Mercurial > repos > ppericard > mixomics_blocksplsda

comparison networkVar.xml @ 4:b0ab97ffc2a1 draft

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planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 0bf5c0745f406f2eca9c708a062c975b1f7ea386
author ppericard
date Mon, 09 Mar 2020 11:53:32 -0400
parents 0a3c83f2197a
children bc28839b17fb
comparison
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3:0a3c83f2197a 4:b0ab97ffc2a1
1 <tool id="networkVar" name="networkVar" version="0.2.0" profile="16.04" workflow_compatible="true"> 1 <tool id="networkVar" name="networkVar" version="0.3.0" profile="16.04" workflow_compatible="true">
2 2
3 <description></description> 3 <description>creates a network between selected variables of datasets and the response variables. In the network, the similarity between two variables is associated with the link between these two variables.</description>
4 4
5 <requirements> 5 <requirements>
6 <requirement type="package" version="6.8">bioconductor-mixomics</requirement> 6 <requirement type="package" version="6.8">bioconductor-mixomics</requirement>
7 <requirement type="package" version="1.2">r-igraph</requirement> 7 <requirement type="package" version="1.2">r-igraph</requirement>
8 <requirement type="package" version="2.0">r-argparse</requirement> 8 <requirement type="package" version="2.0">r-argparse</requirement>
9 </requirements> 9 </requirements>
10 10
11 <stdio> 11 <stdio>
12 <!-- <exit_code range="1:" level="fatal" /> --> 12 <!-- <exit_code range="1:" level="fatal" /> -->
13 </stdio> 13 </stdio>
14 14
15 <command detect_errors="aggressive"> 15 <command detect_errors="aggressive">
21 --var_list_file ${var_list_file} 21 --var_list_file ${var_list_file}
22 22
23 #if str($var_of_interest_file) !='': 23 #if str($var_of_interest_file) !='':
24 --interest_var_file ${var_of_interest_file} 24 --interest_var_file ${var_of_interest_file}
25 #end if 25 #end if
26 26
27 --responses_var ${select_responses_var} 27 --responses_var ${select_responses_var}
28 28
29 --output_graph ${output_graph} 29 --output_graph ${output_graph}
30 ]]> 30 ]]>
31 </command> 31 </command>
32 32
33 <inputs> 33 <inputs>
34 <param name="mat_similarity_rdata" type="data" format="rdata" label="Input RData file from computeMatSimilarity"/> 34 <param name="mat_similarity_rdata" type="data" format="rdata"
35 <param name="block_splsda_rdata" type="data" format="rdata" label="Input RData file from block.SPLSDA"/> 35 label="Input computeMatSimilarity RData file"
36 <param name="var_list_file" type="data" format="tabular" label="Variables list file" /> 36 help="output RData file from computeMatSimilarity"/>
37 37 <param name="block_splsda_rdata" type="data" format="rdata"
38 label="Input block.SPLSDA RData file"
39 help="output Rdata file from block.SPLSDA"/>
40 <param name="var_list_file" type="data" format="tabular"
41 label="Variables list file"
42 help="output tabular file from circleCor"/>
43
38 <!-- Fichier avec noms de gènes/variables, donné par l'utilisateur --> 44 <!-- 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)" /> 45 <param name="var_of_interest_file" type="data" format="tabular" optional="true"
46 label="Variables of interest (Optional)"
47 help="these variables have to belong to datasets that can be superimposed"/>
40 48
41 <param name="responses_var_list" type="data" format="tabular" label="List of response variables"/> 49 <param name="responses_var_list" type="data" format="txt"
42 <param name="select_responses_var" type="select" display="checkboxes" multiple="true" label="Response variables"> 50 label="List of response variables"
51 help="list of the response variables that will be in the network"/>
52 <param name="select_responses_var" type="select" display="checkboxes" multiple="true"
53 label="Response variables">
43 <!-- <param name="select_responses_var" type="select" multiple="true" label="Response variables"> --> 54 <!-- <param name="select_responses_var" type="select" multiple="true" label="Response variables"> -->
44 <options from_dataset="responses_var_list"> 55 <options from_dataset="responses_var_list">
45 <column name="value" index="0"/> 56 <column name="value" index="0"/>
46 <filter type="unique_value" column="0"/> 57 <filter type="unique_value" column="0"/>
47 <filter type="sort_by" name="sorted_value" column="0"/> 58 <filter type="sort_by" name="sorted_value" column="0"/>