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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="FidoAdapter" name="FidoAdapter" version="2.0.0">
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3 <description>Runs the protein inference engine Fido.</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">FidoAdapter</token>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="stdio"/>
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9 <expand macro="requirements"/>
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10 <command>FidoAdapter
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11 -fidocp_executable FidoChooseParameters
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12 -fido_executable Fido
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13
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14 #if $param_in:
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15 -in $param_in
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16 #end if
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17 #if $param_out:
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18 -out $param_out
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19 #end if
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20 #if $param_prob_param:
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21 -prob_param "$param_prob_param"
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22 #end if
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23 #if $param_separate_runs:
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24 -separate_runs
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25 #end if
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26 #if $param_no_cleanup:
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27 -no_cleanup
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28 #end if
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29 #if $param_all_PSMs:
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30 -all_PSMs
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31 #end if
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32 #if $param_group_level:
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33 -group_level
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34 #end if
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35 #if $param_log2_states:
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36 -log2_states $param_log2_states
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37 #end if
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38 -threads \${GALAXY_SLOTS:-24}
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39 #if $param_prob_protein:
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40 -prob:protein $param_prob_protein
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41 #end if
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42 #if $param_prob_peptide:
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43 -prob:peptide $param_prob_peptide
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44 #end if
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45 #if $param_prob_spurious:
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46 -prob:spurious $param_prob_spurious
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47 #end if
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48 #if $adv_opts.adv_opts_selector=='advanced':
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49 #if $adv_opts.param_keep_zero_group:
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50 -keep_zero_group
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51 #end if
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52 #if $adv_opts.param_accuracy:
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53 -accuracy
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54 #if " " in str($adv_opts.param_accuracy):
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55 "$adv_opts.param_accuracy"
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56 #else
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57 $adv_opts.param_accuracy
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58 #end if
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59 #end if
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60 #if $adv_opts.param_log2_states_precalc:
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61 -log2_states_precalc $adv_opts.param_log2_states_precalc
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62 #end if
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63 #if $adv_opts.param_force:
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64 -force
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65 #end if
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66 #end if
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67 </command>
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68 <inputs>
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69 <param name="param_in" type="data" format="idxml" optional="False" label="Input: identification results" help="(-in) "/>
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70 <param name="param_prob_param" type="text" size="30" value="Posterior Probability_score" label="Read the peptide probability from this user parameter ('UserParam') in the input file, instead of from the 'score' field, if available. (Use" help="(-prob_param) e.g. for search results that were processed with the TOPP tools IDPosteriorErrorProbability followed by FalseDiscoveryRate.)">
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71 <sanitizer>
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72 <valid initial="string.printable">
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73 <remove value="'"/>
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74 <remove value="""/>
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75 </valid>
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76 </sanitizer>
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77 </param>
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78 <param name="param_separate_runs" 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"/>
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79 <param name="param_no_cleanup" 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) "/>
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80 <param name="param_all_PSMs" 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) "/>
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81 <param name="param_group_level" 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"/>
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82 <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)"/>
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83 <param name="param_prob_protein" type="float" min="0.0" optional="True" value="0.0" label="Protein prior probability ('gamma' parameter)" help="(-protein) "/>
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84 <param name="param_prob_peptide" type="float" min="0.0" optional="True" value="0.0" label="Peptide emission probability ('alpha' parameter)" help="(-peptide) "/>
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85 <param name="param_prob_spurious" type="float" min="0.0" optional="True" value="0.0" label="Spurious peptide identification probability ('beta' parameter)" help="(-spurious) "/>
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86 <expand macro="advanced_options">
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87 <param name="param_keep_zero_group" 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) "/>
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88 <param name="param_accuracy" 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')">
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89 <option value=""></option>
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90 <option value="best">best</option>
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91 <option value="relaxed">relaxed</option>
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92 <option value="sloppy">sloppy</option>
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93 </param>
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94 <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) "/>
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95 <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
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96 </expand>
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97 </inputs>
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98 <outputs>
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99 <data name="param_out" format="idxml"/>
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100 </outputs>
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101 <help>**What it does**
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102
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103 Runs the protein inference engine Fido.
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104
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105
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106 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FidoAdapter.html</help>
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107 <expand macro="references"/>
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108 </tool>
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