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

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author bgruening
date Wed, 27 Jan 2016 10:06:49 -0500
parents 3d84209d3178
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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: [Quantitation]-->
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4 <tool id="TMTAnalyzer" name="TMTAnalyzer" version="2.0.0">
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5 <description>Calculates TMT quantitative values for peptides</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">TMTAnalyzer</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>TMTAnalyzer
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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_out_mzq:
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22 -out_mzq $param_out_mzq
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23 #end if
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24 #if $param_out_stats:
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25 -out_stats $param_out_stats
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26 #end if
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27 -threads \${GALAXY_SLOTS:-24}
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28 #if $param_algorithm_Extraction_select_activation:
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29 -algorithm:Extraction:select_activation
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30 #if &quot; &quot; in str($param_algorithm_Extraction_select_activation):
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31 &quot;$param_algorithm_Extraction_select_activation&quot;
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32 #else
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33 $param_algorithm_Extraction_select_activation
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34 #end if
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35 #end if
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36 #if $param_algorithm_Extraction_reporter_mass_shift:
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37 -algorithm:Extraction:reporter_mass_shift $param_algorithm_Extraction_reporter_mass_shift
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38 #end if
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39
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40 #if $rep_param_algorithm_Extraction_channel_active:
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41 -algorithm:Extraction:channel_active
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42 #for token in $rep_param_algorithm_Extraction_channel_active:
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43 #if &quot; &quot; in str(token):
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44 &quot;$token.param_algorithm_Extraction_channel_active&quot;
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45 #else
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46 $token.param_algorithm_Extraction_channel_active
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47 #end if
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48 #end for
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49 #end if
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50 #if $param_algorithm_Quantification_channel_reference:
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51 -algorithm:Quantification:channel_reference $param_algorithm_Quantification_channel_reference
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52 #end if
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53 #if $adv_opts.adv_opts_selector=='advanced':
4
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54 #if $adv_opts.param_force:
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55 -force
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56 #end if
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57
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58 #if $rep_param_algorithm_Quantification_isotope_correction_tmt_6plex:
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59 -algorithm:Quantification:isotope_correction:tmt-6plex
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60 #for token in $rep_param_algorithm_Quantification_isotope_correction_tmt_6plex:
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61 #if &quot; &quot; in str(token):
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62 &quot;$token.param_algorithm_Quantification_isotope_correction_tmt_6plex&quot;
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63 #else
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64 $token.param_algorithm_Quantification_isotope_correction_tmt_6plex
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65 #end if
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66 #end for
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67 #end if
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68 #if $adv_opts.param_algorithm_Quantification_do_normalization:
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69 -algorithm:Quantification:do_normalization
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70 #end if
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71 #if $adv_opts.param_algorithm_MetaInformation_Program:
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72 -algorithm:MetaInformation:Program &quot;$adv_opts.param_algorithm_MetaInformation_Program&quot;
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73 #end if
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74 #end if
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75 </command>
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76 <inputs>
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77 <param format="mzml" help="(-in) " label="input raw/picked data file" name="param_in" optional="False" type="data"/>
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78 <param help="(-select_activation) Set to empty string if you want to disable filtering" label="Operate only on MSn scans where any of its precursors features a certain activation method (usually HCD for iTRAQ)" name="param_algorithm_Extraction_select_activation" optional="True" type="select" value="High-energy collision-induced dissociation">
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79 <option value="Collision-induced dissociation">Collision-induced dissociation</option>
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80 <option value="Post-source decay">Post-source decay</option>
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81 <option value="Plasma desorption">Plasma desorption</option>
