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"planemo upload commit 0f9b7614c566b65a022efcc1cdab4a8cdb452a82-dirty"
author prog
date Tue, 26 Apr 2022 09:33:16 +0000
parents e91327d6e034
children
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1 <!-- vi: se fdm=marker : -->
1
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2 <tool id="isa2w4m" name="ISA to W4M" version="1.1.3">
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3
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4 <description>Convert ISA data type into W4M format</description>
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5
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6 <requirements>
1
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7 <requirement type="package" version="1.2.5">pandas</requirement>
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8 <requirement type="package" version="0.12.2">isatools</requirement>
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9 </requirements>
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10
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11 <!-- Command {{{1 -->
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12
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13 <command><![CDATA[
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14 ## @@@BEGIN_CHEETAH@@@
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15
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16 $__tool_directory__/isa2w4m.py
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17 -i '$isa.extra_files_path'
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18 -s '$w4m_sample_metadata'
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19 -v '$w4m_variable_metadata'
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20 -m '$w4m_data_matrix'
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21
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22 ## Choose study to output
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23 #if $study:
1
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24 -n '$study'
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25 #end if
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26
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27 ## Choose assay to output
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28 #if $assay:
1
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29 -f '$assay'
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30 #end if
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31
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32 ## Filtering
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33 #if $sample_na_filtering:
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34 -S '$sample_na_filtering'
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35 #end if
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36 #if $variable_na_filtering:
1
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37 -V '$variable_na_filtering'
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38 #end if
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39
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40 ## Redirect stderr to stdout otherwise Galaxy thinks the tool fails if
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41 ## it sees just one character on stderr.
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42 2>&1
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43
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44 ## @@@END_CHEETAH@@@
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45 ]]></command>
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46
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47 <!-- Inputs {{{1 -->
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48
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49 <inputs>
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50 <param name="isa" label="ISA" type="data" format="isa-tab"/>
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51 <param name="study" type="text" size="256" value="" help="Type here the name of the assay file you want to extract from the ISA archive. If unset, the first listed study will be used."/>
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52 <param name="assay" type="text" size="256" value="" help="Type here the name of the study file you want to extract from the ISA archive. If unset, the first listed assay in the study will be used"/>
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53 <param name="sample_na_filtering" type="text" label="Sample metadata columns NA filtering" help="The rows that contain NA value in the specified columns will be filtered out. Column names must be separated by commas."/>
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54 <param name="variable_na_filtering" type="text" label="Variable metadata columns NA filtering" help="The rows that contain NA value in the specified columns will be filtered out. Column names must be separated by commas."/>
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55 </inputs>
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56
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57 <!-- Outputs {{{1 -->
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58
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59 <outputs>
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60 <data name="w4m_variable_metadata" label="${isa.name} W4M var" format="tabular"/>
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61 <data name="w4m_sample_metadata" label="${isa.name} W4M samp" format="tabular"/>
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62 <data name="w4m_data_matrix" label="${isa.name} W4M data" format="tabular"/>
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63 </outputs>
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64
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65 <!-- Tests {{{1 -->
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66 <tests>
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67 <test>
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68 <param name="isa" value="MTBLS30.zip" ftype="isa-tab"/>
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69 <output name="w4m_variable_metadata" file="MTBLS30-w4m-variable-metadata.tsv"/>
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70 <output name="w4m_sample_metadata" file="MTBLS30-w4m-sample-metadata.tsv"/>
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71 <output name="w4m_data_matrix" file="MTBLS30-w4m-sample-variable-matrix.tsv"/>
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72 </test>
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73 <test>
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74 <param name="isa" value="MTBLS174.zip" ftype="isa-tab"/>
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75 <output name="w4m_variable_metadata" file="MTBLS174-w4m-variable-metadata.tsv"/>
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76 <output name="w4m_sample_metadata" file="MTBLS174-w4m-sample-metadata.tsv"/>
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77 <output name="w4m_data_matrix" file="MTBLS174-w4m-sample-variable-matrix.tsv"/>
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78 </test>
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79 </tests>
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80
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81 <!-- Help {{{1 -->
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82 <help>
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83 <!-- @@@BEGIN_RST@@@ -->
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84
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85 ====================
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86 ISA to W4M converter
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87 ====================
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88
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89 Converts an ISA-Tab dataset into W4M 3 files format.
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90
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91 ------
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92 Inputs
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93 ------
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94
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95 ISA dataset
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96 ===========
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97
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98 The ISA-Tab dataset to convert to W4M format.
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99
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100 Study to extract
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101 ================
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102
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103 The file name of the study to extract from the ISA dataset.
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104
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105 Assay to extract
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106 ================
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107
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108 The file name of the assay to extract from the ISA dataset chosen study.
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109
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110 Sample NA filtering
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111 ===================
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112
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113 This is a comma separated list of column names from the sample metadata dataset.
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114 Rows containg NA values in one or more of the listed columns will be removed from the dataset.
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115
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116 Variable NA filtering
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117 =====================
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118
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119 This is a comma separated list of column names from the variable metadata dataset.
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120 Rows containg NA values in one or more of the listed columns will be removed from the dataset.
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121
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122 -------
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123 Outputs
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124 -------
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125
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126 The output is a set of 3 datasets:
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127
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128 - Samples metadata.
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129 - Variables metadata.
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130 - Samples x variables matrix.
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131
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132 <!-- @@@END_RST@@@ -->
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133 </help>
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134
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135 <!-- Citations {{{1 -->
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136 <citations>
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137 <citation type="doi">10.1038/ng.1054</citation> <!-- ISA -->
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138 <citation type="doi">10.1093/bioinformatics/btu813</citation> <!-- W4M -->
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139 </citations>
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140
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141 </tool>