Mercurial > repos > galaxyp > openms_featurelinkerunlabeled

annotate FeatureLinkerUnlabeled.xml @ 9:bc21e5dd5ff0 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
author galaxyp
date Wed, 15 May 2019 08:19:18 -0400
parents df7f4ac9a2c6
children 6b88274392ce
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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: [Map Alignment]-->
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4 <tool id="FeatureLinkerUnlabeled" name="FeatureLinkerUnlabeled" version="2.3.0">
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5 <description>Groups corresponding features from multiple maps.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">FeatureLinkerUnlabeled</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 detect_errors="aggressive"><![CDATA[FeatureLinkerUnlabeled
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14
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15 -in
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16 #for token in $param_in:
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17 $token
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18 #end for
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19 #if $param_out:
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20 -out $param_out
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21 #end if
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22 #if $param_design:
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23 -design $param_design
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24 #end if
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25 #if $param_keep_subelements:
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26 -keep_subelements
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27 #end if
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28 #if $param_algorithm_second_nearest_gap:
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29 -algorithm:second_nearest_gap $param_algorithm_second_nearest_gap
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30 #end if
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31 #if $param_algorithm_use_identifications:
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32 -algorithm:use_identifications
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33 #end if
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34 #if $param_algorithm_ignore_charge:
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35 -algorithm:ignore_charge
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36 #end if
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37 #if $param_algorithm_distance_RT_max_difference:
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38 -algorithm:distance_RT:max_difference $param_algorithm_distance_RT_max_difference
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39 #end if
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40 #if $param_algorithm_distance_MZ_max_difference:
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41 -algorithm:distance_MZ:max_difference $param_algorithm_distance_MZ_max_difference
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42 #end if
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43 #if $param_algorithm_distance_MZ_unit:
1
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44 -algorithm:distance_MZ:unit
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45 #if " " in str($param_algorithm_distance_MZ_unit):
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46 "$param_algorithm_distance_MZ_unit"
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47 #else
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48 $param_algorithm_distance_MZ_unit
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49 #end if
0
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50 #end if
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51 #if $adv_opts.adv_opts_selector=='advanced':
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52 #if $adv_opts.param_force:
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53 -force
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54 #end if
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55 #if $adv_opts.param_algorithm_distance_RT_exponent:
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56 -algorithm:distance_RT:exponent $adv_opts.param_algorithm_distance_RT_exponent
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57 #end if
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58 #if $adv_opts.param_algorithm_distance_RT_weight:
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59 -algorithm:distance_RT:weight $adv_opts.param_algorithm_distance_RT_weight
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60 #end if
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61 #if $adv_opts.param_algorithm_distance_MZ_exponent:
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62 -algorithm:distance_MZ:exponent $adv_opts.param_algorithm_distance_MZ_exponent
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63 #end if
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64 #if $adv_opts.param_algorithm_distance_MZ_weight:
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65 -algorithm:distance_MZ:weight $adv_opts.param_algorithm_distance_MZ_weight
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66 #end if
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67 #if $adv_opts.param_algorithm_distance_intensity_exponent:
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68 -algorithm:distance_intensity:exponent $adv_opts.param_algorithm_distance_intensity_exponent
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69 #end if
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70 #if $adv_opts.param_algorithm_distance_intensity_weight:
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71 -algorithm:distance_intensity:weight $adv_opts.param_algorithm_distance_intensity_weight
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72 #end if
3
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73 #if $adv_opts.param_algorithm_distance_intensity_log_transform:
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74 -algorithm:distance_intensity:log_transform
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75 #if " " in str($adv_opts.param_algorithm_distance_intensity_log_transform):
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76 "$adv_opts.param_algorithm_distance_intensity_log_transform"
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77 #else
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78 $adv_opts.param_algorithm_distance_intensity_log_transform
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79 #end if
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80 #end if
0
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81 #end if
