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comparison queue_genotype_workflow.xml @ 3:36f8098ff528 draft

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author greg
date Mon, 18 Nov 2019 11:27:29 -0500
parents fa50d7c895c2
children 934acc64b30c
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2:fa50d7c895c2 3:36f8098ff528
53 **What it does** 53 **What it does**
54 54
55 Uses the Galaxy/Bioblend API to execute the complete multilocus genotype analysis pipeline for corals or symbiants. 55 Uses the Galaxy/Bioblend API to execute the complete multilocus genotype analysis pipeline for corals or symbiants.
56 This tool must be able to access the corals (stag) database. 56 This tool must be able to access the corals (stag) database.
57 57
58 **Required options**
59
60 * **Affymetrix 96 well plate metadata file** - a tabular file created by the user to describe their samples - it can be exported from Excel using this example as a template: http://baumslab.org/documents/SNPChip/STAG_Metadata_Template_v3.xlsm
61 * **Sample attributes file** - the Sample Attributes tabular file created by the Affymetrix sequencer for the plate
62 * **Probeset annotation file** - the annotation CSV file created by the Affymetrix sequencer for the plate
63 * **Apt-probeset genotype summary file** - the summary CSV file created by the Affymetrix sequencer for the plate
64 * **Apt-probeset genotype snp-posteriors file** - the snp-posteriors CSV file created by the Affymetrix sequencer for the plate
65 * **Apt-probeset genotype report file** - the report CSV file created by the Affymetrix sequencer for the plate
66 * **Apt-probeset genotype confidences file** - the confidences CSV file created by the Affymetrix sequencer for the plate
67 * **Apt-probeset genotype calls file** - the calls CSV file created by the Affymetrix sequencer for the plate
68 * **Fasta reference sequence** - selected fasta reference dataset for the samples
69
58 </help> 70 </help>
59 <citations> 71 <citations>
60 <citation type="bibtex"> 72 <citation type="bibtex">
61 @misc{None, 73 @misc{None,
62 journal = {None}, 74 journal = {None},