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

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author bgruening
date Wed, 27 Jan 2016 10:06:49 -0500
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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="ConsensusID" name="ConsensusID" version="2.0.0">
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5 <description>Computes a consensus of peptide identifications of several identification engines.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">ConsensusID</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>ConsensusID
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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 #if $param_rt_delta:
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22 -rt_delta $param_rt_delta
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23 #end if
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24 #if $param_mz_delta:
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25 -mz_delta $param_mz_delta
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26 #end if
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27 #if $param_algorithm:
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28 -algorithm
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29 #if &quot; &quot; in str($param_algorithm):
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30 &quot;$param_algorithm&quot;
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31 #else
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32 $param_algorithm
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33 #end if
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34 #end if
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35 -threads \${GALAXY_SLOTS:-24}
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36 #if $param_filter_considered_hits:
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37 -filter:considered_hits $param_filter_considered_hits
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38 #end if
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39 #if $param_filter_min_support:
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40 -filter:min_support $param_filter_min_support
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41 #end if
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42 #if $param_filter_count_empty:
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43 -filter:count_empty
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44 #end if
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45 #if $param_PEPIons_mass_tolerance:
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46 -PEPIons:mass_tolerance $param_PEPIons_mass_tolerance
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47 #end if
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48 #if $param_PEPIons_min_shared:
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49 -PEPIons:min_shared $param_PEPIons_min_shared
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50 #end if
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51 #if $param_PEPMatrix_matrix:
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52 -PEPMatrix:matrix
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53 #if &quot; &quot; in str($param_PEPMatrix_matrix):
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54 &quot;$param_PEPMatrix_matrix&quot;
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55 #else
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56 $param_PEPMatrix_matrix
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57 #end if
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58 #end if
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59 #if $param_PEPMatrix_penalty:
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60 -PEPMatrix:penalty $param_PEPMatrix_penalty
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61 #end if
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62 #if $adv_opts.adv_opts_selector=='advanced':
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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 format="xml,consensusxml" help="(-in) " label="input file" name="param_in" optional="False" type="data"/>
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70 <param help="(-rt_delta) " label="[idXML input only] Maximum allowed retention time deviation between identifications belonging to the same spectrum" min="0.0" name="param_rt_delta" optional="True" type="float" value="0.1"/>
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71 <param help="(-mz_delta) " label="[idXML input only] Maximum allowed precursor m/z deviation between identifications belonging to the same spectrum" min="0.0" name="param_mz_delta" optional="True" type="float" value="0.1"/>
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72 <param help="(-algorithm) &lt;br&gt;* PEPMatrix: Scoring based on posterior error probabilities (PEPs) and peptide sequence similarities (scored by a substitution matrix). Requires PEPs as scores. &lt;br&gt;* PEPIons: Scoring based on posterior error probabilities (PEPs) and fragment ion similarities ('shared peak count'). Requires PEPs as scores. &lt;br&gt;* best: For each peptide ID, use the best score of any search engine as the consensus score. Requires the same score type in all ID runs. &lt;br&gt;* worst: For each peptide ID, use the worst score of any search engine as the consensus score. Requires the same score type in all ID runs. &lt;br&gt;* average: For each peptide ID, use the average score of all search engines as the consensus. Requires the same score type in all ID runs. &lt;br&gt;* ranks: Calculates a consensus score based on the ranks of peptide IDs in the results of different search engines. The final score is in the range (0, 1], with 1 being the best score. No requirements about score types" label="Algorithm used for consensus scoring" name="param_algorithm" optional="True" type="select" value="PEPMatrix">
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73 <option value="PEPMatrix">PEPMatrix</option>
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74 <option value="PEPIons">PEPIons</option>
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75 <option value="best">best</option>
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76 <option value="worst">worst</option>
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77 <option value="average">average</option>
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78 <option value="ranks">ranks</option>
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79 </param>
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80 <param help="(-considered_hits) " label="The number of top hits in each ID run that are considered for consensus scoring ('0' for all hits)" min="0" name="param_filter_considered_hits" optional="True" type="integer" value="0"/>
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81 <param help="(-min_support) " label="For each peptide hit from an ID run, the fraction of other ID runs that must support that hit (otherwise it is removed)" max="1.0" min="0.0" name="param_filter_min_support" optional="True" type="float" value="0.0"/>
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82 <param checked="false" falsevalue="" help="(-count_empty) those containing no peptide hit for the current spectrum) when calculating 'min_support'?" label="Count empty ID runs (i.e" name="param_filter_count_empty" optional="True" truevalue="-filter:count_empty" type="boolean"/>
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83 <param help="(-mass_tolerance) " label="Maximum difference between fragment masses (in Da) for fragments to be considered 'shared' between peptides" min="0.0" name="param_PEPIons_mass_tolerance" optional="True" type="float" value="0.5"/>
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84 <param help="(-min_shared) " label="The minimal number of 'shared' fragments (between two suggested peptides) that is necessary to evaluate the similarity based on shared peak count (SPC)" min="1" name="param_PEPIons_min_shared" optional="True" type="integer" value="2"/>
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85 <param help="(-matrix) " label="Substitution matrix to use for alignment-based similarity scoring" name="param_PEPMatrix_matrix" optional="True" type="select" value="identity">
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86 <option value="identity">identity</option>
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87 <option value="PAM30MS">PAM30MS</option>
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88 </param>
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89 <param help="(-penalty) " label="Alignment gap penalty (the same value is used for gap opening and extension)" min="1" name="param_PEPMatrix_penalty" optional="True" type="integer" value="5"/>
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90 <expand macro="advanced_options">
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91 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
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92 </expand>
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93 </inputs>
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94 <outputs>
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95 <data format="input" metadata_source="param_in" name="param_out"/>
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96 </outputs>
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97 <help>Computes a consensus of peptide identifications of several identification engines.
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98
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99
4
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100 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_ConsensusID.html</help>
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101 </tool>