Mercurial > repos > prog > isa2w4m
annotate isa2w4m.xml @ 1:1facef3ba64a draft default tip
"planemo upload commit 9683b1655539660ed1e983783a72a5c3016238bd-dirty"
author | prog |
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date | Wed, 27 Apr 2022 16:38:56 +0000 |
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1 <!-- vi: se fdm=marker : --> |
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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> |
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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 $study: |
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24 -n '$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 $assay: |
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29 -f '$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 $variable_na_filtering: |
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37 -V '$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> |