Mercurial > repos > galaxyp > openms_fidoadapter

annotate FidoAdapter.xml @ 8:46ac10575c5f draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 981be1bde91d6d565693cd691553f77465e653bb
author galaxyp
date Tue, 20 Mar 2018 14:50:06 -0400
parents ef332f82a0e1
children d4965c549fd9
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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 CTDConverter.-->
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3 <!--Proposed Tool Section: [ID Processing]-->
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4 <tool id="FidoAdapter" name="FidoAdapter" version="2.3.0">
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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 -fidocp_executable FidoChooseParameters
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15 -fido_executable Fido
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16
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17 #if $param_in:
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18 -in $param_in
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19 #end if
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20 #if $param_out:
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21 -out $param_out
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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_greedy_group_resolution:
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27 -greedy_group_resolution
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28 #end if
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29 #if $param_no_cleanup:
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30 -no_cleanup
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31 #end if
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32 #if $param_all_PSMs:
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33 -all_PSMs
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34 #end if
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35 #if $param_group_level:
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36 -group_level
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37 #end if
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38 #if $param_log2_states:
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39 -log2_states $param_log2_states
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40 #end if
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41 #if $param_prob_protein:
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42 -prob:protein $param_prob_protein
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43 #end if
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44 #if $param_prob_peptide:
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45 -prob:peptide $param_prob_peptide
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46 #end if
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47 #if $param_prob_spurious:
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48 -prob:spurious $param_prob_spurious
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49 #end if
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50 #if $adv_opts.adv_opts_selector=='advanced':
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51 #if $adv_opts.param_keep_zero_group:
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52 -keep_zero_group
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53 #end if
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54 #if $adv_opts.param_accuracy:
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55 -accuracy
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56 #if " " in str($adv_opts.param_accuracy):
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57 "$adv_opts.param_accuracy"
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58 #else
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59 $adv_opts.param_accuracy
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60 #end if
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61 #end if
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62 #if $adv_opts.param_log2_states_precalc:
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63 -log2_states_precalc $adv_opts.param_log2_states_precalc
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64 #end if
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65 #if $adv_opts.param_force:
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66 -force
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67 #end if
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68 #end if
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69 </command>
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70 <inputs>
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71 <param name="param_in" type="data" format="idxml" optional="False" label="Input: identification results" help="(-in) "/>
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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"/>
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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"/>
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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) "/>
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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) "/>
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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"/>
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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)"/>
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78 <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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79 <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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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) "/>
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81 <expand macro="advanced_options">
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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) "/>
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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')">
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84 <option value=""></option>
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85 <option value="best">best</option>
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86 <option value="relaxed">relaxed</option>
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87 <option value="sloppy">sloppy</option>
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88 </param>
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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) "/>
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90 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
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91 </expand>
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92 </inputs>
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93 <outputs>
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94 <data name="param_out" format="idxml"/>
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95 </outputs>
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96 <help>Runs the protein inference engine Fido.
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97
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98
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99 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FidoAdapter.html</help>
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100 </tool>