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comparison mixomics_plotindiv.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
parents e93350dc99f1
children d4e9f7546dfa
comparison
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1:e93350dc99f1 2:c8533e9298e5
1 <tool id="mixomics_plotindiv" name="mixOmics plotIndiv" version="6.12+galaxy0" profile="16.04" workflow_compatible="true"> 1 <tool id="mixomics_plotindiv" name="mixOmics plotIndiv" version="@TOOL_VERSION@+galaxy1" profile="16.04" workflow_compatible="true">
2 2
3 <description>provides scatter plots for individuals (experimental units) representation in (sparse)(I)PCA,(regularized)CCA, (sparse)PLS(DA) and (sparse)(R)GCCA(DA)</description> 3 <description>provides scatter plots for individuals (experimental units) representation in (sparse)(I)PCA,(regularized)CCA, (sparse)PLS(DA) and (sparse)(R)GCCA(DA)</description>
4 4
5 <requirements> 5 <macros>
6 <requirement type="package" version="6.12">bioconductor-mixomics</requirement> 6 <import>macros.xml</import>
7 <requirement type="package" version="2.0">r-argparse</requirement> 7 <import>macros_mixomics.xml</import>
8 </requirements> 8 </macros>
9 9
10 <stdio> 10 <expand macro="requirements"/>
11 <!-- <exit_code range="1:" level="fatal" /> --> 11 <expand macro="stdio"/>
12 </stdio>
13 12
14 <command detect_errors="aggressive"> 13 <command detect_errors="aggressive"><![CDATA[
15 <![CDATA[ 14
16 Rscript 15 @COMMAND_RSCRIPT@/mixomics_plotindiv.R
17 ${__tool_directory__}/mixomics_plotindiv_script.R 16
18 --input_rdata $input_rdata 17 --input_rdata $input_rdata
18
19 $adv.legend 19 $adv.legend
20 $adv.ellipse 20 $adv.ellipse
21
21 --output_pdf $output_pdf 22 --output_pdf $output_pdf
22 ]]> 23
23 </command> 24 @COMMAND_LOG_EXIT@
25
26 ]]></command>
24 27
25 <inputs> 28 <inputs>
26 <param name="input_rdata" type="data" format="rdata" 29 <param name="input_rdata" type="data" format="rdata"
27 label="Input RData file from (sparse)(I)PCA, (regularized)CCA, (sparse)PLS(DA) or (sparse)(R)GCCA(DA)" 30 label="Input RData file from (sparse)(I)PCA, (regularized)CCA, (sparse)PLS(DA) or (sparse)(R)GCCA(DA)"
28 help="This is the RData output file from the block.splsda function." /> 31 help="This is the RData output file from the block.splsda function." />
43 <param name="input_rdata" value="out_rdata.rdata" /> 46 <param name="input_rdata" value="out_rdata.rdata" />
44 <output name="output_pdf" value="out_plotIndiv.pdf" /> 47 <output name="output_pdf" value="out_plotIndiv.pdf" />
45 </test> 48 </test>
46 </tests> 49 </tests>
47 50
48 <help> 51 <help><![CDATA[
49 <![CDATA[
50 .. class:: infomark
51 52
52 **Authors** Pierre Pericard (pierre.pericard@pasteur-lille.fr) 53 @HELP_AUTHORS@
53
54 ---------------------------------------------------
55
56 .. class:: infomark
57
58 **Please cite**
59
60 Rohart F, Gautier B, Singh A, Lê Cao KA (2017) mixOmics: An R package for ‘omics feature selection and multiple data integration.
61 PLOS Computational Biology 13(11): e1005752. https://doi.org/10.1371/journal.pcbi.1005752
62
63 ---------------------------------------------------
64 54
65 ================== 55 ==================
66 mixOmics plotIndiv 56 mixOmics plotIndiv
67 ================== 57 ==================
68 58
70 Description 60 Description
71 ----------- 61 -----------
72 62
73 The plotIndiv function is part of the mixOmics package for exploration and integration of Omics datasets. 63 The plotIndiv function is part of the mixOmics package for exploration and integration of Omics datasets.
74 Provides scatter plots for individuals (experimental units) representation in (sparse)(I)PCA,(regularized)CCA, (sparse)PLS(DA) and (sparse)(R)GCCA(DA). 64 Provides scatter plots for individuals (experimental units) representation in (sparse)(I)PCA,(regularized)CCA, (sparse)PLS(DA) and (sparse)(R)GCCA(DA).
65
66 -----------------
67 Workflow position
68 -----------------
69
70 **Upstream tools**
71
72 ======================= =================================== ========
73 Name Output file Format
74 ======================= =================================== ========
75 mixOmics.block.splsda mixomics_blocksplsda_output.RData rdata
76 ======================= =================================== ========
77
78 ---------------------------------------------------
75 79
76 ----------- 80 -----------
77 Input files 81 Input files
78 ----------- 82 -----------
79 83
92 96
93 Plot legend 97 Plot legend
94 98
95 Plot ellipse plots 99 Plot ellipse plots
96 100
101
102 @HELP_MANUAL@
103
97 ------------ 104 ------------
98 Output files 105 Output files
99 ------------ 106 ------------
100 107
101 plotIndiv.pdf 108 plotIndiv.pdf
102 A pdf file with scatter plots for individuals 109 A pdf file with scatter plots for individuals
103 110
104 ]]> 111 ]]></help>
105 </help>
106 112
107 <citations> 113 <expand macro="citations" />
108 <citation type="doi">10.1371/journal.pcbi.1005752</citation>
109 </citations>
110 114
111 </tool> 115 </tool>