diff spring_minz.xml @ 9:4ac5d5a9b21c draft

"planemo upload commit f465445ebca0307953f59938494a2244ca8ea23c"

--- a/spring_minz.xml	Sat Aug 01 00:35:20 2020 -0400
+++ b/spring_minz.xml	Sat Aug 01 02:13:31 2020 -0400
@@ -7,13 +7,14 @@
             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 '$crossreference' -o '$output' -l input_list -i inputs
+        python3 '$__tool_directory__/spring_minz.py' -m '$minscore' -t '$target' -c '$crossreference' -x '$idx' -o '$output' -l input_list -i inputs
     ]]></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="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 pairs from SPRING database protocol."/>
+        <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."/>
+        <param name="idx" type="integer" label="Identifier length" value="6" min="1" max="10" help="Specify the length of the identifier e.g. `1ACB_A` has length 6."/>
     </inputs>
     <outputs>
         <data format="txt" name="output" />