Mercurial > repos > greg > queue_genotype_workflow
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author | greg |
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date | Thu, 15 Jul 2021 20:39:52 +0000 |
parents | 560dcf3f9f3d |
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<tool id="queue_genotype_workflow" name="Queue genotype workflow" version="1.0.0"> <description></description> <command detect_errors="exit_code"><![CDATA[ #set history_id = $__app__.security.encode_id($affy_metadata.history.id) python $__tool_directory__/queue_genotype_workflow.py --affy_metadata '$affy_metadata' --annot '$annot' --api_key $get_user_api_key --calls '$calls' --confidences '$confidences' --config_file $__tool_directory__/qgw_config.ini --history_id $history_id --reference_genome '$locally_cached_item.fields.path' --dbkey '$locally_cached_item.fields.value' --report '$report' --sample_attributes '$sample_attributes' --snp-posteriors '$snp_posteriors' --summary '$summary' #if str($output_nj_phylogeny_tree) == "yes": --output_nj_phylogeny_tree '$output_nj_phylogeny_tree' #end if --output '$output']]></command> <configfiles> <configfile name="get_user_api_key"><![CDATA[#from galaxy.managers import api_keys#${api_keys.ApiKeyManager( $__app__ ).get_or_create_api_key($__user__)} ]]></configfile> </configfiles> <inputs> <param name="affy_metadata" type="data" format="tabular" label="Affymetrix 96 well plate metadata file" help="The word 'metadata' must be in the file name."> <validator type="expression" message="96 well plate data must have 32 columns"><![CDATA[value is not None and value.metadata.columns==32]]></validator> </param> <param name="sample_attributes" type="data" format="tabular" label="Sample attributes file" help="The word 'attributes' must be in the file name."/> <param name="annot" type="data" format="csv" label="Probeset annotation file" help="The word 'annotation' must be in the file name."/> <param name="summary" type="data" format="txt" label="Apt-probeset genotype summary file" help="The word 'summary' must be in the file name."/> <param name="snp_posteriors" type="data" format="txt" label="Apt-probeset genotype snp-posteriors file" help="The word 'snp-posteriors' must be in the file name."/> <param name="report" type="data" format="txt" label="Apt-probeset genotype report file" help="The word 'report' must be in the file name."/> <param name="confidences" type="data" format="txt" label="Apt-probeset genotype confidences file" help="The word 'confidences' must be in the file name."/> <param name="calls" type="data" format="txt" label="Apt-probeset genotype calls file" help="The word 'calls' must be in the file name."/> <param name="locally_cached_item" type="select" format="fasta" label="Fasta reference sequence"> <options from_data_table="all_fasta"> <column name="name" index="2"/> <column name="value" index="0"/> <column name="path" index="3"/> <filter type="sort_by" column="1"/> <validator type="no_options" message="No cached Fasta genome references are available for the build associated with the selected probeset annotation file." /> </options> </param> <param name="output_nj_phylogeny_tree" type="select" display="radio" label="Plot neighbor-joining phylogeny tree in Corals Multilocus Genotype outputs?" help="This may significantly extend the tool execution time"> <option value="yes">Yes</option> <option value="no" selected="true">No</option> </param> </inputs> <outputs> <data name="output" label="${tool.name} execution log" format="txt" /> </outputs> <tests> <test> <!--Testing this tool is a bit difficult at the current time.--> </test> </tests> <help> **What it does** Uses the Galaxy/Bioblend API to execute the complete multilocus genotype analysis pipeline for corals or symbionts. Read this tutorial_ if you are not familiar with this tool. This tool must be able to access the corals (stag) database. .. _tutorial: https://github.com/gregvonkuster/galaxy_tools/blob/master/docs/corals/coralsnp_tutorial.md **Required options** * **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 * **Sample attributes file** - the Sample Attributes tabular file created by the Affymetrix sequencer for the plate * **Probeset annotation file** - the annotation CSV file created by the Affymetrix sequencer for the plate * **Apt-probeset genotype summary file** - the summary CSV file created by the Affymetrix sequencer for the plate * **Apt-probeset genotype snp-posteriors file** - the snp-posteriors CSV file created by the Affymetrix sequencer for the plate * **Apt-probeset genotype report file** - the report CSV file created by the Affymetrix sequencer for the plate * **Apt-probeset genotype confidences file** - the confidences CSV file created by the Affymetrix sequencer for the plate * **Apt-probeset genotype calls file** - the calls CSV file created by the Affymetrix sequencer for the plate * **Fasta reference sequence** - selected fasta reference dataset for the samples </help> <citations> <citation type="doi">https://doi.org/10.1038/s41598-020-69101-z</citation> </citations> </tool>