comparison matCorAddVar.xml @ 0:d0b77b926863 draft

"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="matCorAddVar" name="matCorAddVar" version="1.0" profile="16.04" workflow_compatible="true">
2
3 <description>determine the correlation circles that can be overlaid and compute the correlations</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="2.0">r-argparse</requirement>
8 <!-- <requirement type="package" version="0.3">viscorvar</requirement> -->
9 </requirements>
10
11 <stdio>
12 <!-- <exit_code range="1:" level="fatal" /> -->
13 </stdio>
14
15 <command detect_errors="aggressive">
16 <![CDATA[
17 Rscript
18 ${__tool_directory__}/matCorAddVar_wrapper.R
19 --input_rdata ${input_rdata}
20 ##--cutoff_comp ${cutoff_comp}
21 --cutoff_comp 0.775
22 #if str($var_of_interest_file) !='':
23 --interest_var_file ${var_of_interest_file}
24 #end if
25 --block_Y_file ${block_Y}
26 --output_rdata ${output_rdata}
27 --output_response_var ${output_response_var}
28 --output_blocks_comb ${output_blocks_comb}
29 ]]>
30 </command>
31
32 <inputs>
33 <param name="input_rdata" type="data" format="rdata"
34 label="Input RData file from block.SPLSDA"
35 help="This is the RData output file from the block.splsda function." />
36 <param name="block_Y" type="data" format="tabular"
37 label="Block Y"
38 help="[block_Y] (tabular format) This table contains the name of the samples in the first column. The other columns correspond to phenotypes. For each of these other columns, a column determines which sample is associated with this phenotype (value equals to 1) or not (value equals to 0). The name of the samples in Block Y (transposed), in the sample metadata (transposed) and for all datasets have to be in the same order" />
39 <!-- Fichier avec noms de gènes/variables, donné par l'utilisateur -->
40 <param name="var_of_interest_file" type="data" format="txt" optional="true"
41 label="Variables of interest (Optional)"
42 help="these variables have to belong to datasets that can be superimposed"/>
43 <!-- <param name="cutoff_comp" type="float" value="0.775" min="0" max="1"
44 label="Cutoff comp"
45 help="[cutoff_comp] Two correlation circles will be superimposed if the correlation of their first and second axis is greater than cutoff_comp in absolute value." /> -->
46 </inputs>
47
48 <outputs>
49 <data name="output_rdata" format="rdata" label="${tool.name}_output.rdata" />
50 <data name="output_response_var" format="tabular" label="${tool.name}_response_var.tsv" />
51 <data name="output_blocks_comb" format="tabular" label="${tool.name}_blocks_comb.tsv" />
52 </outputs>
53
54 <tests>
55 </tests>
56
57 <help>
58 </help>
59
60 </tool>