Mercurial > repos > prog > isa2w4m
comparison 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 |
parents | 1883d5274962 |
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0:1883d5274962 | 1:1facef3ba64a |
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1 <!-- vi: se fdm=marker : --> | 1 <!-- vi: se fdm=marker : --> |
2 <tool id="isa2w4m" name="ISA to W4M" version="1.1.1"> | 2 <tool id="isa2w4m" name="ISA to W4M" version="1.1.3"> |
3 | 3 |
4 <description>Convert ISA data type into W4M format</description> | 4 <description>Convert ISA data type into W4M format</description> |
5 | 5 |
6 <requirements> | 6 <requirements> |
7 <requirement type="package" version="0.10.3">isatools</requirement> | 7 <requirement type="package" version="1.2.5">pandas</requirement> |
8 <requirement type="package" version="0.12.2">isatools</requirement> | |
8 </requirements> | 9 </requirements> |
9 | 10 |
10 <!-- Command {{{1 --> | 11 <!-- Command {{{1 --> |
11 | 12 |
12 <command><![CDATA[ | 13 <command><![CDATA[ |
13 ## @@@BEGIN_CHEETAH@@@ | 14 ## @@@BEGIN_CHEETAH@@@ |
14 | 15 |
15 $__tool_directory__/isa2w4m.py | 16 $__tool_directory__/isa2w4m.py |
16 -i "$isa.extra_files_path" | 17 -i '$isa.extra_files_path' |
17 -s "$w4m_sample_metadata" | 18 -s '$w4m_sample_metadata' |
18 -v "$w4m_variable_metadata" | 19 -v '$w4m_variable_metadata' |
19 -m "$w4m_data_matrix" | 20 -m '$w4m_data_matrix' |
20 | 21 |
21 ## Choose study to output | 22 ## Choose study to output |
22 #if $study: | 23 #if $study: |
23 -n "$study" | 24 -n '$study' |
24 #end if | 25 #end if |
25 | 26 |
26 ## Choose assay to output | 27 ## Choose assay to output |
27 #if $assay: | 28 #if $assay: |
28 -f "$assay" | 29 -f '$assay' |
29 #end if | 30 #end if |
30 | 31 |
31 ## Filtering | 32 ## Filtering |
32 #if $sample_na_filtering: | 33 #if $sample_na_filtering: |
33 -S "$sample_na_filtering" | 34 -S '$sample_na_filtering' |
34 #end if | 35 #end if |
35 #if $variable_na_filtering: | 36 #if $variable_na_filtering: |
36 -V "$variable_na_filtering" | 37 -V '$variable_na_filtering' |
37 #end if | 38 #end if |
39 | |
40 ## Redirect stderr to stdout otherwise Galaxy thinks the tool fails if | |
41 ## it sees just one character on stderr. | |
42 2>&1 | |
38 | 43 |
39 ## @@@END_CHEETAH@@@ | 44 ## @@@END_CHEETAH@@@ |
40 ]]></command> | 45 ]]></command> |
41 | 46 |
42 <!-- Inputs {{{1 --> | 47 <!-- Inputs {{{1 --> |
62 <test> | 67 <test> |
63 <param name="isa" value="MTBLS30.zip" ftype="isa-tab"/> | 68 <param name="isa" value="MTBLS30.zip" ftype="isa-tab"/> |
64 <output name="w4m_variable_metadata" file="MTBLS30-w4m-variable-metadata.tsv"/> | 69 <output name="w4m_variable_metadata" file="MTBLS30-w4m-variable-metadata.tsv"/> |
65 <output name="w4m_sample_metadata" file="MTBLS30-w4m-sample-metadata.tsv"/> | 70 <output name="w4m_sample_metadata" file="MTBLS30-w4m-sample-metadata.tsv"/> |
66 <output name="w4m_data_matrix" file="MTBLS30-w4m-sample-variable-matrix.tsv"/> | 71 <output name="w4m_data_matrix" file="MTBLS30-w4m-sample-variable-matrix.tsv"/> |
72 </test> | |
73 <test> | |
74 <param name="isa" value="MTBLS174.zip" ftype="isa-tab"/> | |
75 <output name="w4m_variable_metadata" file="MTBLS174-w4m-variable-metadata.tsv"/> | |
76 <output name="w4m_sample_metadata" file="MTBLS174-w4m-sample-metadata.tsv"/> | |
77 <output name="w4m_data_matrix" file="MTBLS174-w4m-sample-variable-matrix.tsv"/> | |
67 </test> | 78 </test> |
68 </tests> | 79 </tests> |
69 | 80 |
70 <!-- Help {{{1 --> | 81 <!-- Help {{{1 --> |
71 <help> | 82 <help> |