--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/analysis_load_gff3.xml	Mon Sep 11 05:51:14 2017 -0400
@@ -0,0 +1,187 @@
+<?xml version="1.0"?>
+<tool id="analysis_load_gff3" profile="16.04" name="Load a GFF3 annotation file" version="@WRAPPER_VERSION@.0">
+    <description>into Tripal</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <code file="tripal.py"/>
+    <expand macro="stdio"/>
+    <command><![CDATA[
+        tmp_dir=`mktemp -d -p "@DATA_DIR@"` && chmod a+rx "\${tmp_dir}"
+
+        &&
+
+        cp '${gff3}' "\${tmp_dir}/annotation.gff3"
+
+        &&
+
+        @AUTH@
+
+        tripaille analysis load_gff3
+
+            --organism_id '${organism}'
+
+            --analysis_id '${analysis}'
+
+            --import_mode '${import_mode}'
+
+            #if str($naming.mode) == 'manual':
+                --re_mrna '${naming.re_mrna}'
+                --re_protein '${naming.re_protein}'
+            #end if
+
+            #if str($advanced.landmark_type):
+                --landmark_type '${advanced.landmark_type}'
+            #end if
+
+            #if str($advanced.alt_id_attr):
+                --alt_id_attr '${advanced.alt_id_attr}'
+            #end if
+
+            ${advanced.create_organism}
+
+            #if str($target.target_organism):
+                --target_organism '${target.target_organism}'
+            #end if
+
+            #if str($target.target_type):
+                --target_type '${target.target_type}'
+            #end if
+
+            ${target.target_create}
+
+            "\${tmp_dir}/annotation.gff3"
+
+        &&
+
+        echo "Data loaded" > $results
+    ]]></command>
+    <inputs>
+        <param name="gff3"
+               type="data"
+               format="gff3"
+               label="Annotation file" />
+
+        <param argument="--organism"
+               type="select"
+               dynamic_options="list_organisms()"
+               label="Organism" />
+
+        <param argument="--analysis"
+               type="select"
+               dynamic_options="list_analyses()"
+               label="Analysis" />
+
+        <param name="import_mode"
+               argument="--import_mode"
+               type="select"
+               label="Loading method">
+            <option value="update" selected="true">Import everything, update when already existing</option>
+            <option value="add_only">Import only new features</option>
+        </param>
+
+        <conditional name="naming">
+            <param name="mode"
+                   type="select"
+                   label="Naming method for proteins"
+                   help="in case your GFF file does not contain polypeptide features">
+                <option value="auto">Automatic</option>
+                <option value="manual">Manual</option>
+            </param>
+            <when value="auto"/>
+            <when value="manual">
+                <param name="re_mrna"
+                       argument="--re_mrna"
+                       type="text"
+                       label="Regular expression for the mRNA name"
+                       help="this regex will be used to extract parts of the mRNA feature name">
+                    <expand macro="sanitized"/>
+                </param>
+
+                <param name="re_protein"
+                       argument="--re_protein"
+                       type="text"
+                       label="Replacement string for the protein name"
+                       help="will be used to generate the protein name based on the mRNA name">
+                    <expand macro="sanitized"/>
+                </param>
+            </when>
+        </conditional>
+
+        <section name="advanced" title="Advanced options" expanded="False">
+            <param name="landmark_type"
+                   argument="--landmark_type"
+                   type="text"
+                   optional="true"
+                   label="Landmark type"
+                   help="A Sequence Ontology type for the landmark sequences in the GFF fie (e.g. \'chromosome\'). Will be used to create them if they don't already exist." />
+
+            <param name="alt_id_attr"
+                   argument="--alt_id_attr"
+                   type="text"
+                   optional="true"
+                   label="ID attribute"
+                   help="Name of the GFF attribute that contains a unique identifier for each feature. Leave empty to use the 'ID' attribute" />
+
+            <param name="create_organism"
+                   argument="--create_organism"
+                   type="boolean"
+                   checked="false"
+                   truevalue="--create_organism"
+                   falsevalue=""
+                   label="Create organisms specified in 'organism' attribute"
+                   help="If not found, create features referenced in the target attribute." />
+        </section>
+
+        <section name="target" title="Target attribute handling" expanded="False">
+            <param name="target_organism"
+                   argument="--target_organism"
+                   type="text"
+                   optional="true"
+                   label="Target organism name"
+                   help="Name of organism corresponding to target attribute. Abbreviation or common name as created with the 'Create Organism' tool." />
+            <param name="target_type"
+                   argument="--target_type"
+                   type="text"
+                   optional="true"
+                   label="Target feature type"
+                   help="Type of features referenced in the target attribute. Should be a Sequence Ontology term." />
+            <param name="target_create"
+                   argument="--target_create"
+                   type="boolean"
+                   checked="false"
+                   truevalue="--target_create"
+                   falsevalue=""
+                   label="Create target features"
+                   help="If not found, create features referenced in the target attribute." />
+        </section>
+    </inputs>
+    <outputs>
+        <data format="txt" name="results" label="Load GFF3 into Tripal" />
+    </outputs>
+    <tests>
+        <test expect_failure="true" expect_exit_code="1">
+            <param name="gff3" value="sample.gff3" />
+            <param name="organism" value="Testus testus" />
+            <param name="analysis" value="Annotation xx" />
+            <conditional name="naming">
+                <param name="mode" value="manual" />
+                <param name="re_mrna" value="([a-z]{4}[0-9]+)_rna" />
+                <param name="re_protein" value="([a-z]{4}[0-9]+)_prot" />
+            </conditional>
+
+            <expand macro="test_result" />
+        </test>
+    </tests>
+    <help><![CDATA[
+        @HELP_OVERVIEW@
+
+        **Load GFF3**
+
+        With this tool, you can load features from a GFF3 file into the Tripal/Chado database.
+
+        @HELP@
+    ]]></help>
+    <expand macro="citation"/>
+</tool>