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comparison circleCor.xml @ 0:d0b77b926863 draft

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"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
author ppericard
date Tue, 23 Jun 2020 19:57:35 -0400
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children e93350dc99f1
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-1:000000000000 0:d0b77b926863
1 <tool id="circleCor" name="circleCor" version="1.0" 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 <requirements>
6 <requirement type="package" version="6.12">bioconductor-mixomics</requirement> <!-- Remove when viscorvar is available via conda -->
7 <!-- <requirement type="package" version="0.4">r-ellipse</requirement> -->
8 <requirement type="package" version="2.0">r-argparse</requirement>
9 <!-- <requirement type="package" version="1.1">r-rcolorbrewer</requirement> -->
10
11 <!-- <requirement type="package" version="6.8">bioconductor-mixomics</requirement> -->
12 </requirements>
13
14 <stdio>
15 <!-- <exit_code range="1:" level="fatal" /> -->
16 </stdio>
17
18 <command detect_errors="aggressive">
19 <![CDATA[
20 Rscript
21 ${__tool_directory__}/circleCor_wrapper.R
22 --input_rdata ${input_rdata}
23 --blocks_vec ${select_blocks.value}
24 --responses_var ${select_responses_var}
25 --x_min ${x_min}
26 --x_max ${x_max}
27 --y_min ${y_min}
28 --y_max ${y_max}
29 --output_var ${output_var}
30 --output_pdf ${output_pdf}
31 ]]>
32 </command>
33
34 <inputs>
35 <param name="input_rdata" type="data" format="rdata"
36 label="Input RData file"
37 help="output RData from matCorAddVar"/>
38 <param name="blocks_vec_list" type="data" format="tabular"
39 label="List of blocks vector."
40 help="output *_blocks_comb.tsv file from matCorAddVar"/>
41 <param name="select_blocks" type="select"
42 label="Blocks"
43 help="list of the blocks that are to be superimposed">
44 <options from_dataset="blocks_vec_list">
45 <column name="value" index="0"/>
46 <filter type="unique_value" column="0"/>
47 <filter type="sort_by" name="sorted_value" column="0"/>
48 </options>
49 </param>
50 <param name="responses_var_list" type="data" format="tabular"
51 label="List of response variables"
52 help="output *_response_var.tsv file from matCorAddVar"/>
53 <param name="select_responses_var" type="select" display="checkboxes"
54 multiple="true" label="Response variables"
55 help="select the response variables which will be plotted in the correlation circle">
56 <!-- <param name="select_responses_var" type="select" multiple="true" label="Response variables"> -->
57 <options from_dataset="responses_var_list">
58 <column name="value" index="0"/>
59 <filter type="unique_value" column="0"/>
60 <filter type="sort_by" name="sorted_value" column="0"/>
61 </options>
62 </param>
63 <param name="x_min" type="float" value="-1" min="-1" max="1"
64 label="X min" help="" />
65 <param name="x_max" type="float" value="1" min="-1" max="1"
66 label="X max" help="" />
67 <param name="y_min" type="float" value="-1" min="-1" max="1"
68 label="Y min" help="" />
69 <param name="y_max" type="float" value="1" min="-1" max="1"
70 label="Y max" help="" />
71 </inputs>
72
73 <outputs>
74 <data name="output_var" format="tabular" label="${tool.name}_selected_var.tsv" />
75 <data name="output_pdf" format="pdf" label="${tool.name}.pdf" />
76 </outputs>
77
78 <tests>
79 </tests>
80
81 <help>
82 </help>
83
84 </tool>