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comparison viscorvar_circlecor.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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children df8428358b7f
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1:e93350dc99f1 2:c8533e9298e5
1 <tool id="viscorvar_circlecor" name="visCorVar circleCor" version="@TOOL_VERSION@+galaxy1" profile="16.04" workflow_compatible="true">
2
3 <description>plots a correlation circle for the datasets whose correlation circles can be superimposed. This correlation circle contains the selected variables of these datasets which are included in a rectangle and the response 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_circlecor.R
16
17 --input_rdata ${input_rdata}
18
19 --blocks_vec ${select_blocks.value}
20 --responses_var ${select_responses_var}
21 --x_min ${x_min}
22 --x_max ${x_max}
23 --y_min ${y_min}
24 --y_max ${y_max}
25
26 --output_var ${output_var}
27 --output_pdf ${output_pdf}
28
29 @COMMAND_LOG_EXIT@
30
31 ]]></command>
32
33 <inputs>
34 <param name="input_rdata" type="data" format="rdata"
35 label="Input RData file"
36 help="output RData from matCorAddVar"/>
37 <param name="blocks_vec_list" type="data" format="tabular"
38 label="List of blocks vector."
39 help="output *_blocks_comb.tsv file from matCorAddVar"/>
40 <param name="select_blocks" type="select"
41 label="Blocks"
42 help="list of the blocks that are to be superimposed">
43 <options from_dataset="blocks_vec_list">
44 <column name="value" index="0"/>
45 <filter type="unique_value" column="0"/>
46 <filter type="sort_by" name="sorted_value" column="0"/>
47 </options>
48 </param>
49 <param name="responses_var_list" type="data" format="tabular"
50 label="List of response variables"
51 help="output *_response_var.tsv file from matCorAddVar"/>
52 <param name="select_responses_var" type="select" display="checkboxes"
53 multiple="true" label="Response variables"
54 help="select the response variables which will be plotted in the correlation circle">
55 <!-- <param name="select_responses_var" type="select" multiple="true" label="Response variables"> -->
56 <options from_dataset="responses_var_list">
57 <column name="value" index="0"/>
58 <filter type="unique_value" column="0"/>
59 <filter type="sort_by" name="sorted_value" column="0"/>
60 </options>
61 </param>
62 <param name="x_min" type="float" value="-1" min="-1" max="1"
63 label="X min" help="" />
64 <param name="x_max" type="float" value="1" min="-1" max="1"
65 label="X max" help="" />
66 <param name="y_min" type="float" value="-1" min="-1" max="1"
67 label="Y min" help="" />
68 <param name="y_max" type="float" value="1" min="-1" max="1"
69 label="Y max" help="" />
70 </inputs>
71
72 <outputs>
73 <data name="output_var" format="tabular" label="${tool.name}_selected_var.tsv" />
74 <data name="output_pdf" format="pdf" label="${tool.name}.pdf" />
75 </outputs>
76
77 <tests>
78 </tests>
79
80 <help><![CDATA[
81
82 @HELP_AUTHORS@
83
84 ===================
85 visCorVar circleCor
86 ===================
87
88 -----------
89 Description
90 -----------
91
92 Bla bla...
93
94 -----------------
95 Workflow position
96 -----------------
97
98 **Upstream tools**
99
100 ======================== ===================================== ========
101 Name Output file Format
102 ======================== ===================================== ========
103 visCorVar.matCorAddVar viscorvar_matcoraddvar_output.RData rdata
104 ======================== ===================================== ========
105
106 **Downstream tools**
107
108 ====================== ====================================== =========
109 Name Output file Format
110 ====================== ====================================== =========
111 visCorVar.networkVar viscorvar_circlecor_selected_var.tsv tabular
112 ====================== ====================================== =========
113
114 ---------------------------------------------------
115
116 -----------
117 Input files
118 -----------
119
120 +-------------------------------------------------------+-----------+
121 | Parameter : num + label | Format |
122 +=======================================================+===========+
123 | 1 : Rdata visCorVar.matCorAddVar output | rdata |
124 +-------------------------------------------------------+-----------+
125 | 2 : \*_blocks_comb.tsv visCorVar.matCorAddVar output | tabular |
126 +-------------------------------------------------------+-----------+
127 | 3 : \*_response_var.tsv visCorVar.matCorAddVar output | tabular |
128 +-------------------------------------------------------+-----------+
129
130 ----------
131 Parameters
132 ----------
133
134 @HELP_MANUAL@
135
136 ------------
137 Output files
138 ------------
139
140 viscorvar_circlecor.pdf
141 Correlation circle pdf file
142
143 viscorvar_circlecor_selected_var.tsv
144 List of variables selected in the correlation circle
145
146 ]]></help>
147
148 <expand macro="citations" />
149
150 </tool>