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82 ]]></command>
0
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83 <inputs>
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84 <param name="param_in" type="data" format="featurexml,consensusxml" multiple="true" optional="False" size="30" label="input files separated by blanks" help="(-in) ">
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85 <sanitizer>
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86 <valid initial="string.printable">
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87 <remove value="'"/>
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88 <remove value="&quot;"/>
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89 </valid>
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90 </sanitizer>
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91 </param>
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92 <param name="param_design" type="data" format="tabular" optional="True" label="input file containing the experimental design" help="(-design) "/>
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93 <param name="param_keep_subelements" display="radio" type="boolean" truevalue="-keep_subelements" falsevalue="" checked="false" optional="True" label="For consensusXML input only: If set, the sub-features of the inputs are transferred to the output" help="(-keep_subelements) "/>
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94 <param name="param_algorithm_second_nearest_gap" type="float" min="1.0" optional="True" value="2.0" label="Only link features whose distance to the second nearest neighbors (for both sides) is larger by 'second_nearest_gap' than the distance between the matched pair itself" help="(-second_nearest_gap) "/>
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95 <param name="param_algorithm_use_identifications" display="radio" type="boolean" truevalue="-algorithm:use_identifications" falsevalue="" checked="false" optional="True" label="Never link features that are annotated with different peptides (features without ID's always match; only the best hit per peptide identification is considered)" help="(-use_identifications) "/>
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96 <param name="param_algorithm_ignore_charge" display="radio" type="boolean" truevalue="-algorithm:ignore_charge" falsevalue="" checked="false" optional="True" label="false [default]: pairing requires equal charge state (or at least one unknown charge '0'); true: Pairing irrespective of charge state" help="(-ignore_charge) "/>
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97 <param name="param_algorithm_distance_RT_max_difference" type="float" min="0.0" optional="True" value="100.0" label="Never pair features with a larger RT distance (in seconds)" help="(-max_difference) "/>
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98 <param name="param_algorithm_distance_MZ_max_difference" type="float" min="0.0" optional="True" value="0.3" label="Never pair features with larger m/z distance (unit defined by 'unit')" help="(-max_difference) "/>
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99 <param name="param_algorithm_distance_MZ_unit" display="radio" type="select" optional="False" value="Da" label="Unit of the 'max_difference' paramete" help="(-unit) ">
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100 <option value="Da" selected="true">Da</option>
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101 <option value="ppm">ppm</option>
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102 </param>
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103 <expand macro="advanced_options">
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104 <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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105 <param name="param_algorithm_distance_RT_exponent" type="float" min="0.0" optional="True" value="1.0" label="Normalized RT differences ([0-1], relative to 'max_difference') are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help="(-exponent) "/>
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106 <param name="param_algorithm_distance_RT_weight" type="float" min="0.0" optional="True" value="1.0" label="Final RT distances are weighted by this facto" help="(-weight) "/>
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107 <param name="param_algorithm_distance_MZ_exponent" type="float" min="0.0" optional="True" value="2.0" label="Normalized ([0-1], relative to 'max_difference') m/z differences are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help="(-exponent) "/>
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108 <param name="param_algorithm_distance_MZ_weight" type="float" min="0.0" optional="True" value="1.0" label="Final m/z distances are weighted by this facto" help="(-weight) "/>
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109 <param name="param_algorithm_distance_intensity_exponent" type="float" min="0.0" optional="True" value="1.0" label="Differences in relative intensity ([0-1]) are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help="(-exponent) "/>
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110 <param name="param_algorithm_distance_intensity_weight" type="float" min="0.0" optional="True" value="0.0" label="Final intensity distances are weighted by this facto" help="(-weight) "/>
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111 <param name="param_algorithm_distance_intensity_log_transform" display="radio" type="select" optional="False" value="disabled" label="Log-transform intensities?" help="(-log_transform) If disabled, d = |int_f2 - int_f1| / int_max. If enabled, d = |log(int_f2 + 1) - log(int_f1 + 1)| / log(int_max + 1))">
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112 <option value="enabled">enabled</option>
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113 <option value="disabled" selected="true">disabled</option>
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114 </param>
0
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115 </expand>
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116 </inputs>
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117 <outputs>
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118 <data name="param_out" format="consensusxml"/>
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119 </outputs>
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120 <help>Groups corresponding features from multiple maps.
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121
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122
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123 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_FeatureLinkerUnlabeled.html</help>
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124 </tool>