Mercurial > repos > galaxyp > openms_openswathassaygenerator

annotate OpenSwathAssayGenerator.xml @ 13:de7a553552a6 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author galaxyp
date Thu, 01 Dec 2022 19:07:50 +0000
parents a41cd777ced9
children 74d39f98b0c4
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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 CTDConverter.-->
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3 <!--Proposed Tool Section: [Targeted Experiments]-->
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4 <tool id="OpenSwathAssayGenerator" name="OpenSwathAssayGenerator" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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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="requirements"/>
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11 <expand macro="stdio"/>
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12 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
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13 @EXT_FOO@
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14 #import re
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16 ## Preprocessing
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17 mkdir in &&
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18 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
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19 mkdir out &&
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20 #if $swath_windows_file:
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21 mkdir swath_windows_file &&
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22 ln -s '$swath_windows_file' 'swath_windows_file/${re.sub("[^\w\-_]", "_", $swath_windows_file.element_identifier)}.$gxy2omsext($swath_windows_file.ext)' &&
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23 #end if
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24 #if $unimod_file:
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25 mkdir unimod_file &&
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26 ln -s '$unimod_file' 'unimod_file/${re.sub("[^\w\-_]", "_", $unimod_file.element_identifier)}.$gxy2omsext($unimod_file.ext)' &&
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27 #end if
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29 ## Main program call
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31 set -o pipefail &&
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32 @EXECUTABLE@ -write_ctd ./ &&
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33 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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34 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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35 -in
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36 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
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37 -out
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38 'out/output.${out_type}'
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39 #if $swath_windows_file:
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40 -swath_windows_file
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41 'swath_windows_file/${re.sub("[^\w\-_]", "_", $swath_windows_file.element_identifier)}.$gxy2omsext($swath_windows_file.ext)'
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42 #end if
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43 #if $unimod_file:
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44 -unimod_file
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45 'unimod_file/${re.sub("[^\w\-_]", "_", $unimod_file.element_identifier)}.$gxy2omsext($unimod_file.ext)'
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46 #end if
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47
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48 ## Postprocessing
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49 && mv 'out/output.${out_type}' '$out'
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50 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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51 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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52 #end if]]></command>
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53 <configfiles>
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54 <inputs name="args_json" data_style="paths"/>
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55 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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56 </configfiles>
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57 <inputs>
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58 <param argument="-in" type="data" format="mrm,pqp,tabular,traml" optional="false" label="Input file" help=" select mrm,pqp,tabular,traml data sets(s)"/>
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59 <param argument="-out_type" display="radio" type="select" optional="false" label="Output file type -- default: determined from file extension or content" help="">
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60 <option value="TraML">traml</option>
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61 <option value="pqp">pqp</option>
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62 <option value="tsv">tabular (tsv)</option>
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63 <expand macro="list_string_san" name="out_type"/>
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64 </param>
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65 <param argument="-min_transitions" type="integer" optional="true" value="6" label="minimal number of transitions" help=""/>
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66 <param argument="-max_transitions" type="integer" optional="true" value="6" label="maximal number of transitions" help=""/>
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67 <param argument="-allowed_fragment_types" type="text" optional="true" value="b,y" label="allowed fragment types" help="">
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68 <expand macro="list_string_san" name="allowed_fragment_types"/>
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69 </param>
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70 <param argument="-allowed_fragment_charges" type="text" optional="true" value="1,2,3,4" label="allowed fragment charge states" help="">
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71 <expand macro="list_string_san" name="allowed_fragment_charges"/>
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72 </param>
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73 <param argument="-enable_detection_specific_losses" type="boolean" truevalue="true" falsevalue="false" checked="false" label="set this flag if specific neutral losses for detection fragment ions should be allowed" help=""/>
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74 <param argument="-enable_detection_unspecific_losses" type="boolean" truevalue="true" falsevalue="false" checked="false" label="set this flag if unspecific neutral losses (H2O1, H3N1, C1H2N2, C1H2N1O1) for detection fragment ions should be allowed" help=""/>
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75 <param argument="-precursor_mz_threshold" type="float" optional="true" value="0.025" label="MZ threshold in Thomson for precursor ion selection" help=""/>
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76 <param argument="-precursor_lower_mz_limit" type="float" optional="true" value="400.0" label="lower MZ limit for precursor ions" help=""/>
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77 <param argument="-precursor_upper_mz_limit" type="float" optional="true" value="1200.0" label="upper MZ limit for precursor ions" help=""/>
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78 <param argument="-product_mz_threshold" type="float" optional="true" value="0.025" label="MZ threshold in Thomson for fragment ion annotation" help=""/>
