Mercurial > repos > pieterlukasse > prims_proteomics

comparison quantifere.xml @ 19:d31c6978d9d0

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fixes for NapQ
author pieter.lukasse@wur.nl
date Mon, 26 Jan 2015 06:24:15 +0100
parents 40ec8770780d
children 5215b5cfdc53
comparison
equal deleted inserted replaced
18:ad911e9aaf33 19:d31c6978d9d0
54 help="Add the CSV list of codes that occur in the file names 54 help="Add the CSV list of codes that occur in the file names
55 and that stand for a fraction code. E.g. '_F1,_F2,_F3,etc.' In this 55 and that stand for a fraction code. E.g. '_F1,_F2,_F3,etc.' In this
56 way different peptide identifications from the same sample but measured 56 way different peptide identifications from the same sample but measured
57 in different fractions can be merged together. Otherwise each (fraction) file 57 in different fractions can be merged together. Otherwise each (fraction) file
58 is seen as a separate sample."/> <!-- could do regular expressions as well but this would be hard for biologists, e.g. _F\d\b --> 58 is seen as a separate sample."/> <!-- could do regular expressions as well but this would be hard for biologists, e.g. _F\d\b -->
59 <!-- on help above: the given codes are removed from source name...separate features are clustered, not peptides, peptides
60 are quantified based on summing features (raw), or summing patterns : TODO document the quantification columns present in the output CSV -->
59 </when> 61 </when>
60 <when value="No"> 62 <when value="No">
61 </when> 63 </when>
62 </conditional> 64 </conditional>
63 65
87 <!-- TODO let minCorrel default value vary according to quantification type chosen above --> 89 <!-- TODO let minCorrel default value vary according to quantification type chosen above -->
88 <param name="minCorrel" type="float" size="10" value="0.85" label="Minimum correlation in a cluster" help="Features will be grouped by their protein annotation and 90 <param name="minCorrel" type="float" size="10" value="0.85" label="Minimum correlation in a cluster" help="Features will be grouped by their protein annotation and
89 sample intensity values correlation. Set here the minimum correlation expected between grouped members. This is used to guide the clustering algorithm."/> 91 sample intensity values correlation. Set here the minimum correlation expected between grouped members. This is used to guide the clustering algorithm."/>
90 92
91 <!-- simple extra heuristics to remove some "noise" protein hits --> 93 <!-- simple extra heuristics to remove some "noise" protein hits -->
92 <param name="minProtCoverage" type="float" size="10" value="5.0" label="Minimum protein coverage (%)" help="This will remove proteins that have a too small 94 <param name="minProtCoverage" type="float" size="10" value="0.0" label="Minimum protein coverage (%)" help="Set this to e.g. 5.0 if you have protein coverage
93 portion of their sequence covered by peptide matches."/> 95 information in your data. This will remove proteins that have a too small portion of their sequence covered by peptide matches."/>
96 <!-- TODO : ADD warning to report if this is left 0 and no coverage is found ...or maybe validate the other way around-->
94 97
95 <param name="minAboveAverageHits" type="integer" size="10" value="1" label="Minimum number of different peptide matches with a score above average" 98 <param name="minAboveAverageHits" type="integer" size="10" value="1" label="Minimum number of different peptide matches with a score above average"
96 help="This will remove proteins that do not have enough reasonable peptides hits."/> 99 help="This will remove proteins that do not have enough reasonable peptides hits."/>
97 100
98 <param name="minNrIdsForInferencePeptide" type="integer" size="10" value="1" label="Minimum number of peptide identifications for inference peptides" 101 <param name="minNrIdsForInferencePeptide" type="integer" size="10" value="1" label="Minimum number of peptide identifications for inference peptides"
99 help="Minimum number of peptide identifications a peptide needs to be used as inference peptide for secondary proteins."/> 102 help="Minimum number of peptide identifications a peptide needs to be used as inference peptide for secondary proteins."/>
100 103 <!-- currently, when one feature clusters with foreign peptide, then it is not inference peptide anymore...quite strict, could be less strict
104 by letting user indicate for example: 90% of features should be inference features...then it is an inference pep. See QuantifereTool.inferSecondaryProteins() -->
101 105
102 <param name="functionalAnnotationCSV" type="data" format="csv,txt,tsv" optional="true" 106 <param name="functionalAnnotationCSV" type="data" format="csv,txt,tsv" optional="true"
103 label="(Functional)annotation mapping file (csv or tsv format)" 107 label="(Functional)annotation mapping file (csv or tsv format)"
104 help="Optional file that maps protein accessions to a network, pathway or other higher level annotations. In this file a header line is expected with these 2 columns (names and lower case is important): accession,annotation"/> 108 help="Optional file that maps protein accessions to a network, pathway or other higher level annotations. In this file a header line is expected with these 2 columns (names and lower case is important): accession,annotation"/>
105 109
205 . 209 .
206 210
207 .. _Cytoscape chartplugin: http://apps.cytoscape.org/apps/chartplugin 211 .. _Cytoscape chartplugin: http://apps.cytoscape.org/apps/chartplugin
208 212
209 213
214 **References**
215
216 If you use this Galaxy tool in work leading to a scientific publication please
217 cite the following papers:
218
219 Pieter N. J. Lukasse and Antoine H. P. America (2014).
220 Protein Inference Using Peptide Quantification Patterns.
221 http://dx.doi.org/10.1021/pr401072g
222
210 223
211 </help> 224 </help>
225 <citations>
226 <citation type="doi">10.1021/pr401072g</citation> <!-- example
227 see also https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Ccitations.3E_tag_set
228 -->
229 </citations>
212 </tool> 230 </tool>