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comparison matCorAddVar.xml @ 1:e93350dc99f1 draft

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"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 1eda261d4fe137d6e8806b0c6af7eaf12d11ac95"
author ppericard
date Thu, 15 Oct 2020 12:22:25 +0000
parents d0b77b926863
children
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0:d0b77b926863 1:e93350dc99f1
1 <tool id="matCorAddVar" name="matCorAddVar" version="1.0" profile="16.04" workflow_compatible="true"> 1 <tool id="matCorAddVar" name="matCorAddVar" version="0.6+galaxy0" profile="16.04" workflow_compatible="true">
2 2
3 <description>determine the correlation circles that can be overlaid and compute the correlations</description> 3 <description>determine the correlation circles that can be overlaid and compute the correlations</description>
4 4
5 <requirements> 5 <requirements>
6 <requirement type="package" version="6.12">bioconductor-mixomics</requirement> <!-- Remove when viscorvar is available via conda --> 6 <requirement type="package" version="0.6">r-viscorvar</requirement>
7 <requirement type="package" version="2.0">r-argparse</requirement> 7 <requirement type="package" version="2.0">r-argparse</requirement>
8 <!-- <requirement type="package" version="0.3">viscorvar</requirement> -->
9 </requirements> 8 </requirements>
10 9
11 <stdio> 10 <stdio>
12 <!-- <exit_code range="1:" level="fatal" /> --> 11 <!-- <exit_code range="1:" level="fatal" /> -->
13 </stdio> 12 </stdio>
14 13
15 <command detect_errors="aggressive"> 14 <command detect_errors="aggressive">
16 <![CDATA[ 15 <![CDATA[
17 Rscript 16 Rscript
18 ${__tool_directory__}/matCorAddVar_wrapper.R 17 ${__tool_directory__}/matCorAddVar_wrapper.R
19 --input_rdata ${input_rdata} 18 --input_rdata ${input_rdata}
20 ##--cutoff_comp ${cutoff_comp} 19 ##--cutoff_comp ${cutoff_comp}
21 --cutoff_comp 0.775 20 --cutoff_comp 0.75
22 #if str($var_of_interest_file) !='': 21 #if str($var_of_interest_file) !='':
23 --interest_var_file ${var_of_interest_file} 22 --interest_var_file ${var_of_interest_file}
24 #end if 23 #end if
25 --block_Y_file ${block_Y} 24 --block_Y_file ${block_Y}
26 --output_rdata ${output_rdata} 25 --output_rdata ${output_rdata}
37 label="Block Y" 36 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" /> 37 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 --> 38 <!-- Fichier avec noms de gènes/variables, donné par l'utilisateur -->
40 <param name="var_of_interest_file" type="data" format="txt" optional="true" 39 <param name="var_of_interest_file" type="data" format="txt" optional="true"
41 label="Variables of interest (Optional)" 40 label="Variables of interest (Optional)"
42 help="these variables have to belong to datasets that can be superimposed"/> 41 help="variables not belonging to any block will not be considered"/>
43 <!-- <param name="cutoff_comp" type="float" value="0.775" min="0" max="1" 42 <!-- <param name="cutoff_comp" type="float" value="0.775" min="0" max="1"
44 label="Cutoff comp" 43 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." /> --> 44 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> 45 </inputs>
47 46