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79 <param argument="-product_lower_mz_limit" type="float" optional="true" value="350.0" label="lower MZ limit for fragment ions" help=""/>
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80 <param argument="-product_upper_mz_limit" type="float" optional="true" value="2000.0" label="upper MZ limit for fragment ions" help=""/>
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81 <param argument="-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="Note that the first line is a header and will be skipped select txt data sets(s)"/>
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82 <param argument="-unimod_file" type="data" format="xml" optional="true" label="(Modified) Unimod XML file (http://www.unimod.org/xml/unimod.xml) describing residue modifiability" help=" select xml data sets(s)"/>
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83 <param argument="-enable_ipf" type="boolean" truevalue="true" falsevalue="false" checked="false" label="IPF: set this flag if identification transitions should be generated for IPF" help="Note: Requires setting 'unimod_file'"/>
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84 <expand macro="adv_opts_macro">
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85 <param argument="-max_num_alternative_localizations" type="integer" optional="true" value="10000" label="IPF: maximum number of site-localization permutations" help=""/>
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86 <param argument="-disable_identification_ms2_precursors" type="boolean" truevalue="true" falsevalue="false" checked="false" label="IPF: set this flag if MS2-level precursor ions for identification should not be allowed for extraction of the precursor signal from the fragment ion data (MS2-level)" help=""/>
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87 <param argument="-disable_identification_specific_losses" type="boolean" truevalue="true" falsevalue="false" checked="false" label="IPF: set this flag if specific neutral losses for identification fragment ions should not be allowed" help=""/>
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88 <param argument="-enable_identification_unspecific_losses" type="boolean" truevalue="true" falsevalue="false" checked="false" label="IPF: set this flag if unspecific neutral losses (H2O1, H3N1, C1H2N2, C1H2N1O1) for identification fragment ions should be allowed" help=""/>
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89 <param argument="-enable_swath_specifity" type="boolean" truevalue="true" falsevalue="false" checked="false" label="IPF: set this flag if identification transitions without precursor specificity" help="(i.e. across whole precursor isolation window instead of precursor MZ) should be generated"/>
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90 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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91 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
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92 <expand macro="list_string_san" name="test"/>
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93 </param>
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94 </expand>
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95 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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96 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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97 </param>
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98 </inputs>
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99 <outputs>
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100 <data name="out" label="${tool.name} on ${on_string}: out" format="traml">
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101 <change_format>
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102 <when input="out_type" value="pqp" format="pqp"/>
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103 <when input="out_type" value="tsv" format="tabular"/>
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104 </change_format>
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105 </data>
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106 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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107 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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108 </data>
0
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109 </outputs>
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110 <tests><!-- TOPP_OpenSwathAssayGenerator_test_1 -->
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111 <test expect_num_outputs="2">
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112 <section name="adv_opts">
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113 <param name="max_num_alternative_localizations" value="10000"/>
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114 <param name="disable_identification_ms2_precursors" value="false"/>
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115 <param name="disable_identification_specific_losses" value="false"/>
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116 <param name="enable_identification_unspecific_losses" value="false"/>
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117 <param name="enable_swath_specifity" value="false"/>
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118 <param name="force" value="false"/>
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119 <param name="test" value="true"/>
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120 </section>
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121 <param name="in" value="OpenSwathAssayGenerator_input.TraML"/>
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122 <output name="out" file="OpenSwathAssayGenerator_output.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/>
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123 <param name="out_type" value="TraML"/>
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124 <param name="min_transitions" value="6"/>
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125 <param name="max_transitions" value="6"/>
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126 <param name="allowed_fragment_types" value="b,y"/>
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127 <param name="allowed_fragment_charges" value="2,3"/>
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128 <param name="enable_detection_specific_losses" value="true"/>
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129 <param name="enable_detection_unspecific_losses" value="false"/>
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130 <param name="precursor_mz_threshold" value="0.025"/>
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131 <param name="precursor_lower_mz_limit" value="400.0"/>
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132 <param name="precursor_upper_mz_limit" value="1200.0"/>
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133 <param name="product_mz_threshold" value="0.025"/>
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134 <param name="product_lower_mz_limit" value="350.0"/>
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135 <param name="product_upper_mz_limit" value="2000.0"/>
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136 <param name="enable_ipf" value="false"/>
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137 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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138 <output name="ctd_out" ftype="xml">
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139 <assert_contents>
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140 <is_valid_xml/>
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141 </assert_contents>
