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comparison isa2w4m.xml @ 1:1facef3ba64a draft default tip

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"planemo upload commit 9683b1655539660ed1e983783a72a5c3016238bd-dirty"
author prog
date Wed, 27 Apr 2022 16:38:56 +0000
parents 1883d5274962
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0:1883d5274962 1:1facef3ba64a
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>