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annotate ramclustr.xml @ 3:2ec9253a647e draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 8714723083359049eb1a715a946851e07f8a3a20
author recetox
date Tue, 20 Sep 2022 14:43:56 +0000
parents 75dafb766417
children 050cfef6ba65
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2ec9253a647e planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 8714723083359049eb1a715a946851e07f8a3a20
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1 <tool id="ramclustr" name="RAMClustR" version="@TOOL_VERSION@+galaxy2">
2
75dafb766417 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c321421a07bfdcc9ed423e9ed2ee794157984ba1
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2 <description>A feature clustering algorithm for non-targeted mass spectrometric metabolomics data.</description>
0
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="creator"/>
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7
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8 <requirements>
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9 <requirement type="package" version="@TOOL_VERSION@">r-ramclustr</requirement>
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10 <requirement type="package" version="3.14.0">bioconductor-xcms</requirement>
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11 </requirements>
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12
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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13 <command detect_errors="aggressive"><![CDATA[
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14 Rscript
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15 -e 'source("${__tool_directory__}/ramclustr_wrapper.R")'
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16 -e 'source("${ramclustr_method}")'
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17 ]]>
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18 </command>
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19 <configfiles>
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20 <configfile name="ramclustr_method">
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21 store_output(
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22 #if $filetype.type_choice == "xcms":
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23 ramclustr_xcms(
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24 input_xcms = "$filetype.xcms.input_xcms",
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25 use_pheno = $filetype.xcms.usePheno,
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26 #else:
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27 ramclustr_csv(
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28 ms = "$filetype.ms_csv.ms",
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29 idmsms = "$filetype.ms_csv.idmsms",
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30 #end if
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31 sr = $filetype.required.sr,
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32 #if $filetype.type_choice == "xcms":
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33 #if $filetype.required.st
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34 st = $filetype.required.st,
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35 #end if
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36 #else:
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37 st = $filetype.required.st,
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38 #end if
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39 cor_method = "$filetype.required.cor_method",
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40 maxt = $filetype.required.maxt,
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41 linkage = "$clustering.linkage",
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42 min_module_size = $clustering.minModuleSize,
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43 hmax = $clustering.hmax,
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44 deep_split = "$clustering.deepSplit",
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45 normalize = "$normalisation.normalisation_method.normalize",
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46 #if "$normalisation.normalisation_method.normalize" == "batch.qc":
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47 metadata_file = "$normalisation.normalisation_method.batch_order_qc",
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48 qc_inj_range = $normalisation.normalisation_method.qc_inj_range,
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49 #end if
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50 block_size = $performance.blocksize,
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51 mult = $performance.mult,
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52 mzdec = $msp_output_details.mzdec,
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53 rt_only_low_n = $extras.rt_only_low_n,
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54 replace_zeros = $extras.replace_zeros,
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55 #if $extras.ExpDes:
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56 exp_design = "${$extras.ExpDes}"
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57 #end if
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58 ),
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59 $msp_output_details.merge_msp,
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60 "$spec_abundance",
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61 #if $msp_output_details.merge_msp:
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62 "$mass_spectra_merged"
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63 #else:
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64 NULL
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65 #end if
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66 )
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67 </configfile>
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68 </configfiles>
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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 <expand macro="parameters_xcms" />
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77 <section name="required" title="General parameters" expanded="true">
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78 <param label="Sigma t" name="st" type="float" optional="true" help="Retention time similarity (optional).
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79 A recommended starting point is half the value of your average chromatographic peak width at half max (seconds))."/>
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80 <expand macro="parameters_required" />
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81 </section>
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82 </when>
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83 <when value="csv">
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84 <expand macro="parameters_csv" />
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85 <section name="required" title="General parameters" expanded="true">
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86 <param label="Sigma t" name="st" type="float" value="1" help="Retention time similarity.
