--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/spring_minz.xml	Tue Mar 23 13:56:20 2021 +0000
@@ -0,0 +1,107 @@
+<tool id="spring_minz" name="SPRING Min-Z" license="MIT" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
+    <description>filter operation</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+        mkdir -p targets &&
+        #for target in $targets
+            ln -s '${target}' 'targets/${target.element_identifier}' &&
+            echo '${target.element_identifier}' >> 'target_list' &&
+        #end for
+        #if $input_type.input_type_selector == "yes":
+            mkdir -p ./inputs &&
+            #for input in $input_type.inputs
+                ln -s '${input}' 'inputs/${input.element_identifier}' &&
+                echo '${input.element_identifier}' >> 'input_list' &&
+            #end for
+            spring_minz.py
+            -tl target_list
+            -tp targets
+            -il input_list
+            -ip inputs
+            -m '$minscore'
+            -c '$crossreference'
+            -o '$output'
+            -l '$log'
+        #else
+            spring_minz.py
+            -tl target_list
+            -tp targets
+            -m '$minscore'
+            -c '$crossreference'
+            -o '$output'
+            -l '$log'
+        #end if
+    ]]>    </command>
+    <inputs>
+        <param name="targets" format="hhr" multiple="true" label="Target profiles" help="Homology search result of target/query profiles in 'hhr' format."/>
+        <conditional name="input_type">
+            <param name="input_type_selector" type="select" label="Identify interactions across sets?">
+                <option value="yes" selected="True">yes</option>
+                <option value="no">no</option>
+            </param>
+            <when value="yes">
+                <param name="inputs" format="hhr" multiple="true" label="Input profiles" help="Homology search results of input profiles in 'hhr' format."/>
+            </when>
+            <when value="no"/>
+        </conditional>
+        <param name="crossreference" format="tabular" type="data" label="Cross reference" help="Cross reference of interacting proteins `first_id metadata_id second_id`."/>
+        <param name="minscore" type="integer" value="10" min="1" max="200" label="Score threshold" help="Matching interaction pairs with a score lower than this threshold will be excluded."/>
+        <expand macro="logfile"/>
+    </inputs>
+    <outputs>
+        <data format="tabular" name="output" label="SPRING min-Z Table"/>
+        <data format="txt" name="log" label="SPRING min-Z Log">
+            <filter>logfile</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="targets">
+                <collection type="list">
+                    <element name="NP_000282.1.hhr" value="minz/NP_000282.1.hhr" ftype="hhr"/>
+                    <element name="NP_000290.2.hhr" value="minz/NP_000290.2.hhr" ftype="hhr"/>
+                    <element name="NP_000548.2.hhr" value="minz/NP_000548.2.hhr" ftype="hhr"/>
+                    <element name="NP_000836.2.hhr" value="minz/NP_000836.2.hhr" ftype="hhr"/>
+                </collection>
+            </param>
+            <conditional name="input_type">
+                <param name="input_type_selector" value="false"/>
+            </conditional>
+            <param name="crossreference" value="minz/pdb70_random.txt"/>
+            <output name="output" file="minz/pdb70_result.0.txt"/>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="targets">
+                <collection type="list">
+                    <element name="NP_000282.1.hhr" value="minz/NP_000282.1.hhr" ftype="hhr"/>
+                </collection>
+            </param>
+            <conditional name="input_type">
+                <param name="input_type_selector" value="true"/>
+                <param name="inputs">
+                    <collection type="list">
+                        <element name="NP_000282.1.hhr" value="minz/NP_000282.1.hhr" ftype="hhr"/>
+                        <element name="NP_000290.2.hhr" value="minz/NP_000290.2.hhr" ftype="hhr"/>
+                        <element name="NP_000548.2.hhr" value="minz/NP_000548.2.hhr" ftype="hhr"/>
+                        <element name="NP_000836.2.hhr" value="minz/NP_000836.2.hhr" ftype="hhr"/>
+                    </collection>
+                </param>
+            </conditional>
+            <param name="crossreference" value="minz/pdb70_random.txt"/>
+            <output name="output" file="minz/pdb70_result.1.txt"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+**What it does**
+
+This tool filters HH-search/HH-blits homology results through the protein interaction cross reference generated by SPRING. 
+Putative interactions are identified by evaluating the min-Z score. 
+The min-Z is the smaller of the two Z-scores for a pair of sequences matching an existing protein-protein complex structure.
+
+    ]]>    </help>
+    <expand macro="citations"/>
+</tool>