Mercurial > repos > ppericard > viscorvar

comparison viscorvar_networkvar.xml @ 5:88c1fd2ac110 draft default tip

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"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 21d09ff286a496ff475f32626d88dd42423ae663"
author ppericard
date Tue, 07 Sep 2021 10:40:08 +0000
parents d4e9f7546dfa
children
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4:d4e9f7546dfa 5:88c1fd2ac110
18 --var_list_file ${var_list_file} 18 --var_list_file ${var_list_file}
19 --response_var ${select_response_var} 19 --response_var ${select_response_var}
20 20
21 --output_graph ${output_graph} 21 --output_graph ${output_graph}
22 22
23 @COMMAND_LOG_EXIT@ 23 ]]></command>
24 24
25 ]]></command>
26
27 <inputs> 25 <inputs>
28 <param name="mat_similarity_rdata" type="data" format="rdata" 26 <param name="mat_similarity_rdata" type="data" format="rdata"
29 label="this is the RData output file from the computeMatSimilarity function" 27 label="this is the RData output file from the computeMatSimilarity function"
30 help="output RData file from computeMatSimilarity"/> 28 help="output RData file from the computeMatSimilarity function"/>
31 <param name="var_list_file" type="data" format="tabular" 29 <param name="var_list_file" type="data" format="tabular"
32 label="Variables list file" 30 label="Variables list file"
33 help="selected variables output tabular file from circleCor"/> 31 help="selected variables output tabular file from the circleCor function"/>
34 32
35 <!-- Fichier avec noms de gènes/variables, donné par l'utilisateur --> 33 <!-- Fichier avec noms de gènes/variables, donné par l'utilisateur -->
36 <!-- <param name="var_of_interest_file" type="data" format="txt" optional="true" 34 <!-- <param name="var_of_interest_file" type="data" format="txt" optional="true"
37 label="Variables of interest (Optional)" 35 label="Variables of interest (Optional)"
38 help="these variables have to belong to datasets that can be superimposed"/> --> 36 help="these variables have to belong to datasets that can be superimposed"/> -->
39 37
40 <param name="response_var_list" type="data" format="tabular" 38 <param name="response_var_list" type="data" format="tabular"
41 label="List of response variables" 39 label="List of response variables"
42 help="output *_response_var.tsv file from matCorAddVar"/> 40 help="output *_response_var.tsv file from the matCorAddVar function"/>
43 <param name="select_response_var" type="select" display="checkboxes" multiple="true" 41 <param name="select_response_var" type="select" display="checkboxes" multiple="true"
44 label="Response variables" 42 label="Response variables"
45 help="response variables that will be plotted in the network"> 43 help="response variables that will be plotted in the network">
46 <!-- <param name="select_responses_var" type="select" multiple="true" label="Response variables"> --> 44 <!-- <param name="select_responses_var" type="select" multiple="true" label="Response variables"> -->
47 <options from_dataset="response_var_list"> 45 <options from_dataset="response_var_list">
70 ----------- 68 -----------
71 Description 69 Description
72 ----------- 70 -----------
73 71
74 This tool creates a network of correlated variables for omics datasets. The determination of 72 This tool creates a network of correlated variables for omics datasets. The determination of
75 the omics datasets which can be visualized is made by the tool matCorAddVar. This network can 73 the omics datasets which can be visualized is made by the matCorAddVar tool. This network can
76 be exported to graphml format and visualized with Cytoscape. The link between two variables 74 be exported to graphml format and visualized with Cytoscape. The link between two variables
77 is associated with the correlation between two variables : a threshold can be used in 75 is associated with the correlation between two variables : a threshold can be used in
78 Cytoscape to get a network of variables whose correlation is greater than this threshold 76 Cytoscape to get a network of variables whose correlations are greater than this threshold
79 in absolute value. 77 in absolute value.
80 78
81 ----------------- 79 -----------------
82 Workflow position 80 Workflow position
83 ----------------- 81 -----------------
103 +-----------------------------------------------------------+-----------+ 101 +-----------------------------------------------------------+-----------+
104 | Parameter : num + label | Format | 102 | Parameter : num + label | Format |
105 +===========================================================+===========+ 103 +===========================================================+===========+
106 | 1 : Rdata visCorVar.computeMatSimilarity output | rdata | 104 | 1 : Rdata visCorVar.computeMatSimilarity output | rdata |
107 +-----------------------------------------------------------+-----------+ 105 +-----------------------------------------------------------+-----------+
108 | 2 : ``*``_selected_var.tsv visCorVar.circleCor output | tabular | 106 | 2 : \*_selected_var.tsv visCorVar.circleCor output | tabular |
109 +-----------------------------------------------------------+-----------+ 107 +-----------------------------------------------------------+-----------+
110 | 3 : ``*``_response_var.tsv visCorVar.matCorAddVar output | tabular | 108 | 3 : \*_response_var.tsv visCorVar.matCorAddVar output | tabular |
111 +-----------------------------------------------------------+-----------+ 109 +-----------------------------------------------------------+-----------+
112 110
113 ---------- 111 ----------
114 Parameters 112 Parameters
115 ---------- 113 ----------