Mercurial > repos > prog > isa2w4m
comparison 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 : --> | |
2 <tool id="isa2w4m" name="ISA to W4M" version="1.1.1"> | |
3 | |
4 <description>Convert ISA data type into W4M format</description> | |
5 | |
6 <requirements> | |
7 <requirement type="package" version="0.10.3">isatools</requirement> | |
8 </requirements> | |
9 | |
10 <!-- Command {{{1 --> | |
11 | |
12 <command><![CDATA[ | |
13 ## @@@BEGIN_CHEETAH@@@ | |
14 | |
15 $__tool_directory__/isa2w4m.py | |
16 -i "$isa.extra_files_path" | |
17 -s "$w4m_sample_metadata" | |
18 -v "$w4m_variable_metadata" | |
19 -m "$w4m_data_matrix" | |
20 | |
21 ## Choose study to output | |
22 #if $study: | |
23 -n "$study" | |
24 #end if | |
25 | |
26 ## Choose assay to output | |
27 #if $assay: | |
28 -f "$assay" | |
29 #end if | |
30 | |
31 ## Filtering | |
32 #if $sample_na_filtering: | |
33 -S "$sample_na_filtering" | |
34 #end if | |
35 #if $variable_na_filtering: | |
36 -V "$variable_na_filtering" | |
37 #end if | |
38 | |
39 ## @@@END_CHEETAH@@@ | |
40 ]]></command> | |
41 | |
42 <!-- Inputs {{{1 --> | |
43 | |
44 <inputs> | |
45 <param name="isa" label="ISA" type="data" format="isa-tab"/> | |
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."/> | |
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"/> | |
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."/> | |
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."/> | |
50 </inputs> | |
51 | |
52 <!-- Outputs {{{1 --> | |
53 | |
54 <outputs> | |
55 <data name="w4m_variable_metadata" label="${isa.name} W4M var" format="tabular"/> | |
56 <data name="w4m_sample_metadata" label="${isa.name} W4M samp" format="tabular"/> | |
57 <data name="w4m_data_matrix" label="${isa.name} W4M data" format="tabular"/> | |
58 </outputs> | |
59 | |
60 <!-- Tests {{{1 --> | |
61 <tests> | |
62 <test> | |
63 <param name="isa" value="MTBLS30.zip" ftype="isa-tab"/> | |
64 <output name="w4m_variable_metadata" file="MTBLS30-w4m-variable-metadata.tsv"/> | |
65 <output name="w4m_sample_metadata" file="MTBLS30-w4m-sample-metadata.tsv"/> | |
66 <output name="w4m_data_matrix" file="MTBLS30-w4m-sample-variable-matrix.tsv"/> | |
67 </test> | |
68 </tests> | |
69 | |
70 <!-- Help {{{1 --> | |
71 <help> | |
72 <!-- @@@BEGIN_RST@@@ --> | |
73 | |
74 ==================== | |
75 ISA to W4M converter | |
76 ==================== | |
77 | |
78 Converts an ISA-Tab dataset into W4M 3 files format. | |
79 | |
80 ------ | |
81 Inputs | |
82 ------ | |
83 | |
84 ISA dataset | |
85 =========== | |
86 | |
87 The ISA-Tab dataset to convert to W4M format. | |
88 | |
89 Study to extract | |
90 ================ | |
91 | |
92 The file name of the study to extract from the ISA dataset. | |
93 | |
94 Assay to extract | |
95 ================ | |
96 | |
97 The file name of the assay to extract from the ISA dataset chosen study. | |
98 | |
99 Sample NA filtering | |
100 =================== | |
101 | |
102 This is a comma separated list of column names from the sample metadata dataset. | |
103 Rows containg NA values in one or more of the listed columns will be removed from the dataset. | |
104 | |
105 Variable NA filtering | |
106 ===================== | |
107 | |
108 This is a comma separated list of column names from the variable metadata dataset. | |
109 Rows containg NA values in one or more of the listed columns will be removed from the dataset. | |
110 | |
111 ------- | |
112 Outputs | |
113 ------- | |
114 | |
115 The output is a set of 3 datasets: | |
116 | |
117 - Samples metadata. | |
118 - Variables metadata. | |
119 - Samples x variables matrix. | |
120 | |
121 <!-- @@@END_RST@@@ --> | |
122 </help> | |
123 | |
124 <!-- Citations {{{1 --> | |
125 <citations> | |
126 <citation type="doi">10.1038/ng.1054</citation> <!-- ISA --> | |
127 <citation type="doi">10.1093/bioinformatics/btu813</citation> <!-- W4M --> | |
128 </citations> | |
129 | |
130 </tool> |