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82 <option value="Surface-induced dissociation">Surface-induced dissociation</option>
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83 <option value="Blackbody infrared radiative dissociation">Blackbody infrared radiative dissociation</option>
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84 <option value="Electron capture dissociation">Electron capture dissociation</option>
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85 <option value="Infrared multiphoton dissociation">Infrared multiphoton dissociation</option>
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86 <option value="Sustained off-resonance irradiation">Sustained off-resonance irradiation</option>
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87 <option value="High-energy collision-induced dissociation">High-energy collision-induced dissociation</option>
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88 <option value="Low-energy collision-induced dissociation">Low-energy collision-induced dissociation</option>
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89 <option value="Photodissociation">Photodissociation</option>
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90 <option value="Electron transfer dissociation">Electron transfer dissociation</option>
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91 <option value=""></option>
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92 </param>
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93 <param help="(-reporter_mass_shift) " label="Allowed shift (left to right) in Da from the expected position" max="0.5" min="1e-08" name="param_algorithm_Extraction_reporter_mass_shift" optional="True" type="float" value="0.1"/>
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94 <repeat max="1" min="0" name="rep_param_algorithm_Extraction_channel_active" title="param_algorithm_Extraction_channel_active">
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95 <param help="(-channel_active) e.g. &quot;114:myref&quot;,&quot;115:liver&quot;" label="Each channel that was used in the experiment and its description (126-131 for TMT-6-plex) in format &lt;channel&gt;:&lt;name&gt;," name="param_algorithm_Extraction_channel_active" size="30" type="text" value="126:liver 131:lung">
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96 <sanitizer>
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97 <valid initial="string.printable">
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98 <remove value="'"/>
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99 <remove value="&quot;"/>
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100 </valid>
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101 </sanitizer>
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102 </param>
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103 </repeat>
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104 <param help="(-channel_reference) " label="Number of the reference channel (126-131)" max="131" min="126" name="param_algorithm_Quantification_channel_reference" optional="True" type="integer" value="126"/>
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105 <expand macro="advanced_options">
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106 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
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107 <repeat max="1" min="0" name="rep_param_algorithm_Quantification_isotope_correction_tmt_6plex" title="param_algorithm_Quantification_isotope_correction_tmt_6plex">
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108 <param help="(-tmt-6plex) e.g. '126:0/0.3/4/0' , '128:0.1/0.3/3/0.2'" label="Override default values (see Documentation); use the following format: &lt;channel&gt;:&lt;-2Da&gt;/&lt;-1Da&gt;/&lt;+1Da&gt;/&lt;+2Da&gt; ;" name="param_algorithm_Quantification_isotope_correction_tmt_6plex" size="30" type="text" value="126:0/0/0/0 127:0/0/0/0 128:0/0/0/0 129:0/0/0/0 130:0/0/0/0 131:0/0/0/0">
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109 <sanitizer>
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110 <valid initial="string.printable">
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111 <remove value="'"/>
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112 <remove value="&quot;"/>
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113 </valid>
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114 </sanitizer>
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115 </param>
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116 </repeat>
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117 <param checked="false" falsevalue="" help="(-do_normalization) Done by using the Median of Ratios (every channel / Reference). Also the ratio of medians (from any channel and reference) is provided as control measure!" label="Normalize channels?" name="param_algorithm_Quantification_do_normalization" optional="True" truevalue="-algorithm:Quantification:do_normalization" type="boolean"/>
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118 <param help="(-Program) " label="" name="param_algorithm_MetaInformation_Program" size="30" type="text" value="OpenMS::TMTAnalyzer">
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119 <sanitizer>
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120 <valid initial="string.printable">
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121 <remove value="'"/>
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122 <remove value="&quot;"/>
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123 </valid>
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124 </sanitizer>
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125 </param>
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126 </expand>
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127 </inputs>
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128 <outputs>
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129 <data format="consensusxml" name="param_out"/>
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130 <data format="mzq" name="param_out_mzq"/>
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131 <data format="tabular" name="param_out_stats"/>
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132 </outputs>
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133 <help>Calculates TMT quantitative values for peptides
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134
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135
4
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136 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_TMTAnalyzer.html</help>
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137 </tool>