Mercurial > repos > ppericard > viscorvar

comparison viscorvar_matcoraddvar.xml @ 5:88c1fd2ac110 draft default tip

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"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 21d09ff286a496ff475f32626d88dd42423ae663"
author ppericard
date Tue, 07 Sep 2021 10:40:08 +0000
parents d4e9f7546dfa
children
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4:d4e9f7546dfa 5:88c1fd2ac110
25 25
26 --output_rdata ${output_rdata} 26 --output_rdata ${output_rdata}
27 --output_response_var ${output_response_var} 27 --output_response_var ${output_response_var}
28 --output_blocks_comb ${output_blocks_comb} 28 --output_blocks_comb ${output_blocks_comb}
29 29
30 @COMMAND_LOG_EXIT@
31
32 ]]></command> 30 ]]></command>
33 31
34 <inputs> 32 <inputs>
35 <param name="input_rdata" type="data" format="rdata" 33 <param name="input_rdata" type="data" format="rdata"
36 label="Input RData file from block.SPLSDA" 34 label="Input RData file from block.SPLSDA"
37 help="this is the RData output file from the block.splsda function" /> 35 help="this is the RData output file from the block.splsda function" />
38 <param name="block_Y" type="data" format="tabular" 36 <param name="block_Y" type="data" format="tabular"
39 label="Block Y" 37 label="Block Y"
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" /> 38 help="Block Y is a table. A column corresponds to a phenotype and determines which sample is associated with this phenotype or not (value equals to 1 or 0). For the file structure, see below in the section Input files" />
41 <!-- Fichier avec noms de gènes/variables, donné par l'utilisateur --> 39 <!-- Fichier avec noms de gènes/variables, donné par l'utilisateur -->
42 <param name="var_of_interest_file" type="data" format="txt" optional="true" 40 <param name="var_of_interest_file" type="data" format="txt" optional="true"
43 label="Variables of interest (Optional)" 41 label="Variables of interest (Optional)"
44 help="variables not belonging to any block will not be considered. For the file structure, see below in the section Input files"/> 42 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" 43 <!-- <param name="cutoff_comp" type="float" value="0.775" min="0" max="1"
117 115
118 2. Block Y structure 116 2. Block Y structure
119 Block Y is in tabular format (.tsv). 117 Block Y is in tabular format (.tsv).
120 This table contains the name of the samples in the first column. 118 This table contains the name of the samples in the first column.
121 The other columns correspond to phenotypes. 119 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. 120 For each of these other columns, a column corresponds to a phenotype and determines which sample is associated with this phenotype or not (value equals to 1 or 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.
123 121
124 3. Variables of interest structure 122 3. Variables of interest structure
125 All the variables of interest are in the same column. 123 All the variables of interest are in the same column.
126 124
127 ---------- 125 ----------
133 ------------ 131 ------------
134 Output files 132 Output files
135 ------------ 133 ------------
136 134
137 viscorvar_matcoraddvar_output.RData 135 viscorvar_matcoraddvar_output.RData
138 RData output 136 | RData output
139 137 | Contains the `matCorAddVar_result` R object containing the result of the matCorAddVar function
140 viscorvar_matcoraddvar_response_var.tsv
141
142 138
143 viscorvar_matcoraddvar_blocks_comb.tsv 139 viscorvar_matcoraddvar_blocks_comb.tsv
144 140 | viscorvar_matcoraddvar_blocks_comb.tsv contains the block names whose correlation circles can be overlaid
145 141
146 ]]></help> 142 ]]></help>
147 143
148 <expand macro="citations" /> 144 <expand macro="citations" />
149 145