Mercurial > repos > greg > queue_genotype_workflow
diff queue_genotype_workflow.xml @ 0:c80fae8c94c1 draft
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author | greg |
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date | Thu, 15 Aug 2019 11:17:33 -0400 |
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children | fa50d7c895c2 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/queue_genotype_workflow.xml Thu Aug 15 11:17:33 2019 -0400 @@ -0,0 +1,70 @@ +<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 '$summary' +--output '$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 and no more than 96 lines of data"><![CDATA[value is not None and value.metadata.columns==32 and value.metadata.data_lines<=96]]></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> + </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 symbiants. +This tool must be able to access the corals (stag) database. + + </help> + <citations> + <citation type="bibtex"> + @misc{None, + journal = {None}, + author = {Baums I}, + title = {Manuscript in preparation}, + year = {None}, + url = {http://baumslab.org} + </citation> + </citations> +</tool> +