--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/spring_mcc.xml	Tue Mar 23 13:56:55 2021 +0000
@@ -0,0 +1,83 @@
+<tool id="spring_mcc" name="SPRING MCC" license="MIT" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
+    <description>plot generator</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+    spring_mcc.py
+        -i '$input'
+        -b '$database'
+        -e '$experiment'
+        -l '$sampling.locations'
+        -ra '$sampling.regiona'
+        -rb '$sampling.regionb'
+        -n '$sampling.negative'
+        -o '$output'
+    ]]>    </command>
+    <inputs>
+        <param name="experiment" type="text" label="Title" help="Experiment title" value="Results" />
+        <param name="input" type="data" format="tabular" label="Interacting Pairs" help="Prediction input containing UniProt Accession codes (2-columns)." />
+        <conditional name="sampling">
+            <param name="type" type="select" label="Non-interacting Pairs" display="radio" help="Specify how to determine non-interacting pairs.">
+                <option value="random">Random Sampling</option>
+                <option value="uniprot">Sampling with UniProt Localization</option>
+                <option value="negative">Specify non-interacting pairs</option>
+            </param>
+            <when value="uniprot">
+                <param name="locations" type="data" format="tabular" label="UniProt Localization Database" help="UniProt tabular export with localization column to sample non-interacting pairs." />
+                <param name="negative" type="hidden" value="" />
+                <param name="regiona" type="select" label="Choose First Subcellular Location">
+                    <option value="Cell">Cell</option>
+                    <option value="Cytoplasm">Cytoplasm</option>
+                    <option value="Membrane" selected="True">Membrane</option>
+                    <option value="Mitochondrion" selected="True">Mitochondrion</option>
+                    <option value="Nucleus">Nucleus</option>
+                    <option value="Periplasm">Periplasm</option>
+                    <option value="Secreted">Secreted</option>
+                </param>
+                <param name="regionb" type="select" label="Choose Second Subcellular Location">
+                    <option value="Cell">Cell</option>
+                    <option value="Cytoplasm">Cytoplasm</option>
+                    <option value="Membrane" selected="True">Membrane</option>
+                    <option value="Mitochondrion" selected="True">Mitochondrion</option>
+                    <option value="Nucleus">Nucleus</option>
+                    <option value="Periplasm">Periplasm</option>
+                    <option value="Secreted">Secreted</option>
+                </param>
+            </when>
+            <when value="random">
+                <param name="locations" type="hidden" value="" />
+                <param name="negative" type="hidden" value="" />
+                <param name="regiona" type="hidden" value="" />
+                <param name="regionb" type="hidden" value="" />
+            </when>
+            <when value="negative">
+                <param name="locations" type="hidden" value="" />
+                <param name="negative" type="data" format="tabular" label="Non-interacting Pairs" help="Tabular file containing non-interacting pairs (2-columns)." />
+                <param name="regiona" type="hidden" value="" />
+                <param name="regionb" type="hidden" value="" />
+            </when>
+        </conditional>
+        <param name="database" type="data" format="tabular" label="BioGRID Database" help="BioGRID Database in TAB 3.0 format." />
+    </inputs>
+    <outputs>
+        <data format="png" name="output" label="SPRING MCC Image" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="mcc/human_hv1h2.txt" />
+            <param name="database" value="mcc/biogrid_fret.txt" />
+            <output name="output" file="mcc/human_hv1h2.png" compare="sim_size" />
+        </test>
+    </tests>
+    <help><![CDATA[
+
+**What it does**
+
+This tool generates a MCC plot for a given 2-column tabular prediction file containing UniProt Accession codes. The prediction is compared
+to a given BioGRID database file in TAB 3.0 format. Non-interacting protein pairs are randomly sampled.
+
+    ]]>    </help>
+    <expand macro="citations" />
+</tool>
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