Mercurial > repos > ppericard > viscorvar

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

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"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
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
4
d4e9f7546dfa "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 579dc54316e8ede493f86f434a87d3d7b692b023"
ppericard
parents: 3
diff changeset
1 <tool id="viscorvar_networkvar" name="visCorVar networkVar" version="@TOOL_VERSION@+galaxy0" profile="16.04" workflow_compatible="true">
2
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
2
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
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>
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
4
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
5 <macros>
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
6 <import>macros.xml</import>
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
7 <import>macros_viscorvar.xml</import>
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
8 </macros>
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
9
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
10 <expand macro="requirements"/>
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
11 <expand macro="stdio"/>
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
12
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
13 <command detect_errors="aggressive"><![CDATA[
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
14
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
15 @COMMAND_RSCRIPT@/viscorvar_networkvar.R
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
16
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
17 --mat_similarity_rdata ${mat_similarity_rdata}
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
18 --var_list_file ${var_list_file}
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
19 --response_var ${select_response_var}
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
20
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
21 --output_graph ${output_graph}
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
22
5
88c1fd2ac110 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 21d09ff286a496ff475f32626d88dd42423ae663"
ppericard
parents: 4
diff changeset
23 ]]></command>
2
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
24
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
25 <inputs>
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
26 <param name="mat_similarity_rdata" type="data" format="rdata"
4
d4e9f7546dfa "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 579dc54316e8ede493f86f434a87d3d7b692b023"
ppericard
parents: 3
diff changeset
27 label="this is the RData output file from the computeMatSimilarity function"
5
88c1fd2ac110 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 21d09ff286a496ff475f32626d88dd42423ae663"
ppericard
parents: 4
diff changeset
28 help="output RData file from the computeMatSimilarity function"/>
2
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
29 <param name="var_list_file" type="data" format="tabular"
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
30 label="Variables list file"
5
88c1fd2ac110 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 21d09ff286a496ff475f32626d88dd42423ae663"
ppericard
parents: 4
diff changeset
31 help="selected variables output tabular file from the circleCor function"/>
2
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
32
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
33 <!-- Fichier avec noms de gènes/variables, donné par l'utilisateur -->
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
34 <!-- <param name="var_of_interest_file" type="data" format="txt" optional="true"
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
35 label="Variables of interest (Optional)"
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
36 help="these variables have to belong to datasets that can be superimposed"/> -->
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
37
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
38 <param name="response_var_list" type="data" format="tabular"
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
39 label="List of response variables"
5
88c1fd2ac110 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 21d09ff286a496ff475f32626d88dd42423ae663"
ppericard
parents: 4
diff changeset
40 help="output *_response_var.tsv file from the matCorAddVar function"/>
2
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
41 <param name="select_response_var" type="select" display="checkboxes" multiple="true"
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
42 label="Response variables"
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
43 help="response variables that will be plotted in the network">
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
44 <!-- <param name="select_responses_var" type="select" multiple="true" label="Response variables"> -->
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
45 <options from_dataset="response_var_list">
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
46 <column name="value" index="0"/>
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
47 <filter type="unique_value" column="0"/>
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
48 <filter type="sort_by" name="sorted_value" column="0"/>
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
49 </options>
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
50 </param>
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
51 </inputs>
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
52
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
53 <outputs>
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
54 <data name="output_graph" format="xml" label="${tool.name}_graph.graphml" />
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
55 </outputs>
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
56
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
57 <tests>
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
58 </tests>
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
59
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
60 <help><![CDATA[
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
61
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
62 @HELP_AUTHORS@
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
63
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
64 ====================
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
65 visCorVar networkVar
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
66 ====================
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
67
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
68 -----------
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
69 Description
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
70 -----------
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
71
4
d4e9f7546dfa "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 579dc54316e8ede493f86f434a87d3d7b692b023"
ppericard
parents: 3
diff changeset
72 This tool creates a network of correlated variables for omics datasets. The determination of
5
88c1fd2ac110 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 21d09ff286a496ff475f32626d88dd42423ae663"
ppericard
parents: 4
diff changeset
73 the omics datasets which can be visualized is made by the matCorAddVar tool. This network can
4
d4e9f7546dfa "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 579dc54316e8ede493f86f434a87d3d7b692b023"
ppericard
parents: 3
diff changeset
74 be exported to graphml format and visualized with Cytoscape. The link between two variables
d4e9f7546dfa "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 579dc54316e8ede493f86f434a87d3d7b692b023"
ppericard
parents: 3
diff changeset
75 is associated with the correlation between two variables : a threshold can be used in
5
88c1fd2ac110 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 21d09ff286a496ff475f32626d88dd42423ae663"
ppericard
parents: 4
diff changeset
76 Cytoscape to get a network of variables whose correlations are greater than this threshold
4
d4e9f7546dfa "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 579dc54316e8ede493f86f434a87d3d7b692b023"
ppericard
parents: 3
diff changeset
77 in absolute value.
