Mercurial > repos > recetox > ramclustr

annotate ramclustr.xml @ 4:69e0da4703b5 draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit b514d9bf91b62bb06d39e6ceee21d8f18876e12b"
author recetox
date Fri, 04 Feb 2022 08:31:26 +0000
parents 211cd88b5148
children 10ded21d47c0
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1 <tool id="ramclustr" name="RAMClustR" version="@TOOL_VERSION@+galaxy1">
0
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2 <macros>
3
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3 <import>macros.xml</import>
0
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4 </macros>
3
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5 <expand macro="creator"/>
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6
0
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7 <requirements>
1
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8 <requirement type="package" version="@TOOL_VERSION@">r-ramclustr</requirement>
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9 <requirement type="package" version="3.14.0">bioconductor-xcms</requirement>
0
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10 </requirements>
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11
0
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12 <command detect_errors="aggressive"><![CDATA[
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13 Rscript
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14 -e 'source("${__tool_directory__}/ramclustr_wrapper.R")'
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15 -e 'source("${ramclustr_method}")'
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16 ]]>
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17 </command>
2
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18 <configfiles>
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19 <configfile name="ramclustr_method">
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20 store_output(
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21 #if $filetype.type_choice == "xcms":
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22 ramclustr_xcms(
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23 input_xcms = "$filetype.input_xcms",
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24 #else:
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25 ramclustr_csv(
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26 ms="$filetype.ms_csv.ms",
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27 idmsms="$filetype.ms_csv.idmsms",
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28 feature_delimiter="$filetype.ms_csv.feature_delimiter",
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29 sample_name_column = $filetype.ms_csv.sample_name_column,
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30 retention_time_column= $filetype.ms_csv.retention_time_column,
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31 #end if
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32 sr = $filetype.required.sr,
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33 deep_split = $filetype.required.deepSplit,
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34 block_size = $filetype.required.blocksize,
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35 mult = $filetype.required.mult,
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36 hmax = $filetype.required.hmax,
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37 collapse = $filetype.required.collapse,
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38 use_pheno = $filetype.required.usePheno,
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39 qc_inj_range = $filetype.required.qc_inj_range,
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40 normalize = "$filetype.required.normalize",
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41 min_module_size = $filetype.required.minModuleSize,
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42 linkage = "$filetype.required.linkage",
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43 mzdec = $filetype.required.mzdec,
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44 cor_method = "$filetype.required.cor_method",
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45 rt_only_low_n = $filetype.required.rt_only_low_n,
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46 replace_zeros = $filetype.required.replace_zeros,
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47 #if $filetype.type_choice == "xcms":
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48 #if $filetype.optional.st
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49 st = $filetype.optional.st,
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50 #end if
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51 #else:
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52 st = $filetype.ms_csv.st,
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53 #end if
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54 #if $filetype.optional.maxt
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55 maxt = $filetype.optional.maxt,
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56 #end if
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57 #if $filetype.optional.fftempdir
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58 fftempdir = $filetype.optional.fftempdir,
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59 #end if
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60 #if $filetype.metadata.batch_order_qc
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61 metadata_file = "${filetype.metadata.batch_order_qc}",
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62 #end if
4
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63 #if $filetype.metadata.ExpDes
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64 exp_design = "${filetype.metadata.ExpDes}"
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65 #end if
2
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66 ),
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67 "$result", "$method_metadata", $filetype.required.merge_msp, "$spec_abundance")
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68 </configfile>
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69 </configfiles>
0
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70 <inputs>
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71 <conditional name="filetype">
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72 <param name="type_choice" type="select" label="Choose input format:">
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73 <option value="xcms" selected="true">XCMS</option>
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74 <option value="csv">CSV</option>
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75 </param>
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76 <when value="xcms">
3
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77 <param name="input_xcms" label="input_xcms" type="data" format="rdata.xcms.fillpeaks" help="Grouped feature data for clustering by ramclustR" />
0
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78 <expand macro="parameters_required" />
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79 <expand macro="parameters_optional_xcms" />
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80 <expand macro="parameters_optional_metadata" />
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81 </when>
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82 <when value="csv">
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83 <expand macro="parameters_csv" />
