Mercurial > repos > galaxyp > openms_openswathassaygenerator

annotate OpenSwathAssayGenerator.xml @ 0:c5136f02a0fa draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
author galaxyp
date Wed, 01 Mar 2017 12:22:47 -0500
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children 1c46da1a81a7
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c5136f02a0fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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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: [Targeted Experiments]-->
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4 <tool id="OpenSwathAssayGenerator" name="OpenSwathAssayGenerator" version="2.1.0">
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5 <description>Generates assays according to different models for a specific TraML</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">OpenSwathAssayGenerator</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>OpenSwathAssayGenerator
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14
c5136f02a0fa planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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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_min_transitions:
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22 -min_transitions $param_min_transitions
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23 #end if
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24 #if $param_max_transitions:
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25 -max_transitions $param_max_transitions
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26 #end if
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27 #if $param_allowed_fragment_types:
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28 -allowed_fragment_types "$param_allowed_fragment_types"
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29 #end if
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30 #if $param_allowed_fragment_charges:
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31 -allowed_fragment_charges "$param_allowed_fragment_charges"
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32 #end if
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33 #if $param_enable_detection_specific_losses:
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34 -enable_detection_specific_losses
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35 #end if
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36 #if $param_enable_detection_unspecific_losses:
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37 -enable_detection_unspecific_losses
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38 #end if
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39 #if $param_enable_identification_specific_losses:
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40 -enable_identification_specific_losses
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41 #end if
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42 #if $param_enable_identification_unspecific_losses:
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43 -enable_identification_unspecific_losses
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44 #end if
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45 #if $param_enable_identification_ms2_precursors:
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46 -enable_identification_ms2_precursors
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47 #end if
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48 #if $param_enable_ms1_uis_scoring:
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49 -enable_ms1_uis_scoring
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50 #end if
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51 #if $param_enable_ms2_uis_scoring:
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52 -enable_ms2_uis_scoring
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53 #end if
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54 #if $param_max_num_alternative_localizations:
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55 -max_num_alternative_localizations $param_max_num_alternative_localizations
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56 #end if
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57 #if $param_enable_reannotation:
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58 -enable_reannotation
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59 #end if
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60 #if $param_precursor_mz_threshold:
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61 -precursor_mz_threshold $param_precursor_mz_threshold
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62 #end if
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63 #if $param_precursor_lower_mz_limit:
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64 -precursor_lower_mz_limit $param_precursor_lower_mz_limit
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65 #end if
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66 #if $param_precursor_upper_mz_limit:
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67 -precursor_upper_mz_limit $param_precursor_upper_mz_limit
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68 #end if
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69 #if $param_product_mz_threshold:
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70 -product_mz_threshold $param_product_mz_threshold
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71 #end if
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72 #if $param_product_lower_mz_limit:
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73 -product_lower_mz_limit $param_product_lower_mz_limit
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74 #end if
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75 #if $param_product_upper_mz_limit:
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76 -product_upper_mz_limit $param_product_upper_mz_limit
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77 #end if
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78 #if $adv_opts.adv_opts_selector=='advanced':
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79 #if $adv_opts.param_swath_windows_file:
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80 -swath_windows_file $adv_opts.param_swath_windows_file
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81 #end if
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82 #if $adv_opts.param_force:
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83 -force
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84 #end if
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85 #end if
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86 </command>
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87 <inputs>
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88 <param name="param_in" type="data" format="traml" optional="False" label="input file ('traML')" help="(-in) "/>
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89 <param name="param_min_transitions" type="integer" value="6" label="minimal number of transitions" help="(-min_transitions) "/>
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90 <param name="param_max_transitions" type="integer" value="6" label="maximal number of transitions" help="(-max_transitions) "/>