2
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
78
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
79 -----------------
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
80 Workflow position
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
81 -----------------
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
82
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
83 **Upstream tools**
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
84
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
85 ================================ ============================================= =========
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
86 Name Output file Format
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
87 ================================ ============================================= =========
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
88 visCorVar.computeMatSimilarity viscorvar_computematsimilarity_output.RData rdata
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
89 -------------------------------- --------------------------------------------- ---------
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
90 visCorVar.circleCor viscorvar_circlecor_selected_var.tsv tabular
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
91 -------------------------------- --------------------------------------------- ---------
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
92 visCorVar.matCorAddVar viscorvar_matcoraddvar_response_var.tsv tabular
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
93 ================================ ============================================= =========
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
94
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
95 ---------------------------------------------------
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
96
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
97 -----------
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
98 Input files
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
99 -----------
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
100
3
df8428358b7f "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit d930da2982ffb689ba4fdf7599c8971f8c52339d"
ppericard
parents: 2
diff changeset
101 +-----------------------------------------------------------+-----------+
df8428358b7f "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit d930da2982ffb689ba4fdf7599c8971f8c52339d"
ppericard
parents: 2
diff changeset
102 | Parameter : num + label | Format |
df8428358b7f "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit d930da2982ffb689ba4fdf7599c8971f8c52339d"
ppericard
parents: 2
diff changeset
103 +===========================================================+===========+
df8428358b7f "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit d930da2982ffb689ba4fdf7599c8971f8c52339d"
ppericard
parents: 2
diff changeset
104 | 1 : Rdata visCorVar.computeMatSimilarity output | rdata |
df8428358b7f "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit d930da2982ffb689ba4fdf7599c8971f8c52339d"
ppericard
parents: 2
diff changeset
105 +-----------------------------------------------------------+-----------+
5
88c1fd2ac110 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 21d09ff286a496ff475f32626d88dd42423ae663"
ppericard
parents: 4
diff changeset
106 | 2 : \*_selected_var.tsv visCorVar.circleCor output | tabular |
3
df8428358b7f "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit d930da2982ffb689ba4fdf7599c8971f8c52339d"
ppericard
parents: 2
diff changeset
107 +-----------------------------------------------------------+-----------+
5
88c1fd2ac110 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 21d09ff286a496ff475f32626d88dd42423ae663"
ppericard
parents: 4
diff changeset
108 | 3 : \*_response_var.tsv visCorVar.matCorAddVar output | tabular |
3
df8428358b7f "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit d930da2982ffb689ba4fdf7599c8971f8c52339d"
ppericard
parents: 2
diff changeset
109 +-----------------------------------------------------------+-----------+
2
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
110
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
111 ----------
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
112 Parameters
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
113 ----------
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
114
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
115 @HELP_MANUAL@
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
116
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
117 ------------
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
118 Output files
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
119 ------------
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
120
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
121 viscorvar_networkvar_graph.graphml
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
122 GraphML file
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
123
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
124 ]]></help>
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
125
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
126 <expand macro="citations" />
c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
ppericard
parents:
diff changeset
127
5
88c1fd2ac110 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 21d09ff286a496ff475f32626d88dd42423ae663"
ppericard
parents: 4
diff changeset
128 </tool>