--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/analysis_load_fasta.xml	Mon Sep 11 05:50:45 2017 -0400
@@ -0,0 +1,191 @@
+<?xml version="1.0"?>
+<tool id="analysis_load_fasta" profile="16.04" name="Load a Fasta 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 '${fasta}' "\${tmp_dir}/content.fasta"
+
+        &&
+
+        @AUTH@
+
+        tripaille analysis load_fasta
+
+            --organism_id '${organism}'
+
+            --analysis_id '${analysis}'
+
+            --sequence_type '${sequence_type}'
+
+            --method '${loading.method}'
+
+            --match_type '${loading.match_type}'
+
+            #if str($naming.re_name):
+                --re_name '${naming.re_name}'
+            #end if
+
+            #if str($naming.re_uniquename):
+                --re_uniquename '${naming.re_uniquename}'
+            #end if
+
+            #if str($relationships.rel_type) != "none":
+                --rel_type '${relationships.rel_type}'
+                --rel_subject_re '${relationships.rel_subject_re}'
+                --rel_subject_type '${relationships.rel_subject_type}'
+            #end if
+
+            #if str($ext_db.db_ext_id):
+                --db_ext_id '${ext_db.db_ext_id}'
+            #end if
+
+            #if str($ext_db.re_accession):
+                --re_accession '${ext_db.re_accession}'
+            #end if
+
+            "\${tmp_dir}/content.fasta"
+
+        &&
+
+        echo "Data loaded" > $results
+    ]]></command>
+    <inputs>
+        <param name="fasta"
+               type="data"
+               format="fasta"
+               label="Fasta file to load" />
+
+        <param argument="--organism"
+               type="select"
+               dynamic_options="list_organisms()"
+               label="Organism" />
+
+        <param argument="--analysis"
+               type="select"
+               dynamic_options="list_analyses()"
+               label="Analysis" />
+
+        <param name="sequence_type"
+               argument="--sequence_type"
+               type="text"
+               label="Sequence type"
+               value="contig"
+               help="this should be a Sequence Ontology term" />
+
+        <conditional name="loading">
+            <param name="method"
+                   argument="--method"
+                   type="select"
+                   label="Loading method"
+                   help="select wether you expect feature to be already existing or not">
+                <option value="insup" selected="true">Insert and update</option>
+                <option value="insert">Insert only</option>
+                <option value="update">Update only</option>
+            </param>
+            <when value="insup">
+                <expand macro="match_type" />
+            </when>
+            <when value="insert"/>
+            <when value="update">
+                <expand macro="match_type" />
+            </when>
+        </conditional>
+
+        <section name="naming" title="Feature naming">
+            <param name="re_name"
+                   argument="--re_name"
+                   type="text"
+                   optional="true"
+                   label="Regular expression to extract feature name"
+                   help="this regex will be applied on the fasta definition line to generate the feature name">
+                <expand macro="sanitized"/>
+            </param>
+
+            <param name="re_uniquename"
+                   argument="--re_uniquename"
+                   type="text"
+                   optional="true"
+                   label="Regular expression to extract feature uniquename"
+                   help="this regex will be applied on the fasta definition line to generate the feature uniquename">
+                <expand macro="sanitized"/>
+            </param>
+        </section>
+
+        <conditional name="relationships">
+            <param name="rel_type"
+                   argument="--rel_type"
+                   type="select"
+                   label="Relationship type"
+                   help="Use this when inserting features that should be associated to other already existing features">
+                <option value="none" selected="true">No relationship</option>
+                <option value="part_of">Part of (for CDS sequences)</option>
+                <option value="derives_from">Derives from (for peptide sequences)</option>
+            </param>
+            <when value="none"/>
+            <when value="part_of">
+                <expand macro="feature_rel" />
+            </when>
+            <when value="derives_from">
+                <expand macro="feature_rel" />
+            </when>
+        </conditional>
+
+        <section name="ext_db" title="Cross references to external database">
+            <param name="db_ext_id"
+                   argument="--db_ext_id"
+                   type="integer"
+                   optional="true"
+                   label="External Database ID"
+                   help="Numeric ID from the Chado database" />
+
+            <param name="re_accession"
+                   argument="--re_accession"
+                   type="text"
+                   optional="true"
+                   label="Regular expression to extract the accession from external DB"
+                   help="this regex will be applied on the fasta definition line to generate the accession from external DB" />
+        </section>
+    </inputs>
+    <outputs>
+        <data format="txt" name="results" label="Load Fasta into Tripal" />
+    </outputs>
+    <tests>
+        <test expect_failure="true" expect_exit_code="1">
+            <param name="fasta" value="citrus_genome.fasta" />
+            <param name="organism" value="Testus testus" />
+            <param name="analysis" value="Annotation xx" />
+            <param name="sequence_type" value="mRNA" />
+            <conditional name="loading">
+                <param name="method" value="insup" />
+                <param name="match_type" value="uniquename" />
+            </conditional>
+            <section name="naming">
+                <param name="re_name" value="([a-z]{4}[0-9]+)_suffix" />
+                <param name="re_uniquename" value="([a-z]{4}[0-9]+_suffix)" />
+            </section>
+
+            <expand macro="test_result" />
+        </test>
+    </tests>
+    <help><![CDATA[
+        @HELP_OVERVIEW@
+
+        **Load Fasta**
+
+        With this tool, you can load sequences from a Fasta file into the Tripal/Chado database.
+
+        Corresponding features can be created if needed.
+
+        @HELP@
+    ]]></help>
+    <expand macro="citation"/>
+</tool>