Mercurial > repos > ppericard > mixomics_blocksplsda

comparison circleCor.xml @ 3:0a3c83f2197a draft

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planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
author ppericard
date Fri, 25 Oct 2019 07:10:59 -0400
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children b0ab97ffc2a1
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2:655d1fbcd3e6 3:0a3c83f2197a
1 <tool id="circleCor" name="circleCor" version="0.2.0" profile="16.04" workflow_compatible="true">
2
3 <description></description>
4
5 <requirements>
6 <requirement type="package">r-base</requirement>
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 ${output_pdf}
31 ]]>
32 </command>
33
34 <inputs>
35 <param name="input_rdata" type="data" format="rdata" label="Input RData file from block.SPLSDA"/>
36 <param name="blocks_vec_list" type="data" format="tabular" label="List of blocks vector"/>
37 <param name="select_blocks" type="select" label="Blocks">
38 <options from_dataset="blocks_vec_list">
39 <column name="value" index="0"/>
40 <filter type="unique_value" column="0"/>
41 <filter type="sort_by" name="sorted_value" column="0"/>
42 </options>
43 </param>
44 <param name="responses_var_list" type="data" format="tabular" label="List of response variables"/>
45 <param name="select_responses_var" type="select" display="checkboxes" multiple="true" label="Response variables">
46 <!-- <param name="select_responses_var" type="select" multiple="true" label="Response variables"> -->
47 <options from_dataset="responses_var_list">
48 <column name="value" index="0"/>
49 <filter type="unique_value" column="0"/>
50 <filter type="sort_by" name="sorted_value" column="0"/>
51 </options>
52 </param>
53 <param name="x_min" type="float" value="-1" min="-1" max="1" label="X min" help="" />
54 <param name="x_max" type="float" value="1" min="-1" max="1" label="X max" help="" />
55 <param name="y_min" type="float" value="-1" min="-1" max="1" label="Y min" help="" />
56 <param name="y_max" type="float" value="1" min="-1" max="1" label="Y max" help="" />
57 </inputs>
58
59 <outputs>
60 <data name="output_var" format="tabular" label="${tool.name}_var.tsv" />
61 <data name="output_pdf" format="pdf" label="${tool.name}.pdf" />
62 </outputs>
63
64 <tests>
65 </tests>
66
67 <help>
68 </help>
69
70 </tool>