--- /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>
+