diff spring_minz.xml @ 17:c790d25086dc draft

"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"

--- a/spring_minz.xml	Sat Oct 24 17:48:06 2020 +0000
+++ b/spring_minz.xml	Wed Oct 28 05:11:56 2020 +0000
@@ -7,10 +7,12 @@
             link '${str(input)}' 'inputs/${input.element_identifier}' &&
             echo '${input.element_identifier}' >> 'input_list' &&
         #end for
+		mkdir -p targets &&
         #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 &&
+            link '${str(target)}' 'targets/${target.element_identifier}' &&
+            echo '${target.element_identifier}' >> 'target_list' &&
         #end for
-        echo 0
+		python3 '$__tool_directory__/spring_minz.py' -il input_list -ip inputs -tl target_list -tp targets -m '$minscore' -c '$crossreference' -x '$idx' -o '$output'
     ]]></command>
     <inputs>
         <param format="txt" name="targets" type="data_collection" label="Target Profiles" help="Homology search result of target/query profiles `hhr`."/>
@@ -73,8 +75,7 @@
         </test>
     </tests>
     <help><![CDATA[
-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.
+This tool creates 3D models from HH-search/HH-blits homology results utilized by SPRING.
     ]]></help>
     <citations>
         <citation type="bibtex">