79 73
80 Given a set of peptide assignments from MS/MS spectra in the form of a pepXML file, this tool estimates probabilities at the protein level. As output, the tool produces a protXML file, which contains proteins along with the estimated probabilities that those proteins were present. Probabilities are estimated using a statistical model based on the number of peptides corresponding to that protein and the confidence that each of those peptides were assigned correctly. It takes account of the fact that peptides may correspond to more than one protein. 74 Given a set of peptide assignments from MS/MS spectra in the form of a pepXML file, this tool estimates probabilities at the protein level. As output, the tool produces a protXML file, which contains proteins along with the estimated probabilities that those proteins were present. Probabilities are estimated using a statistical model based on the number of peptides corresponding to that protein and the confidence that each of those peptides were assigned correctly. It takes account of the fact that peptides may correspond to more than one protein.
81 75
86 If you use this tool please read and cite the paper describing the statistical model implemented by Protein Prophet 80 If you use this tool please read and cite the paper describing the statistical model implemented by Protein Prophet
87 81
88 Nesvizhskii A., et al. “A Statistical Model for Identifying Proteins by Tandem Mass Spectrometry” *Anal. Chem.* 75, 4646-4658 (2003). 82 Nesvizhskii A., et al. “A Statistical Model for Identifying Proteins by Tandem Mass Spectrometry” *Anal. Chem.* 75, 4646-4658 (2003).
89 83
90 84
91 </help> 85 </help>
92
93 </tool> 86 </tool>