Mercurial > repos > ppericard > viscorvar

comparison viscorvar_matcoraddvar.xml @ 4:d4e9f7546dfa draft

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"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 579dc54316e8ede493f86f434a87d3d7b692b023"
author ppericard
date Tue, 17 Nov 2020 13:01:44 +0000
parents df8428358b7f
children 88c1fd2ac110
comparison
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3:df8428358b7f 4:d4e9f7546dfa
1 <tool id="viscorvar_matcoraddvar" name="visCorVar matCorAddVar" version="@TOOL_VERSION@+galaxy1" profile="16.04" workflow_compatible="true"> 1 <tool id="viscorvar_matcoraddvar" name="visCorVar matCorAddVar" version="@TOOL_VERSION@+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 <macros> 5 <macros>
6 <import>macros.xml</import> 6 <import>macros.xml</import>
32 ]]></command> 32 ]]></command>
33 33
34 <inputs> 34 <inputs>
35 <param name="input_rdata" type="data" format="rdata" 35 <param name="input_rdata" type="data" format="rdata"
36 label="Input RData file from block.SPLSDA" 36 label="Input RData file from block.SPLSDA"
37 help="This is the RData output file from the block.splsda function." /> 37 help="this is the RData output file from the block.splsda function" />
38 <param name="block_Y" type="data" format="tabular" 38 <param name="block_Y" type="data" format="tabular"
39 label="Block Y" 39 label="Block Y"
40 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" /> 40 help="Block Y is a table. A column determines which sample is associated with a phenotype (value equals to 1) or not (value equals to 0). For the file structure, see below in the section Input files" />
41 <!-- Fichier avec noms de gènes/variables, donné par l'utilisateur --> 41 <!-- Fichier avec noms de gènes/variables, donné par l'utilisateur -->
42 <param name="var_of_interest_file" type="data" format="txt" optional="true" 42 <param name="var_of_interest_file" type="data" format="txt" optional="true"
43 label="Variables of interest (Optional)" 43 label="Variables of interest (Optional)"
44 help="variables not belonging to any block will not be considered"/> 44 help="variables not belonging to any block will not be considered. For the file structure, see below in the section Input files"/>
45 <!-- <param name="cutoff_comp" type="float" value="0.775" min="0" max="1" 45 <!-- <param name="cutoff_comp" type="float" value="0.775" min="0" max="1"
46 label="Cutoff comp" 46 label="Cutoff comp"
47 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." /> --> 47 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." /> -->
48 </inputs> 48 </inputs>
49 49
66 66
67 ----------- 67 -----------
68 Description 68 Description
69 ----------- 69 -----------
70 70
71 Bla bla... 71 This tool is a pre-processing step of the pipeline. It computes the correlations
72 between omics datasets variables, variables of interest (optional), response variables and
73 the components which are output of the data integration. The variables of interest are omics
74 datasets variables that will be added to the network. It also determines the omics datasets
75 for which the correlated variables of these omics datasets can be visualized with correlation
76 circles and networks.
72 77
73 ----------------- 78 -----------------
74 Workflow position 79 Workflow position
75 ----------------- 80 -----------------
76 81
108 | 2 : Block Y | tabular | 113 | 2 : Block Y | tabular |
109 +-----------------------------------------+-----------+ 114 +-----------------------------------------+-----------+
110 | 3 : [opt] Variables of interest | txt | 115 | 3 : [opt] Variables of interest | txt |
111 +-----------------------------------------+-----------+ 116 +-----------------------------------------+-----------+
112 117
118 2. Block Y structure
119 Block Y is in tabular format (.tsv).
120 This table contains the name of the samples in the first column.
121 The other columns correspond to phenotypes.
122 For each of these other columns, a column determines which sample is associated with a phenotype (value equals to 1) or not (value equals to 0). The names of the samples in Block Y (transposed), in the sample metadata (transposed) and for all datasets have to be in the same order.
123
124 3. Variables of interest structure
125 All the variables of interest are in the same column.
126
113 ---------- 127 ----------
114 Parameters 128 Parameters
115 ---------- 129 ----------
116 130
117 @HELP_MANUAL@ 131 @HELP_MANUAL@