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comparison FidoAdapter.xml @ 0:0ca1787a59a7 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
author galaxyp
date Wed, 01 Mar 2017 12:17:44 -0500
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-1:000000000000 0:0ca1787a59a7
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="2.1.0">
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 -fidocp_executable fido_choose_parameters
15 -fido_executable fido
16
17 #if $param_in:
18 -in $param_in
19 #end if
20 #if $param_out:
21 -out $param_out
22 #end if
23 #if $param_separate_runs:
24 -separate_runs
25 #end if
26 #if $param_greedy_group_resolution:
27 -greedy_group_resolution
28 #end if
29 #if $param_no_cleanup:
30 -no_cleanup
31 #end if
32 #if $param_all_PSMs:
33 -all_PSMs
34 #end if
35 #if $param_group_level:
36 -group_level
37 #end if
38 #if $param_log2_states:
39 -log2_states $param_log2_states
40 #end if
41 #if $param_prob_protein:
42 -prob:protein $param_prob_protein
43 #end if
44 #if $param_prob_peptide:
45 -prob:peptide $param_prob_peptide
46 #end if
47 #if $param_prob_spurious:
48 -prob:spurious $param_prob_spurious
49 #end if
50 #if $adv_opts.adv_opts_selector=='advanced':
51 #if $adv_opts.param_keep_zero_group:
52 -keep_zero_group
53 #end if
54 #if $adv_opts.param_accuracy:
55 -accuracy
56 #if " " in str($adv_opts.param_accuracy):
57 "$adv_opts.param_accuracy"
58 #else
59 $adv_opts.param_accuracy
60 #end if
61 #end if
62 #if $adv_opts.param_log2_states_precalc:
63 -log2_states_precalc $adv_opts.param_log2_states_precalc
64 #end if
65 #if $adv_opts.param_force:
66 -force
67 #end if
68 #end if
69 </command>
70 <inputs>
71 <param name="param_in" type="data" format="idxml" optional="False" label="Input: identification results" help="(-in) "/>
72 <param name="param_separate_runs" display="radio" type="boolean" truevalue="-separate_runs" falsevalue="" checked="false" optional="True" label="Process multiple protein identification runs in the input separately, don't merge them" help="(-separate_runs) Merging results in loss of descriptive information of the single protein identification runs"/>
73 <param name="param_greedy_group_resolution" display="radio" type="boolean" truevalue="-greedy_group_resolution" falsevalue="" checked="false" optional="True" label="Post-process Fido output with greedy resolution of shared peptides based on the protein probabilities" help="(-greedy_group_resolution) Also adds the resolved ambiguity groups to output"/>
74 <param name="param_no_cleanup" display="radio" type="boolean" truevalue="-no_cleanup" falsevalue="" checked="false" optional="True" label="Omit clean-up of peptide sequences (removal of non-letter characters, replacement of I with L)" help="(-no_cleanup) "/>
75 <param name="param_all_PSMs" display="radio" type="boolean" truevalue="-all_PSMs" falsevalue="" checked="false" optional="True" label="Consider all PSMs of each peptide, instead of only the best one" help="(-all_PSMs) "/>
76 <param name="param_group_level" display="radio" type="boolean" truevalue="-group_level" falsevalue="" checked="false" optional="True" label="Perform inference on protein group level (instead of individual protein level)" help="(-group_level) This will lead to higher probabilities for (bigger) protein groups"/>
77 <param name="param_log2_states" type="integer" min="0" optional="True" value="0" label="Binary logarithm of the max" 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)"/>
78 <param name="param_prob_protein" type="float" min="0.0" optional="True" value="0.0" label="Protein prior probability ('gamma' parameter)" help="(-protein) "/>
79 <param name="param_prob_peptide" type="float" min="0.0" optional="True" value="0.0" label="Peptide emission probability ('alpha' parameter)" help="(-peptide) "/>
80 <param name="param_prob_spurious" type="float" min="0.0" optional="True" value="0.0" label="Spurious peptide identification probability ('beta' parameter)" help="(-spurious) "/>
81 <expand macro="advanced_options">
82 <param name="param_keep_zero_group" display="radio" type="boolean" truevalue="-keep_zero_group" falsevalue="" checked="false" optional="True" label="Keep the group of proteins with estimated probability of zero, which is otherwise removed (it may be very large)" help="(-keep_zero_group) "/>
83 <param name="param_accuracy" display="radio" type="select" optional="True" label="Accuracy level of start parameters" help="(-accuracy) There is a trade-off between accuracy and runtime. Empty uses the default ('best')">
84 <option value=""></option>
85 <option value="best">best</option>
86 <option value="relaxed">relaxed</option>
87 <option value="sloppy">sloppy</option>
88 </param>
89 <param name="param_log2_states_precalc" type="integer" min="0" optional="True" value="0" label="Like 'log2_states', but allows to set a separate limit for the precalculation" help="(-log2_states_precalc) "/>
90 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
91 </expand>
92 </inputs>
93 <outputs>
94 <data name="param_out" format="idxml"/>
95 </outputs>
96 <help>Runs the protein inference engine Fido.
97
98
99 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FidoAdapter.html</help>
100 </tool>