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91 <param name="param_allowed_fragment_types" type="text" size="30" value="b,y" label="allowed fragment types" help="(-allowed_fragment_types) ">
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92 <sanitizer>
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93 <valid initial="string.printable">
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94 <remove value="'"/>
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95 <remove value="&quot;"/>
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96 </valid>
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97 </sanitizer>
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98 </param>
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99 <param name="param_allowed_fragment_charges" type="text" size="30" value="1,2,3,4" label="allowed fragment charge states" help="(-allowed_fragment_charges) ">
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100 <sanitizer>
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101 <valid initial="string.printable">
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102 <remove value="'"/>
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103 <remove value="&quot;"/>
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104 </valid>
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105 </sanitizer>
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106 </param>
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107 <param name="param_enable_detection_specific_losses" display="radio" type="boolean" truevalue="-enable_detection_specific_losses" falsevalue="" checked="false" optional="True" label="set this flag if specific neutral losses for detection fragment ions should be allowed" help="(-enable_detection_specific_losses) "/>
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108 <param name="param_enable_detection_unspecific_losses" display="radio" type="boolean" truevalue="-enable_detection_unspecific_losses" falsevalue="" checked="false" optional="True" label="set this flag if unspecific neutral losses (H2O1, H3N1, C1H2N2, C1H2N1O1) for detection fragment ions should be allowed" help="(-enable_detection_unspecific_losses) "/>
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109 <param name="param_enable_identification_specific_losses" display="radio" type="boolean" truevalue="-enable_identification_specific_losses" falsevalue="" checked="false" optional="True" label="set this flag if specific neutral losses for identification fragment ions should be allowed" help="(-enable_identification_specific_losses) "/>
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110 <param name="param_enable_identification_unspecific_losses" display="radio" type="boolean" truevalue="-enable_identification_unspecific_losses" falsevalue="" checked="false" optional="True" label="set this flag if unspecific neutral losses (H2O1, H3N1, C1H2N2, C1H2N1O1) for identification fragment ions should be allowed" help="(-enable_identification_unspecific_losses) "/>
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111 <param name="param_enable_identification_ms2_precursors" display="radio" type="boolean" truevalue="-enable_identification_ms2_precursors" falsevalue="" checked="false" optional="True" label="set this flag if MS2-level precursor ions for identification should be allowed to enable extraction of the precursor signal from the fragment ion data (MS2-level)" help="(-enable_identification_ms2_precursors) This may help in identification if the MS1 signal is weak"/>
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112 <param name="param_enable_ms1_uis_scoring" display="radio" type="boolean" truevalue="-enable_ms1_uis_scoring" falsevalue="" checked="false" optional="True" label="set this flag if MS1-UIS assays for UIS scoring should be generated" help="(-enable_ms1_uis_scoring) "/>
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113 <param name="param_enable_ms2_uis_scoring" display="radio" type="boolean" truevalue="-enable_ms2_uis_scoring" falsevalue="" checked="false" optional="True" label="set this flag if MS2-UIS assays for UIS scoring should be generated" help="(-enable_ms2_uis_scoring) "/>
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114 <param name="param_max_num_alternative_localizations" type="integer" value="20" label="maximum number of site-localization permutations" help="(-max_num_alternative_localizations) "/>
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115 <param name="param_enable_reannotation" display="radio" type="boolean" truevalue="-enable_reannotation" falsevalue="" checked="false" optional="True" label="set this flag if reannotation of fragment ions should be allowed" help="(-enable_reannotation) "/>
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116 <param name="param_precursor_mz_threshold" type="float" value="0.025" label="MZ threshold in Thomson for precursor ion selection" help="(-precursor_mz_threshold) "/>
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117 <param name="param_precursor_lower_mz_limit" type="float" value="400.0" label="lower MZ limit for precursor ions" help="(-precursor_lower_mz_limit) "/>
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118 <param name="param_precursor_upper_mz_limit" type="float" value="1200.0" label="upper MZ limit for precursor ions" help="(-precursor_upper_mz_limit) "/>
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119 <param name="param_product_mz_threshold" type="float" value="0.025" label="MZ threshold in Thomson for fragment ion annotation" help="(-product_mz_threshold) "/>
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120 <param name="param_product_lower_mz_limit" type="float" value="350.0" label="lower MZ limit for fragment ions" help="(-product_lower_mz_limit) "/>
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121 <param name="param_product_upper_mz_limit" type="float" value="2000.0" label="upper MZ limit for fragment ions" help="(-product_upper_mz_limit) "/>
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122 <expand macro="advanced_options">
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123 <param name="param_swath_windows_file" type="data" format="txt" optional="True" label="Tab separated file containing the SWATH windows for exclusion of fragment ions falling into the precursor isolation window: lower_offset upper_offset \newline 400 425 \newline .." help="(-swath_windows_file) Note that the first line is a header and will be skipped"/>
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124 <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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125 </expand>
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126 </inputs>
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127 <outputs>
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128 <data name="param_out" format="traml"/>
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129 </outputs>
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130 <help>Generates assays according to different models for a specific TraML
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131
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132
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133 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathAssayGenerator.html</help>
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134 </tool>