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comparison viscorvar_networkvar.xml @ 2:c8533e9298e5 draft

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"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
author ppericard
date Fri, 23 Oct 2020 10:15:56 +0000
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1:e93350dc99f1 2:c8533e9298e5
1 <tool id="viscorvar_networkvar" name="visCorVar networkVar" version="@TOOL_VERSION@+galaxy1" profile="16.04" workflow_compatible="true">
2
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
5 <macros>
6 <import>macros.xml</import>
7 <import>macros_viscorvar.xml</import>
8 </macros>
9
10 <expand macro="requirements"/>
11 <expand macro="stdio"/>
12
13 <command detect_errors="aggressive"><![CDATA[
14
15 @COMMAND_RSCRIPT@/viscorvar_networkvar.R
16
17 --mat_similarity_rdata ${mat_similarity_rdata}
18 --var_list_file ${var_list_file}
19 --response_var ${select_response_var}
20
21 --output_graph ${output_graph}
22
23 @COMMAND_LOG_EXIT@
24
25 ]]></command>
26
27 <inputs>
28 <param name="mat_similarity_rdata" type="data" format="rdata"
29 label="Input computeMatSimilarity RData file"
30 help="output RData file from computeMatSimilarity"/>
31 <param name="var_list_file" type="data" format="tabular"
32 label="Variables list file"
33 help="selected variables output tabular file from circleCor"/>
34
35 <!-- Fichier avec noms de gènes/variables, donné par l'utilisateur -->
36 <!-- <param name="var_of_interest_file" type="data" format="txt" optional="true"
37 label="Variables of interest (Optional)"
38 help="these variables have to belong to datasets that can be superimposed"/> -->
39
40 <param name="response_var_list" type="data" format="tabular"
41 label="List of response variables"
42 help="output *_response_var.tsv file from matCorAddVar"/>
43 <param name="select_response_var" type="select" display="checkboxes" multiple="true"
44 label="Response variables"
45 help="response variables that will be plotted in the network">
46 <!-- <param name="select_responses_var" type="select" multiple="true" label="Response variables"> -->
47 <options from_dataset="response_var_list">
48 <column name="value" index="0"/>
49 <filter type="unique_value" column="0"/>
50 <filter type="sort_by" name="sorted_value" column="0"/>
51 </options>
52 </param>
53 </inputs>
54
55 <outputs>
56 <data name="output_graph" format="xml" label="${tool.name}_graph.graphml" />
57 </outputs>
58
59 <tests>
60 </tests>
61
62 <help><![CDATA[
63
64 @HELP_AUTHORS@
65
66 ====================
67 visCorVar networkVar
68 ====================
69
70 -----------
71 Description
72 -----------
73
74 Bla bla...
75
76 -----------------
77 Workflow position
78 -----------------
79
80 **Upstream tools**
81
82 ================================ ============================================= =========
83 Name Output file Format
84 ================================ ============================================= =========
85 visCorVar.computeMatSimilarity viscorvar_computematsimilarity_output.RData rdata
86 -------------------------------- --------------------------------------------- ---------
87 visCorVar.circleCor viscorvar_circlecor_selected_var.tsv tabular
88 -------------------------------- --------------------------------------------- ---------
89 visCorVar.matCorAddVar viscorvar_matcoraddvar_response_var.tsv tabular
90 ================================ ============================================= =========
91
92 ---------------------------------------------------
93
94 -----------
95 Input files
96 -----------
97
98 +-------------------------------------------------------+------------+
99 | Parameter : num + label | Format |
100 +=======================================================+============+
101 | 1 : Rdata visCorVar.computeMatSimilarity output | rdata |
102 +-------------------------------------------------------+------------+
103 | 2 : *_selected_var.tsv visCorVar.circleCor output | tabular |
104 +-------------------------------------------------------+------------+
105 | 3 : *_response_var.tsv visCorVar.matCorAddVar output | tabular |
106 +-------------------------------------------------------+------------+
107
108 ----------
109 Parameters
110 ----------
111
112 @HELP_MANUAL@
113
114 ------------
115 Output files
116 ------------
117
118 viscorvar_networkvar_graph.graphml
119 GraphML file
120
121 ]]></help>
122
123 <expand macro="citations" />
124
125 </tool>