Mercurial > repos > ppericard > viscorvar
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 |
| parents | |
| children | e93350dc99f1 |
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| -1:000000000000 | 0:d0b77b926863 |
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| 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> |