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142 </output>
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143 </test>
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144 <!-- TOPP_OpenSwathAssayGenerator_test_2 -->
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145 <test expect_num_outputs="2">
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146 <section name="adv_opts">
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147 <param name="max_num_alternative_localizations" value="10000"/>
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148 <param name="disable_identification_ms2_precursors" value="false"/>
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149 <param name="disable_identification_specific_losses" value="false"/>
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150 <param name="enable_identification_unspecific_losses" value="false"/>
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151 <param name="enable_swath_specifity" value="false"/>
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152 <param name="force" value="false"/>
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153 <param name="test" value="true"/>
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154 </section>
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155 <param name="in" value="OpenSwathAssayGenerator_input_2.TraML"/>
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156 <output name="out" file="OpenSwathAssayGenerator_output_2.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/>
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157 <param name="out_type" value="TraML"/>
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158 <param name="min_transitions" value="6"/>
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159 <param name="max_transitions" value="6"/>
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160 <param name="allowed_fragment_types" value="b,y"/>
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161 <param name="allowed_fragment_charges" value="1,2,3,4"/>
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162 <param name="enable_detection_specific_losses" value="false"/>
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163 <param name="enable_detection_unspecific_losses" value="false"/>
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164 <param name="precursor_mz_threshold" value="0.025"/>
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165 <param name="precursor_lower_mz_limit" value="400.0"/>
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166 <param name="precursor_upper_mz_limit" value="1200.0"/>
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167 <param name="product_mz_threshold" value="0.025"/>
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168 <param name="product_lower_mz_limit" value="350.0"/>
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169 <param name="product_upper_mz_limit" value="2000.0"/>
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170 <param name="unimod_file" value="OpenSwathAssayGenerator_input_2_unimod.xml"/>
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171 <param name="enable_ipf" value="true"/>
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172 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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173 <output name="ctd_out" ftype="xml">
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174 <assert_contents>
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175 <is_valid_xml/>
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176 </assert_contents>
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177 </output>
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178 </test>
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179 <!-- TOPP_OpenSwathAssayGenerator_test_3 -->
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180 <test expect_num_outputs="2">
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181 <section name="adv_opts">
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182 <param name="max_num_alternative_localizations" value="10000"/>
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183 <param name="disable_identification_ms2_precursors" value="false"/>
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184 <param name="disable_identification_specific_losses" value="false"/>
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185 <param name="enable_identification_unspecific_losses" value="false"/>
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186 <param name="enable_swath_specifity" value="false"/>
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187 <param name="force" value="false"/>
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188 <param name="test" value="true"/>
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189 </section>
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190 <param name="in" value="OpenSwathAssayGenerator_input_2.TraML"/>
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191 <output name="out" file="OpenSwathAssayGenerator_output_3.TraML" compare="sim_size" delta_frac="0.7" ftype="traml"/>
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192 <param name="out_type" value="TraML"/>
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193 <param name="min_transitions" value="6"/>
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194 <param name="max_transitions" value="6"/>
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195 <param name="allowed_fragment_types" value="b,y"/>
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196 <param name="allowed_fragment_charges" value="1,2,3,4"/>
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197 <param name="enable_detection_specific_losses" value="false"/>
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198 <param name="enable_detection_unspecific_losses" value="false"/>
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199 <param name="precursor_mz_threshold" value="0.025"/>
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200 <param name="precursor_lower_mz_limit" value="400.0"/>
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201 <param name="precursor_upper_mz_limit" value="1200.0"/>
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202 <param name="product_mz_threshold" value="0.025"/>
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203 <param name="product_lower_mz_limit" value="350.0"/>
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204 <param name="product_upper_mz_limit" value="2000.0"/>
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205 <param name="unimod_file" value="OpenSwathAssayGenerator_input_3_unimod.xml"/>
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206 <param name="enable_ipf" value="true"/>
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207 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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208 <output name="ctd_out" ftype="xml">
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209 <assert_contents>
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210 <is_valid_xml/>
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211 </assert_contents>
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212 </output>
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213 </test>
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214 </tests>
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215 <help><![CDATA[Generates assays according to different models for a specific TraML
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216
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217
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218 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_OpenSwathAssayGenerator.html]]></help>
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219 <expand macro="references"/>
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220 </tool>