Mercurial > repos > galaxyp > openms_openswathdecoygenerator

annotate OpenSwathDecoyGenerator.xml @ 7:5cc0f0e55785 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
author galaxyp
date Fri, 17 May 2019 04:51:51 -0400
parents 829f134aab22
children 1814187218fe
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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: [Targeted Experiments]-->
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4 <tool id="OpenSwathDecoyGenerator" name="OpenSwathDecoyGenerator" version="2.3.0">
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5 <description>Generates decoys according to different models for a specific TraML</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">OpenSwathDecoyGenerator</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[OpenSwathDecoyGenerator
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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 $param_method:
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22 -method "$param_method"
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23 #end if
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24 #if $param_decoy_tag:
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25 -decoy_tag "$param_decoy_tag"
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26 #end if
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27 #if $param_mz_threshold:
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28 -mz_threshold $param_mz_threshold
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29 #end if
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30 #if $param_exclude_similar:
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31 -exclude_similar
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32 #end if
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33 #if $param_similarity_threshold:
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34 -similarity_threshold $param_similarity_threshold
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35 #end if
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36 #if $param_append:
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37 -append
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38 #end if
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39 #if $param_remove_CNterm_mods:
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40 -remove_CNterm_mods
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41 #end if
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42 #if $param_remove_unannotated:
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43 -remove_unannotated
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44 #end if
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45 #if $param_identity_threshold:
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46 -identity_threshold $param_identity_threshold
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47 #end if
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48 #if $param_max_attempts:
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49 -max_attempts $param_max_attempts
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50 #end if
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51 #if $param_mz_shift:
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52 -mz_shift $param_mz_shift
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53 #end if
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54 #if $param_precursor_mass_shift:
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55 -precursor_mass_shift $param_precursor_mass_shift
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56 #end if
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57 #if $param_allowed_fragment_types:
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58 -allowed_fragment_types "$param_allowed_fragment_types"
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59 #end if
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60 #if $param_allowed_fragment_charges:
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61 -allowed_fragment_charges "$param_allowed_fragment_charges"
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62 #end if
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63 #if $param_enable_detection_specific_losses:
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64 -enable_detection_specific_losses
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65 #end if
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66 #if $param_enable_detection_unspecific_losses:
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67 -enable_detection_unspecific_losses
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68 #end if
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69 #if $adv_opts.adv_opts_selector=='advanced':
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70 #if $adv_opts.param_force:
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71 -force
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72 #end if
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73 #end if
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74 ]]></command>
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75 <inputs>
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76 <param name="param_in" type="data" format="traml" optional="False" label="input file ('traML')" help="(-in) "/>
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77 <param name="param_method" type="text" size="30" value="shuffle" label="decoy generation method ('shuffle','pseudo-reverse','reverse','shift')" help="(-method) ">
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78 <sanitizer>
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79 <valid initial="string.printable">
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80 <remove value="'"/>
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81 <remove value="&quot;"/>
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82 </valid>
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83 </sanitizer>
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84 </param>
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85 <param name="param_decoy_tag" type="text" size="30" value="DECOY_" label="decoy tag" help="(-decoy_tag) ">
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86 <sanitizer>
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87 <valid initial="string.printable">
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88 <remove value="'"/>
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89 <remove value="&quot;"/>
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90 </valid>
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91 </sanitizer>
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92 </param>
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93 <param name="param_mz_threshold" type="float" value="0.05" label="MZ threshold in Thomson for fragment ion annotation" help="(-mz_threshold) "/>
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94 <param name="param_exclude_similar" display="radio" type="boolean" truevalue="-exclude_similar" falsevalue="" checked="false" optional="True" label="set this flag if decoy assays with similarity of the peptide sequence to the target assays higher than the identity_threshold should be excluded" help="(-exclude_similar) If similarity_threshold is over 0, decoy assays with an absolute difference of the decoy and target product mz smaller than similarity_threshold are further excluded"/>
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95 <param name="param_similarity_threshold" type="float" value="-1.0" label="Similarity threshold for absolute difference of the product mz of target and decoy assays for exclusion in Dalton" help="(-similarity_threshold) Suggested value: 0.05"/>
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96 <param name="param_append" display="radio" type="boolean" truevalue="-append" falsevalue="" checked="false" optional="True" label="set this flag if non-decoy TraML should be appended to the output" help="(-append) "/>
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97 <param name="param_remove_CNterm_mods" display="radio" type="boolean" truevalue="-remove_CNterm_mods" falsevalue="" checked="false" optional="True" label="set this flag to remove decoy peptides with C/N terminal modifications (may be necessary depending on the decoy generation method)" help="(-remove_CNterm_mods) "/>
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98 <param name="param_remove_unannotated" display="radio" type="boolean" truevalue="-remove_unannotated" falsevalue="" checked="false" optional="True" label="set this flag if target assays with unannotated ions should be ignored from decoy generation" help="(-remove_unannotated) "/>
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99 <param name="param_identity_threshold" type="float" value="0.7" label="shuffle: identity threshold for the shuffle algorithm" help="(-identity_threshold) "/>
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100 <param name="param_max_attempts" type="integer" value="10" label="shuffle: maximum attempts to lower the sequence identity between target and decoy for the shuffle algorithm" help="(-max_attempts) "/>
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101 <param name="param_mz_shift" type="float" value="20.0" label="shift: MZ shift in Thomson for shift decoy method" help="(-mz_shift) "/>
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102 <param name="param_precursor_mass_shift" type="float" value="0.0" label="Mass shift to apply to the precursor ion" help="(-precursor_mass_shift) "/>
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103 <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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104 <sanitizer>
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105 <valid initial="string.printable">
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106 <remove value="'"/>
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107 <remove value="&quot;"/>
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108 </valid>
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109 </sanitizer>
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110 </param>
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111 <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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112 <sanitizer>
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113 <valid initial="string.printable">
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114 <remove value="'"/>
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115 <remove value="&quot;"/>
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116 </valid>
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117 </sanitizer>
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118 </param>
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119 <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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120 <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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121 <expand macro="advanced_options">
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122 <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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123 </expand>
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124 </inputs>
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125 <outputs>
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126 <data name="param_out" format="traml"/>
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127 </outputs>
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128 <help>Generates decoys according to different models for a specific TraML
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129
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130
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131 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_OpenSwathDecoyGenerator.html</help>
0
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132 </tool>