Mercurial > repos > recetox > ramclustr

annotate ramclustr.xml @ 2:eac0e6feb850 draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit d4a601c637b18f18a5cda9111208559e72d12657"
author recetox
date Mon, 17 Jan 2022 16:28:54 +0000
parents 15e173c5762c
children 211cd88b5148
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1 <tool id="ramclustr" name="RAMClustR" version="@TOOL_VERSION@+galaxy0">
0
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2 <macros>
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3 <import>ramclustr_macros.xml</import>
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4 </macros>
1
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5 <creator>
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6 <organization
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7 url="https://www.recetox.muni.cz/"
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8 name="RECETOX MUNI" />
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9 </creator>
0
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10 <requirements>
1
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11 <requirement type="package" version="@TOOL_VERSION@">r-ramclustr</requirement>
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12 <requirement type="package" version="3.14.0">bioconductor-xcms</requirement>
0
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13 </requirements>
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14 <command detect_errors="aggressive"><![CDATA[
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15 Rscript
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16 -e 'source("${__tool_directory__}/ramclustr_wrapper.R")'
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17 -e 'source("${ramclustr_method}")'
0
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18 ]]>
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19 </command>
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20 <configfiles>
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21 <configfile name="ramclustr_method">
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22 store_output(
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23 #if $filetype.type_choice == "xcms":
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24 ramclustr_xcms(
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25 input_xcms = "$filetype.input_xcms",
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26 #else:
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27 ramclustr_csv(
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28 ms="$filetype.ms_csv.ms",
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29 idmsms="$filetype.ms_csv.idmsms",
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30 feature_delimiter="$filetype.ms_csv.feature_delimiter",
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31 sample_name_column = $filetype.ms_csv.sample_name_column,
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32 retention_time_column= $filetype.ms_csv.retention_time_column,
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33 #end if
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34 sr = $filetype.required.sr,
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35 deep_split = $filetype.required.deepSplit,
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36 block_size = $filetype.required.blocksize,
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37 mult = $filetype.required.mult,
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38 hmax = $filetype.required.hmax,
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39 collapse = $filetype.required.collapse,
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40 use_pheno = $filetype.required.usePheno,
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41 qc_inj_range = $filetype.required.qc_inj_range,
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42 normalize = "$filetype.required.normalize",
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43 min_module_size = $filetype.required.minModuleSize,
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44 linkage = "$filetype.required.linkage",
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45 mzdec = $filetype.required.mzdec,
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46 cor_method = "$filetype.required.cor_method",
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47 rt_only_low_n = $filetype.required.rt_only_low_n,
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48 replace_zeros = $filetype.required.replace_zeros,
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49 #if $filetype.type_choice == "xcms":
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50 #if $filetype.optional.st
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51 st = $filetype.optional.st,
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52 #end if
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53 #else:
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54 st = $filetype.ms_csv.st,
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55 #end if
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56 #if $filetype.optional.maxt
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57 maxt = $filetype.optional.maxt,
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58 #end if
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59 #if $filetype.optional.fftempdir
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60 fftempdir = $filetype.optional.fftempdir,
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61 #end if
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62 #if $filetype.metadata.batch_order_qc
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63 metadata_file = "${filetype.metadata.batch_order_qc}",
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64 #end if
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65 ),
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66 "$result", "$method_metadata", $filetype.required.merge_msp, "$spec_abundance")
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67 </configfile>
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68 </configfiles>
0
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69 <inputs>
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70 <conditional name="filetype">
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71 <param name="type_choice" type="select" label="Choose input format:">
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72 <option value="xcms" selected="true">XCMS</option>
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73 <option value="csv">CSV</option>
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74 </param>
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75 <when value="xcms">
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76 <param name="input_xcms" label="input_xcms" type="data" format="rdata.xcms.fillpeaks" help=": containing grouped feature data for clustering by ramclustR" />
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77 <expand macro="parameters_required" />
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78 <expand macro="parameters_optional_xcms" />
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79 <expand macro="parameters_optional_metadata" />
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80 </when>
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81 <when value="csv">
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82 <expand macro="parameters_csv" />
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83 <expand macro="parameters_required" />
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84 <expand macro="parameters_optional_csv" />
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85 <expand macro="parameters_optional_metadata" />
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86 </when>
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87 </conditional>
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88 </inputs>
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89
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90 <outputs>
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91 <data label="${tool.name} on ${on_string}" name="result" format="RData" />
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92 <data label="Spec Abundance of ${on_string}" name="spec_abundance" format="csv" />
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93 <data label="Metadata for ${tool.name} on ${on_string}" name="method_metadata" format="txt"/>
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94 <expand macro="output_msp"/>
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95 </outputs>
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96
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97 <tests>
1
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98 <test><!-- TEST 1 -->
0
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99 <param name="type_choice" value="xcms"/>
