Mercurial > repos > ppericard > viscorvar

comparison mixomics_plotvar.xml @ 2:c8533e9298e5 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"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
equal deleted inserted replaced
1:e93350dc99f1 2:c8533e9298e5
1 <tool id="mixomics_plotvar" name="mixOmics plotVar" version="6.12+galaxy0" profile="16.04" workflow_compatible="true"> 1 <tool id="mixomics_plotvar" name="mixOmics plotVar" version="@TOOL_VERSION@+galaxy1" profile="16.04" workflow_compatible="true">
2 2
3 <description>provides variables representation for (regularized) CCA, (sparse) PLS regression, PCA and (sparse) Regularized generalised CCA</description> 3 <description>provides variables representation for (regularized) CCA, (sparse) PLS regression, PCA and (sparse) Regularized generalised CCA</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_plotvar.R
17 ${__tool_directory__}/mixomics_plotvar_script.R 16
18 --input_rdata $input_rdata 17 --input_rdata $input_rdata
18
19 $adv.legend 19 $adv.legend
20 --cutoff $adv.cutoff 20 --cutoff $adv.cutoff
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." />
44 <param name="input_rdata" value="out_rdata.rdata" /> 47 <param name="input_rdata" value="out_rdata.rdata" />
45 <output name="output_pdf" value="out_plotVar.pdf" /> 48 <output name="output_pdf" value="out_plotVar.pdf" />
46 </test> 49 </test>
47 </tests> 50 </tests>
48 51
49 <help> 52 <help><![CDATA[
50 <![CDATA[
51 .. class:: infomark
52 53
53 **Authors** Pierre Pericard (pierre.pericard@pasteur-lille.fr) 54 @HELP_AUTHORS@
54
55 ---------------------------------------------------
56
57 .. class:: infomark
58
59 **Please cite**
60
61 Rohart F, Gautier B, Singh A, Lê Cao KA (2017) mixOmics: An R package for ‘omics feature selection and multiple data integration.
62 PLOS Computational Biology 13(11): e1005752. https://doi.org/10.1371/journal.pcbi.1005752
63
64 ---------------------------------------------------
65 55
66 ================ 56 ================
67 mixOmics plotVar 57 mixOmics plotVar
68 ================ 58 ================
69 59
71 Description 61 Description
72 ----------- 62 -----------
73 63
74 The plotVar function is part of the mixOmics package for exploration and integration of Omics datasets. 64 The plotVar function is part of the mixOmics package for exploration and integration of Omics datasets.
75 Provides variables representation for (regularized) CCA, (sparse) PLS regression, PCA and (sparse) Regularized generalised CCA. 65 Provides variables representation for (regularized) CCA, (sparse) PLS regression, PCA and (sparse) Regularized generalised CCA.
66
67 -----------------
68 Workflow position
69 -----------------
70
71 **Upstream tools**
72
73 ======================= =================================== ========
74 Name Output file Format
75 ======================= =================================== ========
76 mixOmics.block.splsda mixomics_blocksplsda_output.RData rdata
77 ======================= =================================== ========
78
79 ---------------------------------------------------
76 80
77 ----------- 81 -----------
78 Input files 82 Input files
79 ----------- 83 -----------
80 84
93 97
94 Plot legend 98 Plot legend
95 99
96 Cut-off 100 Cut-off
97 101
102
103 @HELP_MANUAL@
104
98 ------------ 105 ------------
99 Output files 106 Output files
100 ------------ 107 ------------
101 108
102 plotIndiv.pdf 109 plotVar.pdf
103 A pdf file with scatter plots for individuals 110 A pdf file with scatter plots for variables
104 111
105 ]]> 112 ]]></help>
106 </help>
107 113
108 <citations> 114 <expand macro="citations" />
109 <citation type="doi">10.1371/journal.pcbi.1005752</citation>
110 </citations>
111 115
112 </tool> 116 </tool>