view queue_genotype_workflow.xml @ 2:fa50d7c895c2 draft

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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 '$summary'
--output '$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>
    </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>