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84 <expand macro="parameters_required" />
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85 <expand macro="parameters_optional_csv" />
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86 <expand macro="parameters_optional_metadata" />
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87 </when>
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88 </conditional>
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89 </inputs>
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90
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91 <outputs>
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92 <data label="${tool.name} on ${on_string}" name="result" format="RData" />
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93 <data label="Spec Abundance of ${on_string}" name="spec_abundance" format="csv" />
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94 <data label="Metadata for ${tool.name} on ${on_string}" name="method_metadata" format="txt"/>
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95 <expand macro="output_msp"/>
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96 </outputs>
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97
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98 <tests>
1
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99 <test><!-- TEST 1 -->
0
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100 <param name="type_choice" value="xcms"/>
1
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101 <param name="input_xcms" value="test1_xcmsObj_1.rdata.xcms.fillpeaks" ftype="rdata.xcms.fillpeaks"/>
4
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102 <param name="ExpDes" value="lc-ramclustr-define-experiment.csv" ftype="csv"/>
1
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103 <output name="result" file="test1_ramclustObj_xcms_1.rdata" ftype="RData" compare="sim_size" delta="200"/>
0
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104 <output_collection name="mass_spectra" type="list">
4
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105 <element name="experiment_lc" file="test1_fill_xcms_1.msp" ftype="msp"/>
0
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106 </output_collection>
1
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107 <output name="method_metadata" file="test1_metadata_xcms_1.txt" ftype="txt"/>
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108 <output name="spec_abundance" file="test1_spec_abundance_xcms_1.csv" ftype="csv" compare="sim_size" delta="100"/>
0
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109 </test>
1
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110 <test><!-- TEST 2 -->
0
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111 <param name="type_choice" value="xcms"/>
1
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112 <param name="input_xcms" value="test2_xcmsObj_2.rdata.xcms.fillpeaks" ftype="rdata.xcms.fillpeaks"/>
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113 <param name="batch_order_qc" value="test2_sample_metadata_xcms_2.csv" ftype="csv" />
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114 <output name="result" file="test2_ramclustObj_xcms_2.rdata" ftype="RData" compare="sim_size" delta="200"/>
0
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115 <output_collection name="mass_spectra" type="list">
1
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116 <element name="fill" file="test2_fill_xcms_2.msp" ftype="msp" compare="diff" lines_diff="10"/>
0
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117 </output_collection>
1
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118 <output name="method_metadata" file="test2_metadata_xcms_2.txt" ftype="txt"/>
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119 <output name="spec_abundance" file="test2_spec_abundance_xcms_2.csv" ftype="csv" compare="sim_size" delta="100"/>
0
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120 </test>
1
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121 <test><!-- TEST 3 -->
0
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122 <param name="type_choice" value="csv"/>
1
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123 <param name="ms" value="test3_csv_test-input_1_2.csv" ftype="csv"/>
0
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124 <param name="st" value="5.0"/>
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125 <param name="blocksize" value="1000"/>
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126 <param name="mult" value="1"/>
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127 <param name="maxt" value="1"/>
1
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128 <output name="result" file="test3_ramclustObj_csv_1.rdata" ftype="RData" compare="sim_size" delta="200"/>
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129 <output name="spec_abundance" file="test3_spec_abundance_csv_1.csv" ftype="csv"/>
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130 <output name="method_metadata" file="test3_metadata_csv_1.txt" ftype="txt"/>
0
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131 <output_collection name="mass_spectra" type="list">
1
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132 <element name="fill" file="test3_spectra_csv_1.msp" ftype="msp"/>
0
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133 </output_collection>
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134 </test>
1
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135 <test><!-- TEST 4 -->
0
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136 <param name="type_choice" value="csv"/>
1
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137 <param name="ms" value="test3_csv_test-input_1_2.csv" ftype="csv"/>
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138 <param name="batch_order_qc" value="test4_sample_metadata_csv_2.csv" ftype="csv" />
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139 <output name="result" file="test4_ramclustObj_csv_2.rdata" ftype="RData" compare="sim_size" delta="200"/>
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140 <output name="spec_abundance" file="test4_spec_abundance_csv_2.csv" ftype="csv"/>
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141 <output name="method_metadata" file="test4_metadata_csv_2.txt" ftype="txt"/>
0
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142 <output_collection name="mass_spectra" type="list">
1
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143 <element name="fill" file="test4_spectra_csv_2.msp" ftype="msp" lines_diff="10"/>
0
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144 </output_collection>
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145 </test>
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146 </tests>
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147
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
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148 <help>
3
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149 <![CDATA[
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150 @HELP@
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151 ]]>
0
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152 </help>
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153
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
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154 <expand macro="citations" />
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155 </tool>