# HG changeset patch
# User guerler
# Date 1601060834 0
# Node ID 21a7dd67b4838f5bd6c434c53c3cfe49d3d8e954
# Parent  860bd6f8f4802119a77583d83e408d4c8e1c4050
"planemo upload commit f208fb81425711754738fc8e612ee2d5cc26377f"

diff -r 860bd6f8f480 -r 21a7dd67b483 spring_minz.py
--- a/spring_minz.py	Sat Aug 01 04:16:19 2020 -0400
+++ b/spring_minz.py	Fri Sep 25 19:07:14 2020 +0000
@@ -41,9 +41,9 @@
 				interactions.append((name, minz))
 				print("Predicting: %s, min-Z: %s" % (name, minz))
 		interactions.sort(key=lambda tup: tup[1], reverse=True)
-	with open(args.output, 'w') as output_file:
+	with open(args.output, 'a+') as output_file:
 		for i in interactions:
-			output_file.write("%s %s\n" % (i[0], i[1]))
+			output_file.write("%s %s %s\n" % (args.name, i[0], i[1]))
 
 def get_template_scores(hhr_file, min_score, identifier_length):
 	result = {}
@@ -63,6 +63,7 @@
 if __name__ == "__main__":
 	parser = argparse.ArgumentParser(description='This script identifies interactions by detecting matching HH-search results.')
 	parser.add_argument('-t', '--target', help='HHR target file result', required=True)
+	parser.add_argument('-n', '--name', help='HHR target name', required=True)
 	parser.add_argument('-c', '--crossreference', help='Cross Reference index file', required=True)
 	parser.add_argument('-x', '--idx', help='Length of identifier', type=int, default=6)
 	parser.add_argument('-l', '--list', help='Text file containing identifiers.', required=True)
diff -r 860bd6f8f480 -r 21a7dd67b483 spring_minz.xml
--- a/spring_minz.xml	Sat Aug 01 04:16:19 2020 -0400
+++ b/spring_minz.xml	Fri Sep 25 19:07:14 2020 +0000
@@ -7,10 +7,12 @@
             link '${str(input)}' 'inputs/${input.element_identifier}' &&
             echo '${input.element_identifier}' >> 'input_list' &&
         #end for
-        python3 '$__tool_directory__/spring_minz.py' -m '$minscore' -t '$target' -c '$crossreference' -x '$idx' -o '$output' -l input_list -i inputs
+        #for target in $targets
+            python3 '$__tool_directory__/spring_minz.py' -m '$minscore' -t '${str(target)}' -n '${target.element_identifier}' -c '$crossreference' -x '$idx' -o '$output' -l input_list -i inputs
+        #end for
     ]]></command>
     <inputs>
-        <param format="txt" name="target" type="data" label="Target Profile" help="Homology search result of target/query profile `hhr`."/>
+        <param format="txt" name="targets" type="data_collection" label="Target Profiles" help="Homology search result of target/query profiles `hhr`."/>
         <param format="txt" name="inputs" type="data_collection" collection_type="list" label="Input Profiles" help="Homology search results of input profiles `hhr`."/>
         <param format="txt" name="crossreference" type="data" label="Cross Reference" help="Cross reference of interacting proteins `first_id metadata_id second_id`."/>
         <param name="minscore" type="integer" label="min-Z score threshold" value="10" min="1" max="100" help="Matching interaction pairs with a score lower than this threshold will be excluded."/>
@@ -21,7 +23,11 @@
     </outputs>
     <tests>
         <test>
-            <param name="target" value="7BQY_A.hhr"/>
+            <param name="targets">
+                <collection type="list">
+                    <element name="7BQY_A.hhr" value="7BQY_A.hhr" />
+                </collection>
+            </param>
             <param name="idx" value="10"/>
             <param name="inputs">
                 <collection type="list">
@@ -39,7 +45,11 @@
             <output name="output" file="dbCAN_result.txt"/>
         </test>
         <test>
-            <param name="target" value="NP_000282.1.hhr"/>
+            <param name="targets">
+                <collection type="list">
+                    <element name="NP_000282.1.hhr" value="NP_000282.1.hhr" />
+                </collection>
+            </param>
             <param name="inputs">
                 <collection type="list">
                     <element name="NP_000282.1.hhr" value="NP_000282.1.hhr" />
diff -r 860bd6f8f480 -r 21a7dd67b483 test-data/dbCAN_result.txt
--- a/test-data/dbCAN_result.txt	Sat Aug 01 04:16:19 2020 -0400
+++ b/test-data/dbCAN_result.txt	Fri Sep 25 19:07:14 2020 +0000
@@ -1,3 +1,3 @@
-6W9C_A.hhr 24.2
-6W4H_B.hhr 24.0
-6W37_A.hhr 14.0
+7BQY_A.hhr 6W9C_A.hhr 24.2
+7BQY_A.hhr 6W4H_B.hhr 24.0
+7BQY_A.hhr 6W37_A.hhr 14.0
diff -r 860bd6f8f480 -r 21a7dd67b483 test-data/pdb70_result.txt
--- a/test-data/pdb70_result.txt	Sat Aug 01 04:16:19 2020 -0400
+++ b/test-data/pdb70_result.txt	Fri Sep 25 19:07:14 2020 +0000
@@ -1,2 +1,2 @@
-NP_000282.1.hhr 875.1
-NP_000290.2.hhr 86.5
+NP_000282.1.hhr NP_000282.1.hhr 875.1
+NP_000282.1.hhr NP_000290.2.hhr 86.5