diff spring_minz.xml @ 25:5d1ae615e4ec draft

"planemo upload commit ff7d7e512b79436c3538078552983762330a920d-dirty"

--- a/spring_minz.xml	Thu Oct 29 13:09:57 2020 +0000
+++ b/spring_minz.xml	Sat Oct 31 22:01:29 2020 +0000
@@ -1,4 +1,4 @@
-<tool id="spring_minz" name="SPRING min-Z" version="0.1.1" python_template_version="3.5">
+<tool id="spring_minz" name="SPRING min-Z" version="0.1.2" python_template_version="3.5">
     <description>filter operation</description>
     <code file="spring_minz.py"/>
     <command detect_errors="exit_code"><![CDATA[
@@ -13,9 +13,9 @@
                 link '${str(input)}' 'inputs/${input.element_identifier}' &&
                 echo '${input.element_identifier}' >> 'input_list' &&
             #end for
-            python3 '$__tool_directory__/spring_minz.py' -tl target_list -tp targets -il input_list -ip inputs -m '$minscore' -c '$crossreference' -x '$idx' -o '$output' -l '$log'
+            python3 '$__tool_directory__/spring_minz.py' -tl target_list -tp targets -il input_list -ip inputs -m '$minscore' -c '$crossreference' -o '$output' -l '$log'
         #else
-            python3 '$__tool_directory__/spring_minz.py' -tl target_list -tp targets -m '$minscore' -c '$crossreference' -x '$idx' -o '$output' -l '$log'
+            python3 '$__tool_directory__/spring_minz.py' -tl target_list -tp targets -m '$minscore' -c '$crossreference' -o '$output' -l '$log'
         #end if
     ]]></command>
     <inputs>
@@ -26,9 +26,8 @@
                 <param format="txt" name="inputs" type="data_collection" collection_type="list" label="Input profiles" help="Homology search results of input profiles `hhr`."/>
             </when>
         </conditional>
-        <param format="txt" name="crossreference" type="data" label="Cross reference" help="Cross reference of interacting proteins `first_id metadata_id second_id`."/>
+        <param format="tabular" 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="Score threshold" value="10" min="1" max="200" 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="20" help="Specify the length of the identifier e.g. `1ACB_A` has length 6."/>
     </inputs>
     <outputs>
         <data format="tabular" name="output" label="SPRING min-Z Table"/>
@@ -38,49 +37,29 @@
         <test>
             <param name="targets">
                 <collection type="list">
-                    <element name="7BQY_A.hhr" value="7BQY_A.hhr" />
-                    <element name="6WLC_A.hhr" value="6WLC_A.hhr" />
-                    <element name="6WJI_A.hhr" value="6WJI_A.hhr" />
-                    <element name="6WEY_A.hhr" value="6WEY_A.hhr" />
-                    <element name="6W37_A.hhr" value="6W37_A.hhr" />
-                    <element name="6W9C_A.hhr" value="6W9C_A.hhr" />
-                    <element name="6W4H_B.hhr" value="6W4H_B.hhr" />
-                    <element name="6W4H_A.hhr" value="6W4H_A.hhr" />
-                    <element name="6W9Q_A.hhr" value="6W9Q_A.hhr" />
-                </collection>
-            </param>
-            <conditional name="input_type">
-                <param name="input_type_selector" type="boolean" checked="false"/>
-            </conditional>
-            <param name="idx" value="10"/>
-            <param name="crossreference" value="dbCAN_random.txt"/>
-            <output name="output" file="dbCAN_result.txt"/>
-            <output name="log" file="dbCAN_log.txt"/>
-        </test>
-        <test>
-            <param name="targets">
-                <collection type="list">
-                    <element name="NP_000282.1.hhr" value="NP_000282.1.hhr" />
+                    <element name="NP_000282.1.hhr" value="minz/NP_000282.1.hhr" />
                 </collection>
             </param>
             <conditional name="input_type">
                 <param name="input_type_selector" type="boolean" checked="true"/>
                 <param name="inputs">
                     <collection type="list">
-                        <element name="NP_000282.1.hhr" value="NP_000282.1.hhr" />
-                        <element name="NP_000290.2.hhr" value="NP_000290.2.hhr" />
-                        <element name="NP_000548.2.hhr" value="NP_000548.2.hhr" />
-                        <element name="NP_000836.2.hhr" value="NP_000836.2.hhr" />
+                        <element name="NP_000282.1.hhr" value="minz/NP_000282.1.hhr" />
+                        <element name="NP_000290.2.hhr" value="minz/NP_000290.2.hhr" />
+                        <element name="NP_000548.2.hhr" value="minz/NP_000548.2.hhr" />
+                        <element name="NP_000836.2.hhr" value="minz/NP_000836.2.hhr" />
                     </collection>
                 </param>
             </conditional>
-            <param name="crossreference" value="pdb70_random.txt"/>
-            <output name="output" file="pdb70_result.txt"/>
-            <output name="log" file="pdb70_log.txt"/>
+            <param name="crossreference" value="minz/pdb70_random.txt"/>
+            <output name="output" file="minz/pdb70_result.txt"/>
+            <output name="log" file="minz/pdb70_log.txt"/>
         </test>
     </tests>
     <help><![CDATA[
-This tool creates 3D models from HH-search/HH-blits homology results utilized by SPRING.
+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>
     <citations>
         <citation type="bibtex">