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87 A recommended starting point is half the value of your average chromatographic peak width at half max (seconds))."/>
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88 <expand macro="parameters_required" />
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89 </section>
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90 </when>
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91 </conditional>
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92 <expand macro="main_parameters" />
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93 </inputs>
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94
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95 <outputs>
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96 <data label="Spec Abundance of ${on_string}" name="spec_abundance" format="csv" />
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97 <expand macro="output_msp"/>
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98 </outputs>
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99
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100 <tests>
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101 <test><!-- TEST 1 -->
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102 <section name="filetype">
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103 <param name="type_choice" value="xcms"/>
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104 <section name="xcms">
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105 <param name="input_xcms" value="test1_xcmsObj_1.rdata.xcms.fillpeaks" ftype="rdata.xcms.fillpeaks"/>
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106 </section>
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107 <section name="required">
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108 <param name="maxt" value="259.8"/>
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109 </section>
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110 </section>
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111 <section name="extras">
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112 <param name="ExpDes" value="lc-ramclustr-define-experiment.csv" ftype="csv"/>
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113 </section>
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114 <output name="mass_spectra_merged" file="test1_fill_xcms_1.msp" ftype="msp"/>
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115 <output name="spec_abundance" file="test1_spec_abundance_xcms_1.csv" ftype="csv" compare="sim_size" delta="100"/>
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116 </test>
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117 <test><!-- TEST 2 -->
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118 <section name="filetype">
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119 <param name="type_choice" value="xcms"/>
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120 <section name="xcms">
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121 <param name="input_xcms" value="test2_xcmsObj_2.rdata.xcms.fillpeaks" ftype="rdata.xcms.fillpeaks"/>
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122 </section>
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123 <section name="required">
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124 <param name="maxt" value="78.4"/>
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125 </section>
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126 </section>
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127 <section name="normalisation">
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128 <section name="normalisation_method">
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129 <param name="batch_order_qc" value="test2_sample_metadata_xcms_2.csv" ftype="csv" />
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130 </section>
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131 </section>
3
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132 <output name="mass_spectra_merged" file="test2_fill_xcms_2.msp" ftype="msp" compare="diff" lines_diff="20"/>
0
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133 <output name="spec_abundance" file="test2_spec_abundance_xcms_2.csv" ftype="csv" compare="sim_size" delta="100"/>
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134 </test>
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135 <test><!-- TEST 3 -->
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136 <section name="filetype">
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137 <param name="type_choice" value="csv"/>
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138 <section name="ms_csv">
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139 <param name="ms" value="test3_csv_test-input_1_2.csv" ftype="csv"/>
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140 </section>
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141 <section name="required">
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142 <param name="st" value="5.0"/>
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143 <param name="maxt" value="1"/>
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144 </section>
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145 </section>
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146 <section name="performance">
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147 <param name="blocksize" value="1000"/>
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148 <param name="mult" value="1"/>
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149 </section>
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150 <output name="mass_spectra_merged" file="test3_spectra_csv_1.msp" ftype="msp"/>
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151 <output name="spec_abundance" file="test3_spec_abundance_csv_1.csv" ftype="csv"/>
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152 </test>
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153 <test><!-- TEST 4 -->
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154 <section name="filetype">
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155 <param name="type_choice" value="csv"/>
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156 <section name="ms_csv">
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157 <param name="ms" value="test3_csv_test-input_1_2.csv" ftype="csv"/>
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158 </section>
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159 </section>
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160 <output name="mass_spectra_merged" file="test4_spectra_csv_2.msp" ftype="msp" lines_diff="10"/>
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161 </test>
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162 </tests>
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163
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164 <help>
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165 <![CDATA[
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166 @HELP@
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167
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168 .. rubric:: **Footnotes**
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169 .. [1] Correlation, Variance and Covariance - `stats::cor <https://www.rdocumentation.org/packages/stats/versions/3.6.2/topics/cor>`_
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170 .. [2] Hierarchical Clustering - `stats::hclust <https://www.rdocumentation.org/packages/stats/versions/3.6.2/topics/hclust>`_
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171 .. [3] Dynamic Dendrogram Pruning Based on Dendrogram Only - `dynamicTreeCut::cutreeDynamicTree <https://www.rdocumentation.org/packages/dynamicTreeCut/versions/1.63-1/topics/cutreeDynamicTree>`_
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172 ]]>
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173 </help>
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174
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175 <expand macro="citations" />
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176 </tool>