Mercurial > repos > recetox > ramclustr_csv

annotate ramclustr_csv.xml @ 3:61035548f46c draft default tip

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3479dea72f19e42832d30cda4283e56e81dd96d5"
author recetox
date Mon, 07 Jun 2021 15:13:41 +0000
parents 08b09930cd73
children
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1 <tool id="ramclustr_csv" name="RAMClustR (CSV)" version="@TOOL_VERSION@+galaxy1">
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2 <macros>
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3 <import>ramclustr_macros.xml</import>
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4 </macros>
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6 <requirements>
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7 <container type="docker">recetox/ramclustr:1.1.0-recetox0</container>
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8 </requirements>
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10 <inputs>
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11 <expand macro="parameters_csv" />
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12 <expand macro="parameters_required" />
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13 <expand macro="parameters_optional_csv" />
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14 <expand macro="parameters_optional_metadata" />
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15 </inputs>
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17 <command detect_errors="aggressive"><![CDATA[
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18 Rscript
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19 -e 'source("${__tool_directory__}/ramclustr_wrapper.R")'
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20 -e 'x <- ramclustr_csv(
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21 ms="$ms_csv.ms",
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22 idmsms="$ms_csv.idmsms",
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23 feature_delimiter="$ms_csv.feature_delimiter",
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24 sample_name_column = $ms_csv.sample_name_column,
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25 retention_time_column= $ms_csv.retention_time_column,
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26 sr = $required.sr,
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27 deep_split = $required.deepSplit,
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28 block_size = $required.blocksize,
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29 mult = $required.mult,
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30 hmax = $required.hmax,
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31 collapse = $required.collapse,
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32 use_pheno = $required.usePheno,
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33 qc_inj_range = $required.qc_inj_range,
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34 normalize = "$required.normalize",
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35 min_module_size = $required.minModuleSize,
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36 linkage = "$required.linkage",
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37 mzdec = $required.mzdec,
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38 cor_method = "$required.cor_method",
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39 rt_only_low_n = $required.rt_only_low_n,
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40 replace_zeros = $required.replace_zeros,
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41 st = $ms_csv.st,
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42 #if $optional.maxt
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43 maxt = $optional.maxt,
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44 #end if
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45 #if $optional.fftempdir
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46 fftempdir = $optional.fftempdir,
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47 #end if
3
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48 #if $metadata.batch_order_qc
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49 metadata = "$metadata.batch_order_qc"
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50 #end if
0
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51 )'
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52 -e 'store_output(x, "$result", "$method_metadata", $required.merge_msp, "$spec_abundance")'
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53
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54 ]]>
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55 </command>
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56
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57 <outputs>
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58 <data label="${tool.name} on ${on_string}" name="result" format="RData" />
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59 <data label="Spec Abundance of ${on_string}" name="spec_abundance" format="csv" />
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60 <data label="Metadata for ${tool.name} on ${on_string}" name="method_metadata" format="txt"/>
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61 <expand macro="output_msp"/>
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62 </outputs>
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63
2
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64 <tests>
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65 <test>
3
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66 <param name="ms" value="csv_test-input_1_2.csv" ftype="csv"/>
2
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67 <param name="sample_name_column" value="1"/>
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68 <param name="feature_delimiter" value="_"/>
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69 <param name="retention_time_column" value="2"/>
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70 <param name="st" value="5.0"/>
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71 <param name="sr" value="0.5"/>
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72 <param name="deepSplit" value="False"/>
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73 <param name="blocksize" value="1000"/>
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74 <param name="mult" value="1"/>
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75 <param name="hmax" value="0.3"/>
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76 <param name="collapse" value="True"/>
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77 <param name="usePheno" value="True"/>
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78 <param name="normalize" value="none"/>
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79 <param name="qc_inj_range" value="20"/>
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80 <param name="minModuleSize" value="2"/>
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81 <param name="linkage" value="average"/>
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82 <param name="mzdec" value="3"/>
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83 <param name="cor_method" value="pearson"/>
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84 <param name="rt_only_low_n" value="True"/>
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85 <param name="replace_zeros" value="True"/>
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86 <param name="Merge MSP Files" value="True"/>
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87 <param name="maxt" value="1"/>
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88 <output name="result" file="ramclustObj_csv_1.rdata"/>
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89 <output name="spec_abundance" file="spec_abundance_csv_1.csv" ftype="csv"/>
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90 <output name="method_metadata" file="metadata_csv_1.txt" ftype="txt"/>
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91 <output_collection name="mass_spectra" type="list">
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92 <element name="fill" file="spectra_csv_1.msp" ftype="msp"/>
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93 </output_collection>
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94 </test>
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95 <test>
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96 <param name="ms" value="csv_test-input_1_2.csv" ftype="csv"/>
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97 <param name="sample_name_column" value="1"/>
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98 <param name="feature_delimiter" value="_"/>
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99 <param name="retention_time_column" value="2"/>
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100 <param name="batch_order_qc" value="sample_metadata_csv_2.csv" ftype="csv" />
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101 <output name="result" file="ramclustObj_csv_2.rdata"/>
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102 <output name="spec_abundance" file="spec_abundance_csv_2.csv" ftype="csv"/>
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103 <output name="method_metadata" file="metadata_csv_2.txt" ftype="txt"/>
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104 <output_collection name="mass_spectra" type="list">
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105 <element name="fill" file="spectra_csv_2.msp" ftype="msp" lines_diff="10"/>
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106 </output_collection>
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107 </test>
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108 </tests>
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109
0
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110 <help>
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111 Documentation
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112 For documentation on the tool see https://github.com/cbroeckl/RAMClustR/blob/master/vignettes/RAMClustR.Rmd
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113
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114 Upstream Tools
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115 +-------+------------------------+--------+------------+
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116 | Name | Output File | Format | Parameter |
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117 +=======+========================+========+============+
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118 | ??? | Feature Table with MS1 | csv | ms |
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119 +-------+------------------------+--------+------------+
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120 | ??? | Feature Table with MS2 | csv | idmsms |
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121 +-------+------------------------+--------+------------+
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122
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123 The tool takes a **csv** table as input which has to fulfill the following requirements
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124
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125 (1) no more than one sample (or file) name column and one feature name row;
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126 (2) feature names that contain the mass and retention times, separated by a constant delimiter; and
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127 (3) features in columns and samples in rows.
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128
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129 Downstream Tools
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130 +---------+--------------+----------------------+
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131 | Name | Output File | Format |
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132 +=========+==============+======================+
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133 | matchMS | Mass Spectra | collection (tgz/msp) |
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134 +---------+--------------+----------------------+
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135
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136 @GENERAL_HELP@
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137 </help>
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138
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139 <expand macro="citations" />
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140 </tool>