Mercurial > repos > bgruening > openms

comparison FidoAdapter.xml @ 4:6ead64a594bd draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
author bgruening
date Wed, 27 Jan 2016 10:06:49 -0500
parents
children
comparison
equal deleted inserted replaced
3:ec62782f6c68 4:6ead64a594bd
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="FidoAdapter" name="FidoAdapter" version="2.0.0">
5 <description>Runs the protein inference engine Fido.</description>
6 <macros>
7 <token name="@EXECUTABLE@">FidoAdapter</token>
8 <import>macros.xml</import>
9 </macros>
10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>FidoAdapter
14
15 #if $param_in:
16 -in $param_in
17 #end if
18 #if $param_out:
19 -out $param_out
20 #end if
21 -fido_executable fido
22 -fidocp_executable fido_choose_parameters
23 #if $param_prob_param:
24 -prob_param &quot;$param_prob_param&quot;
25 #end if
26 #if $param_separate_runs:
27 -separate_runs
28 #end if
29 #if $param_greedy_group_resolution:
30 -greedy_group_resolution
31 #end if
32 #if $param_no_cleanup:
33 -no_cleanup
34 #end if
35 #if $param_all_PSMs:
36 -all_PSMs
37 #end if
38 #if $param_group_level:
39 -group_level
40 #end if
41 #if $param_log2_states:
42 -log2_states $param_log2_states
43 #end if
44 -threads \${GALAXY_SLOTS:-24}
45 #if $param_prob_protein:
46 -prob:protein $param_prob_protein
47 #end if
48 #if $param_prob_peptide:
49 -prob:peptide $param_prob_peptide
50 #end if
51 #if $param_prob_spurious:
52 -prob:spurious $param_prob_spurious
53 #end if
54 #if $adv_opts.adv_opts_selector=='advanced':
55 #if $adv_opts.param_keep_zero_group:
56 -keep_zero_group
57 #end if
58 #if $adv_opts.param_accuracy:
59 -accuracy
60 #if &quot; &quot; in str($adv_opts.param_accuracy):
61 &quot;$adv_opts.param_accuracy&quot;
62 #else
63 $adv_opts.param_accuracy
64 #end if
65 #end if
66 #if $adv_opts.param_log2_states_precalc:
67 -log2_states_precalc $adv_opts.param_log2_states_precalc
68 #end if
69 #if $adv_opts.param_force:
70 -force
71 #end if
72 #end if
73 </command>
74 <inputs>
75 <param format="xml" help="(-in) " label="Input: identification results" name="param_in" optional="False" type="data"/>
76 <param help="(-prob_param) e.g. for search results that were processed with the TOPP tools IDPosteriorErrorProbability followed by FalseDiscoveryRate.)" label="Read the peptide probability from this user parameter ('UserParam') in the input file, instead of from the 'score' field, if available. (Use" name="param_prob_param" size="30" type="text" value="Posterior Probability_score">
77 <sanitizer>
78 <valid initial="string.printable">
79 <remove value="'"/>
80 <remove value="&quot;"/>
81 </valid>
82 </sanitizer>
83 </param>
84 <param checked="false" falsevalue="" help="(-separate_runs) Merging results in loss of descriptive information of the single protein identification runs" label="Process multiple protein identification runs in the input separately, don't merge them" name="param_separate_runs" optional="True" truevalue="-separate_runs" type="boolean"/>
85 <param checked="false" falsevalue="" help="(-greedy_group_resolution) Also adds the resolved ambiguity groups to output" label="Post-process Fido output with greedy resolution of shared peptides based on the protein probabilities" name="param_greedy_group_resolution" optional="True" truevalue="-greedy_group_resolution" type="boolean"/>
86 <param checked="false" falsevalue="" help="(-no_cleanup) " label="Omit clean-up of peptide sequences (removal of non-letter characters, replacement of I with L)" name="param_no_cleanup" optional="True" truevalue="-no_cleanup" type="boolean"/>
87 <param checked="false" falsevalue="" help="(-all_PSMs) " label="Consider all PSMs of each peptide, instead of only the best one" name="param_all_PSMs" optional="True" truevalue="-all_PSMs" type="boolean"/>
88 <param checked="false" falsevalue="" help="(-group_level) This will lead to higher probabilities for (bigger) protein groups" label="Perform inference on protein group level (instead of individual protein level)" name="param_group_level" optional="True" truevalue="-group_level" type="boolean"/>
89 <param help="(-log2_states) number of connected states in a subgraph. For a value N, subgraphs that are bigger than 2^N will be split up, sacrificing accuracy for runtime. '0' uses the default (18)" label="Binary logarithm of the max" min="0" name="param_log2_states" optional="True" type="integer" value="0"/>
90 <param help="(-protein) " label="Protein prior probability ('gamma' parameter)" min="0.0" name="param_prob_protein" optional="True" type="float" value="0.0"/>
91 <param help="(-peptide) " label="Peptide emission probability ('alpha' parameter)" min="0.0" name="param_prob_peptide" optional="True" type="float" value="0.0"/>
92 <param help="(-spurious) " label="Spurious peptide identification probability ('beta' parameter)" min="0.0" name="param_prob_spurious" optional="True" type="float" value="0.0"/>
93 <expand macro="advanced_options">
94 <param checked="false" falsevalue="" help="(-keep_zero_group) " label="Keep the group of proteins with estimated probability of zero, which is otherwise removed (it may be very large)" name="param_keep_zero_group" optional="True" truevalue="-keep_zero_group" type="boolean"/>
95 <param help="(-accuracy) There is a trade-off between accuracy and runtime. Empty uses the default ('best')" label="Accuracy level of start parameters" name="param_accuracy" optional="True" type="select">
96 <option value=""></option>
97 <option value="best">best</option>
98 <option value="relaxed">relaxed</option>
99 <option value="sloppy">sloppy</option>
100 </param>
101 <param help="(-log2_states_precalc) " label="Like 'log2_states', but allows to set a separate limit for the precalculation" min="0" name="param_log2_states_precalc" optional="True" type="integer" value="0"/>
102 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
103 </expand>
104 </inputs>
105 <outputs>
106 <data format="xml" name="param_out"/>
107 </outputs>
108 <help>Runs the protein inference engine Fido.
109
110
111 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FidoAdapter.html</help>
112 </tool>