Mercurial > repos > ppericard > mixomics_blocksplsda

comparison circleCor.xml @ 4:b0ab97ffc2a1 draft

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planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 0bf5c0745f406f2eca9c708a062c975b1f7ea386
author ppericard
date Mon, 09 Mar 2020 11:53:32 -0400
parents 0a3c83f2197a
children
comparison
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3:0a3c83f2197a 4:b0ab97ffc2a1
1 <tool id="circleCor" name="circleCor" version="0.2.0" profile="16.04" workflow_compatible="true"> 1 <tool id="circleCor" name="circleCor" version="0.3.0" profile="16.04" workflow_compatible="true">
2 2
3 <description></description> 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 4
5 <requirements> 5 <requirements>
6 <requirement type="package">r-base</requirement> 6 <requirement type="package">r-base</requirement>
7 <requirement type="package" version="0.4">r-ellipse</requirement> 7 <requirement type="package" version="0.4">r-ellipse</requirement>
8 <requirement type="package" version="2.0">r-argparse</requirement> 8 <requirement type="package" version="2.0">r-argparse</requirement>
9 <requirement type="package" version="1.1">r-rcolorbrewer</requirement> 9 <requirement type="package" version="1.1">r-rcolorbrewer</requirement>
10 10
11 <!-- <requirement type="package" version="6.8">bioconductor-mixomics</requirement> --> 11 <!-- <requirement type="package" version="6.8">bioconductor-mixomics</requirement> -->
12 </requirements> 12 </requirements>
13 13
14 <stdio> 14 <stdio>
15 <!-- <exit_code range="1:" level="fatal" /> --> 15 <!-- <exit_code range="1:" level="fatal" /> -->
16 </stdio> 16 </stdio>
17 17
18 <command detect_errors="aggressive"> 18 <command detect_errors="aggressive">
30 --output_pdf ${output_pdf} 30 --output_pdf ${output_pdf}
31 ]]> 31 ]]>
32 </command> 32 </command>
33 33
34 <inputs> 34 <inputs>
35 <param name="input_rdata" type="data" format="rdata" label="Input RData file from block.SPLSDA"/> 35 <param name="input_rdata" type="data" format="rdata"
36 <param name="blocks_vec_list" type="data" format="tabular" label="List of blocks vector"/> 36 label="Input RData file"
37 <param name="select_blocks" type="select" label="Blocks"> 37 help="output RData from matCor_addVar"/>
38 <param name="blocks_vec_list" type="data" format="tabular"
39 label="List of blocks vector."
40 help="output tsv file from matCor_addVar"/>
41 <param name="select_blocks" type="select"
42 label="Blocks"
43 help="list of the blocks that are to be superimposed">
38 <options from_dataset="blocks_vec_list"> 44 <options from_dataset="blocks_vec_list">
39 <column name="value" index="0"/> 45 <column name="value" index="0"/>
40 <filter type="unique_value" column="0"/> 46 <filter type="unique_value" column="0"/>
41 <filter type="sort_by" name="sorted_value" column="0"/> 47 <filter type="sort_by" name="sorted_value" column="0"/>
42 </options> 48 </options>
43 </param> 49 </param>
44 <param name="responses_var_list" type="data" format="tabular" label="List of response variables"/> 50 <param name="responses_var_list" type="data" format="txt"
51 label="List of response variables"
52 help="list of the response variables which will be plotted in the correlation circle"/>
45 <param name="select_responses_var" type="select" display="checkboxes" multiple="true" label="Response variables"> 53 <param name="select_responses_var" type="select" display="checkboxes" multiple="true" label="Response variables">
46 <!-- <param name="select_responses_var" type="select" multiple="true" label="Response variables"> --> 54 <!-- <param name="select_responses_var" type="select" multiple="true" label="Response variables"> -->
47 <options from_dataset="responses_var_list"> 55 <options from_dataset="responses_var_list">
48 <column name="value" index="0"/> 56 <column name="value" index="0"/>
49 <filter type="unique_value" column="0"/> 57 <filter type="unique_value" column="0"/>
50 <filter type="sort_by" name="sorted_value" column="0"/> 58 <filter type="sort_by" name="sorted_value" column="0"/>
51 </options> 59 </options>
52 </param> 60 </param>
53 <param name="x_min" type="float" value="-1" min="-1" max="1" label="X min" help="" /> 61 <param name="x_min" type="float" value="-1" min="-1" max="1"
54 <param name="x_max" type="float" value="1" min="-1" max="1" label="X max" help="" /> 62 label="X min" help="" />
55 <param name="y_min" type="float" value="-1" min="-1" max="1" label="Y min" help="" /> 63 <param name="x_max" type="float" value="1" min="-1" max="1"
56 <param name="y_max" type="float" value="1" min="-1" max="1" label="Y max" help="" /> 64 label="X max" help="" />
65 <param name="y_min" type="float" value="-1" min="-1" max="1"
66 label="Y min" help="" />
67 <param name="y_max" type="float" value="1" min="-1" max="1"
68 label="Y max" help="" />
57 </inputs> 69 </inputs>
58 70
59 <outputs> 71 <outputs>
60 <data name="output_var" format="tabular" label="${tool.name}_var.tsv" /> 72 <data name="output_var" format="tabular" label="${tool.name}_var.tsv" />
61 <data name="output_pdf" format="pdf" label="${tool.name}.pdf" /> 73 <data name="output_pdf" format="pdf" label="${tool.name}.pdf" />