Mercurial > repos > ppericard > mixomics_blocksplsda

comparison networkVar.xml @ 3:0a3c83f2197a draft

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planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
author ppericard
date Fri, 25 Oct 2019 07:10:59 -0400
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children b0ab97ffc2a1
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2:655d1fbcd3e6 3:0a3c83f2197a
1 <tool id="networkVar" name="networkVar" version="0.2.0" profile="16.04" workflow_compatible="true">
2
3 <description></description>
4
5 <requirements>
6 <requirement type="package" version="6.8">bioconductor-mixomics</requirement>
7 <requirement type="package" version="1.2">r-igraph</requirement>
8 <requirement type="package" version="2.0">r-argparse</requirement>
9 </requirements>
10
11 <stdio>
12 <!-- <exit_code range="1:" level="fatal" /> -->
13 </stdio>
14
15 <command detect_errors="aggressive">
16 <![CDATA[
17 Rscript
18 ${__tool_directory__}/networkVar_wrapper.R
19 --mat_similarity_rdata ${mat_similarity_rdata}
20 --block_splsda_rdata ${block_splsda_rdata}
21 --var_list_file ${var_list_file}
22
23 #if str($var_of_interest_file) !='':
24 --interest_var_file ${var_of_interest_file}
25 #end if
26
27 --responses_var ${select_responses_var}
28
29 --output_graph ${output_graph}
30 ]]>
31 </command>
32
33 <inputs>
34 <param name="mat_similarity_rdata" type="data" format="rdata" label="Input RData file from computeMatSimilarity"/>
35 <param name="block_splsda_rdata" type="data" format="rdata" label="Input RData file from block.SPLSDA"/>
36 <param name="var_list_file" type="data" format="tabular" label="Variables list file" />
37
38 <!-- Fichier avec noms de gènes/variables, donné par l'utilisateur -->
39 <param name="var_of_interest_file" type="data" format="tabular" optional="true" label="Variables of interest (Optional)" />
40
41 <param name="responses_var_list" type="data" format="tabular" label="List of response variables"/>
42 <param name="select_responses_var" type="select" display="checkboxes" multiple="true" label="Response variables">
43 <!-- <param name="select_responses_var" type="select" multiple="true" label="Response variables"> -->
44 <options from_dataset="responses_var_list">
45 <column name="value" index="0"/>
46 <filter type="unique_value" column="0"/>
47 <filter type="sort_by" name="sorted_value" column="0"/>
48 </options>
49 </param>
50 </inputs>
51
52 <outputs>
53 <data name="output_graph" format="xml" label="${tool.name}_graph.graphml" />
54 </outputs>
55
56 <tests>
57 </tests>
58
59 <help>
60 </help>
61
62 </tool>