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

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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
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4
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1 <?xml version="1.0" encoding="UTF-8"?>
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2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
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3 <!--Proposed Tool Section: [ID Processing]-->
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4 <tool id="FidoAdapter" name="FidoAdapter" version="2.0.0">
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5 <description>Runs the protein inference engine Fido.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">FidoAdapter</token>
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8 <import>macros.xml</import>
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9 </macros>
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10 <expand macro="references"/>
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11 <expand macro="stdio"/>
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12 <expand macro="requirements"/>
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13 <command>FidoAdapter
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14
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15 #if $param_in:
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16 -in $param_in
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17 #end if
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18 #if $param_out:
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19 -out $param_out
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20 #end if
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21 -fido_executable fido
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22 -fidocp_executable fido_choose_parameters
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23 #if $param_prob_param:
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24 -prob_param &quot;$param_prob_param&quot;
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25 #end if
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26 #if $param_separate_runs:
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27 -separate_runs
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28 #end if
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29 #if $param_greedy_group_resolution:
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30 -greedy_group_resolution
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31 #end if
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32 #if $param_no_cleanup:
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33 -no_cleanup
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34 #end if
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35 #if $param_all_PSMs:
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36 -all_PSMs
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37 #end if
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38 #if $param_group_level:
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39 -group_level
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40 #end if
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41 #if $param_log2_states:
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42 -log2_states $param_log2_states
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43 #end if
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44 -threads \${GALAXY_SLOTS:-24}
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45 #if $param_prob_protein:
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46 -prob:protein $param_prob_protein
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47 #end if
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48 #if $param_prob_peptide:
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49 -prob:peptide $param_prob_peptide
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50 #end if
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51 #if $param_prob_spurious:
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52 -prob:spurious $param_prob_spurious
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53 #end if
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54 #if $adv_opts.adv_opts_selector=='advanced':
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55 #if $adv_opts.param_keep_zero_group:
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56 -keep_zero_group
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57 #end if
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58 #if $adv_opts.param_accuracy:
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59 -accuracy
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60 #if &quot; &quot; in str($adv_opts.param_accuracy):
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61 &quot;$adv_opts.param_accuracy&quot;
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62 #else
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63 $adv_opts.param_accuracy
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64 #end if
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65 #end if
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66 #if $adv_opts.param_log2_states_precalc:
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67 -log2_states_precalc $adv_opts.param_log2_states_precalc
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68 #end if
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69 #if $adv_opts.param_force:
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70 -force
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71 #end if
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72 #end if
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73 </command>
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74 <inputs>
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75 <param format="xml" help="(-in) " label="Input: identification results" name="param_in" optional="False" type="data"/>
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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">
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77 <sanitizer>
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78 <valid initial="string.printable">
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79 <remove value="'"/>
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80 <remove value="&quot;"/>
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81 </valid>
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82 </sanitizer>
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83 </param>
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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"/>
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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"/>
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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"/>
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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"/>
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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"/>
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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"/>
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90 <param help="(-protein) " label="Protein prior probability ('gamma' parameter)" min="0.0" name="param_prob_protein" optional="True" type="float" value="0.0"/>
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91 <param help="(-peptide) " label="Peptide emission probability ('alpha' parameter)" min="0.0" name="param_prob_peptide" optional="True" type="float" value="0.0"/>
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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"/>
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93 <expand macro="advanced_options">
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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"/>
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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">
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96 <option value=""></option>
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97 <option value="best">best</option>
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98 <option value="relaxed">relaxed</option>
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99 <option value="sloppy">sloppy</option>
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100 </param>
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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"/>
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102 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
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103 </expand>
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104 </inputs>
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105 <outputs>
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106 <data format="xml" name="param_out"/>
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107 </outputs>
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108 <help>Runs the protein inference engine Fido.
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109
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110
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111 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FidoAdapter.html</help>
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112 </tool>