--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/egapx_runner.xml	Sat Aug 03 12:10:13 2024 +0000
@@ -0,0 +1,47 @@
+<tool name="egapx_runner" id="egapx_runner" version="6.0.1" profile="22.05">
+  <!--Source in git at: https://github.com/fubar2/galaxy_tf_overlay-->
+  <!--Created by toolfactory@galaxy.org at 03/08/2024 10:40:32 using the Galaxy Tool Factory.-->
+  <description>Runs egapx</description>
+  <requirements>
+    <requirement version="3.12.3" type="package">python</requirement>
+    <requirement version="24.04.4-0" type="package">nextflow</requirement>
+    <requirement version="6.0.1" type="package">pyyaml</requirement>
+  </requirements>
+  <version_command><![CDATA[echo "6.0.1"]]></version_command>
+  <command><![CDATA[mkdir -p ./egapx_config &&
+#set econfigfile = $econfig + '.config'
+cp  '$__tool_directory__/ui/assets/config/executor/$econfigfile' ./egapx_config/ &&
+python '$__tool_directory__/ui/egapx.py' '$yamlconfig'  -e '$econfig' -o 'egapx_out']]></command>
+  <inputs>
+    <param name="yamlconfig" type="data" optional="false" label="egapx configuration yaml file to execute" help="" format="yaml,txt" multiple="false"/>
+    <param name="econfig" type="select" label="Configuration" help="">
+      <option value="docker_minimal">docker minimal only works for the minimal dust mite sample using 6GB and 4 cores</option>
+      <option value="singularity">singularity requires at least 128GB ram and 32 cores. 256GB and 64 cores recommendd</option>
+      <option value="docker">docker requires at least 128GB ram and 32 cores. 256GB and 64 cores recommend</option>
+    </param>
+  </inputs>
+  <outputs>
+    <collection name="egapx_out" type="list" label="Outputs from egapx">
+      <discover_datasets pattern="__name_and_ext__" directory="egapx_out" visible="false"/>
+    </collection>
+  </outputs>
+  
+
+<tests>
+    <test>
+      <output_collection name="egapx_out" count="8"/>
+      <param name="yamlconfig" value="yamlconfig_sample"/>
+      <param name="econfig" value="docker_minimal"/>
+    </test>
+</tests>
+
+
+
+  <help><![CDATA[
+ **What it Does**
+  ]]></help>
+  <citations>
+    <citation type="doi">10.1093/bioinformatics/bts573</citation>
+  </citations>
+</tool>
+