1
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100 <param name="input_xcms" value="test1_xcmsObj_1.rdata.xcms.fillpeaks" ftype="rdata.xcms.fillpeaks"/>
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101 <output name="result" file="test1_ramclustObj_xcms_1.rdata" ftype="RData" compare="sim_size" delta="200"/>
0
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102 <output_collection name="mass_spectra" type="list">
1
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103 <element name="fill" file="test1_fill_xcms_1.msp" ftype="msp"/>
0
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104 </output_collection>
1
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105 <output name="method_metadata" file="test1_metadata_xcms_1.txt" ftype="txt"/>
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106 <output name="spec_abundance" file="test1_spec_abundance_xcms_1.csv" ftype="csv" compare="sim_size" delta="100"/>
0
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107 </test>
1
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108 <test><!-- TEST 2 -->
0
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109 <param name="type_choice" value="xcms"/>
1
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110 <param name="input_xcms" value="test2_xcmsObj_2.rdata.xcms.fillpeaks" ftype="rdata.xcms.fillpeaks"/>
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111 <param name="batch_order_qc" value="test2_sample_metadata_xcms_2.csv" ftype="csv" />
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112 <output name="result" file="test2_ramclustObj_xcms_2.rdata" ftype="RData" compare="sim_size" delta="200"/>
0
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113 <output_collection name="mass_spectra" type="list">
1
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114 <element name="fill" file="test2_fill_xcms_2.msp" ftype="msp" compare="diff" lines_diff="10"/>
0
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115 </output_collection>
1
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116 <output name="method_metadata" file="test2_metadata_xcms_2.txt" ftype="txt"/>
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117 <output name="spec_abundance" file="test2_spec_abundance_xcms_2.csv" ftype="csv" compare="sim_size" delta="100"/>
0
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118 </test>
1
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119 <test><!-- TEST 3 -->
0
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120 <param name="type_choice" value="csv"/>
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121 <param name="ms" value="test3_csv_test-input_1_2.csv" ftype="csv"/>
0
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122 <param name="st" value="5.0"/>
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123 <param name="blocksize" value="1000"/>
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124 <param name="mult" value="1"/>
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125 <param name="maxt" value="1"/>
1
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126 <output name="result" file="test3_ramclustObj_csv_1.rdata" ftype="RData" compare="sim_size" delta="200"/>
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127 <output name="spec_abundance" file="test3_spec_abundance_csv_1.csv" ftype="csv"/>
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128 <output name="method_metadata" file="test3_metadata_csv_1.txt" ftype="txt"/>
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129 <output_collection name="mass_spectra" type="list">
1
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130 <element name="fill" file="test3_spectra_csv_1.msp" ftype="msp"/>
0
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131 </output_collection>
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132 </test>
1
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133 <test><!-- TEST 4 -->
0
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134 <param name="type_choice" value="csv"/>
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135 <param name="ms" value="test3_csv_test-input_1_2.csv" ftype="csv"/>
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136 <param name="batch_order_qc" value="test4_sample_metadata_csv_2.csv" ftype="csv" />
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137 <output name="result" file="test4_ramclustObj_csv_2.rdata" ftype="RData" compare="sim_size" delta="200"/>
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138 <output name="spec_abundance" file="test4_spec_abundance_csv_2.csv" ftype="csv"/>
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139 <output name="method_metadata" file="test4_metadata_csv_2.txt" ftype="txt"/>
0
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140 <output_collection name="mass_spectra" type="list">
1
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141 <element name="fill" file="test4_spectra_csv_2.msp" ftype="msp" lines_diff="10"/>
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142 </output_collection>
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143 </test>
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144 </tests>
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145
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146 <help>
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147 Documentation
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148 For documentation on the tool see https://github.com/cbroeckl/RAMClustR/blob/master/vignettes/RAMClustR.Rmd
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149
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150 Upstream Tools
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151 +-------+----------------------+----------------------+------------+
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152 | Name | Output File | Format | Parameter |
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153 +=======+======================+======================+============+
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154 | xcms | xset.fillPeaks.RData | rdata.xcms.fillpeaks | xcmsObj |
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155 +-------+----------------------+----------------------+------------+
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156
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157 The tool takes an **xcmsSet** object as input and extracts all relevant information.
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158
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159 +-------+------------------------+--------+------------+
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160 | Name | Output File | Format | Parameter |
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161 +=======+========================+========+============+
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162 | ??? | Feature Table with MS1 | csv | ms |
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163 +-------+------------------------+--------+------------+
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164 | ??? | Feature Table with MS2 | csv | idmsms |
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165 +-------+------------------------+--------+------------+
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166
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167 Alternatively, the tool takes a **csv** table as input which has to fulfill the following requirements
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168
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169 (1) no more than one sample (or file) name column and one feature name row;
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170 (2) feature names that contain the mass and retention times, separated by a constant delimiter; and
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171 (3) features in columns and samples in rows.
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172
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173 Downstream Tools
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174 +---------+--------------+----------------------+
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175 | Name | Output File | Format |
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176 +=========+==============+======================+
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177 | matchMS | Mass Spectra | collection (tgz/msp) |
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178 +---------+--------------+----------------------+
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179
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180 @GENERAL_HELP@
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181 </help>
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182
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183 <expand macro="citations" />
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184 </tool>