Mercurial > repos > prog > isa2w4m
annotate isa2w4m.xml @ 0:1883d5274962 draft
"planemo upload commit 8feeae9c62e2026c018e970bb2252e75e1433058"
author | prog |
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date | Wed, 08 Jan 2020 09:56:00 -0500 |
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children | 1facef3ba64a |
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1 <!-- vi: se fdm=marker : --> |
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2 <tool id="isa2w4m" name="ISA to W4M" version="1.1.1"> |
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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="0.10.3">isatools</requirement> |
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8 </requirements> |
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9 |
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10 <!-- Command {{{1 --> |
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11 |
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12 <command><![CDATA[ |
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13 ## @@@BEGIN_CHEETAH@@@ |
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14 |
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15 $__tool_directory__/isa2w4m.py |
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16 -i "$isa.extra_files_path" |
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17 -s "$w4m_sample_metadata" |
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18 -v "$w4m_variable_metadata" |
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19 -m "$w4m_data_matrix" |
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20 |
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21 ## Choose study to output |
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22 #if $study: |
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23 -n "$study" |
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24 #end if |
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25 |
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26 ## Choose assay to output |
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27 #if $assay: |
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28 -f "$assay" |
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29 #end if |
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30 |
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31 ## Filtering |
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32 #if $sample_na_filtering: |
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33 -S "$sample_na_filtering" |
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34 #end if |
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35 #if $variable_na_filtering: |
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36 -V "$variable_na_filtering" |
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37 #end if |
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38 |
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39 ## @@@END_CHEETAH@@@ |
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40 ]]></command> |
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41 |
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42 <!-- Inputs {{{1 --> |
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43 |
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44 <inputs> |
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45 <param name="isa" label="ISA" type="data" format="isa-tab"/> |
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46 <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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47 <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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48 <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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49 <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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50 </inputs> |
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51 |
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52 <!-- Outputs {{{1 --> |
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53 |
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54 <outputs> |
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55 <data name="w4m_variable_metadata" label="${isa.name} W4M var" format="tabular"/> |
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56 <data name="w4m_sample_metadata" label="${isa.name} W4M samp" format="tabular"/> |
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57 <data name="w4m_data_matrix" label="${isa.name} W4M data" format="tabular"/> |
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58 </outputs> |
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59 |
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60 <!-- Tests {{{1 --> |
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61 <tests> |
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62 <test> |
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63 <param name="isa" value="MTBLS30.zip" ftype="isa-tab"/> |
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64 <output name="w4m_variable_metadata" file="MTBLS30-w4m-variable-metadata.tsv"/> |
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65 <output name="w4m_sample_metadata" file="MTBLS30-w4m-sample-metadata.tsv"/> |
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66 <output name="w4m_data_matrix" file="MTBLS30-w4m-sample-variable-matrix.tsv"/> |
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67 </test> |
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68 </tests> |
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69 |
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70 <!-- Help {{{1 --> |
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71 <help> |
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72 <!-- @@@BEGIN_RST@@@ --> |
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73 |
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74 ==================== |
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75 ISA to W4M converter |
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76 ==================== |
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77 |
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78 Converts an ISA-Tab dataset into W4M 3 files format. |
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79 |
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80 ------ |
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81 Inputs |
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82 ------ |
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83 |
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84 ISA dataset |
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85 =========== |
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86 |
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87 The ISA-Tab dataset to convert to W4M format. |
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88 |
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89 Study to extract |
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90 ================ |
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91 |
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92 The file name of the study to extract from the ISA dataset. |
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93 |
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94 Assay to extract |
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95 ================ |
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96 |
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97 The file name of the assay to extract from the ISA dataset chosen study. |
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98 |
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99 Sample NA filtering |
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100 =================== |
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101 |
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102 This is a comma separated list of column names from the sample metadata dataset. |
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103 Rows containg NA values in one or more of the listed columns will be removed from the dataset. |
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104 |
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105 Variable NA filtering |
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106 ===================== |
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107 |
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108 This is a comma separated list of column names from the variable metadata dataset. |
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109 Rows containg NA values in one or more of the listed columns will be removed from the dataset. |
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110 |
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111 ------- |
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112 Outputs |
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113 ------- |
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114 |
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115 The output is a set of 3 datasets: |
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116 |
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117 - Samples metadata. |
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118 - Variables metadata. |
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119 - Samples x variables matrix. |
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120 |
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121 <!-- @@@END_RST@@@ --> |
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122 </help> |
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123 |
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124 <!-- Citations {{{1 --> |
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125 <citations> |
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126 <citation type="doi">10.1038/ng.1054</citation> <!-- ISA --> |
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127 <citation type="doi">10.1093/bioinformatics/btu813</citation> <!-- W4M --> |
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128 </citations> |
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129 |
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130 </tool> |