comparison ConsensusID.xml @ 0:5c56387ff06a draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
author galaxyp
date Wed, 01 Mar 2017 12:40:02 -0500
parents
children 66388c2e2f38
comparison
equal deleted inserted replaced
-1:000000000000 0:5c56387ff06a
1 <?xml version='1.0' encoding='UTF-8'?>
2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
3 <!--Proposed Tool Section: [ID Processing]-->
4 <tool id="ConsensusID" name="ConsensusID" version="2.1.0">
5 <description>Computes a consensus of peptide identifications of several identification engines.</description>
6 <macros>
7 <token name="@EXECUTABLE@">ConsensusID</token>
8 <import>macros.xml</import>
9 </macros>
10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>ConsensusID
14
15 #if $param_in:
16 -in $param_in
17 #end if
18 #if $param_out:
19 -out $param_out
20 #end if
21 #if $param_rt_delta:
22 -rt_delta $param_rt_delta
23 #end if
24 #if $param_mz_delta:
25 -mz_delta $param_mz_delta
26 #end if
27 #if $param_algorithm:
28 -algorithm $param_algorithm
29 #end if
30 #if $param_filter_considered_hits:
31 -filter:considered_hits $param_filter_considered_hits
32 #end if
33 #if $param_filter_min_support:
34 -filter:min_support $param_filter_min_support
35 #end if
36 #if $param_filter_count_empty:
37 -filter:count_empty
38 #end if
39 #if $param_PEPIons_mass_tolerance:
40 -PEPIons:mass_tolerance $param_PEPIons_mass_tolerance
41 #end if
42 #if $param_PEPIons_min_shared:
43 -PEPIons:min_shared $param_PEPIons_min_shared
44 #end if
45 #if $param_PEPMatrix_matrix:
46 -PEPMatrix:matrix $param_PEPMatrix_matrix
47 #end if
48 #if $param_PEPMatrix_penalty:
49 -PEPMatrix:penalty $param_PEPMatrix_penalty
50 #end if
51 #if $adv_opts.adv_opts_selector=='advanced':
52 #if $adv_opts.param_force:
53 -force
54 #end if
55 #end if
56 </command>
57 <inputs>
58 <param name="param_in" type="data" format="featurexml,consensusxml,idxml" optional="False" label="input file" help="(-in) "/>
59 <param name="param_rt_delta" type="float" min="0.0" optional="True" value="0.1" label="[idXML input only] Maximum allowed retention time deviation between identifications belonging to the same spectrum" help="(-rt_delta) "/>
60 <param name="param_mz_delta" type="float" min="0.0" optional="True" value="0.1" label="[idXML input only] Maximum allowed precursor m/z deviation between identifications belonging to the same spectrum" help="(-mz_delta) "/>
61 <param name="param_algorithm" type="select" optional="False" value="PEPMatrix" label="Algorithm used for consensus scoring" help="(-algorithm) &lt;br&gt;* PEPMatrix: Scoring based on posterior error probabilities (PEPs) and peptide sequence similarities (scored by a substitution matrix). Requires PEPs as scores. &lt;br&gt;* PEPIons: Scoring based on posterior error probabilities (PEPs) and fragment ion similarities ('shared peak count'). Requires PEPs as scores. &lt;br&gt;* best: For each peptide ID, use the best score of any search engine as the consensus score. Requires the same score type in all ID runs. &lt;br&gt;* worst: For each peptide ID, use the worst score of any search engine as the consensus score. Requires the same score type in all ID runs. &lt;br&gt;* average: For each peptide ID, use the average score of all search engines as the consensus. Requires the same score type in all ID runs. &lt;br&gt;* ranks: Calculates a consensus score based on the ranks of peptide IDs in the results of different search engines. The final score is in the range (0, 1], with 1 being the best score. No requirements about score types">
62 <option value="PEPMatrix" selected="true">PEPMatrix</option>
63 <option value="PEPIons">PEPIons</option>
64 <option value="best">best</option>
65 <option value="worst">worst</option>
66 <option value="average">average</option>
67 <option value="ranks">ranks</option>
68 </param>
69 <param name="param_filter_considered_hits" type="integer" min="0" optional="True" value="0" label="The number of top hits in each ID run that are considered for consensus scoring ('0' for all hits)" help="(-considered_hits) "/>
70 <param name="param_filter_min_support" type="float" min="0.0" max="1.0" optional="True" value="0.0" label="For each peptide hit from an ID run, the fraction of other ID runs that must support that hit (otherwise it is removed)" help="(-min_support) "/>
71 <param name="param_filter_count_empty" display="radio" type="boolean" truevalue="-filter:count_empty" falsevalue="" checked="false" optional="True" label="Count empty ID runs (i.e" help="(-count_empty) those containing no peptide hit for the current spectrum) when calculating 'min_support'?"/>
72 <param name="param_PEPIons_mass_tolerance" type="float" min="0.0" optional="True" value="0.5" label="Maximum difference between fragment masses (in Da) for fragments to be considered 'shared' between peptides" help="(-mass_tolerance) "/>
73 <param name="param_PEPIons_min_shared" type="integer" min="1" optional="True" value="2" label="The minimal number of 'shared' fragments (between two suggested peptides) that is necessary to evaluate the similarity based on shared peak count (SPC)" help="(-min_shared) "/>
74 <param name="param_PEPMatrix_matrix" display="radio" type="select" optional="False" value="identity" label="Substitution matrix to use for alignment-based similarity scoring" help="(-matrix) ">
75 <option value="identity" selected="true">identity</option>
76 <option value="PAM30MS">PAM30MS</option>
77 </param>
78 <param name="param_PEPMatrix_penalty" type="integer" min="1" optional="True" value="5" label="Alignment gap penalty (the same value is used for gap opening and extension)" help="(-penalty) "/>
79 <expand macro="advanced_options">
80 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
81 </expand>
82 </inputs>
83 <outputs>
84 <data name="param_out" metadata_source="param_in" format="input"/>
85 </outputs>
86 <help>Computes a consensus of peptide identifications of several identification engines.
87
88
89 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_ConsensusID.html</help>
90 </tool>