diff spring_minz.xml @ 0:d30785e31577 draft

"planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"

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+++ b/spring_minz.xml	Fri Jul 31 00:18:57 2020 -0400
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+<tool id="spring_minz" name="SPRING min-Z" version="0.1.0" python_template_version="3.5">
+    <description>filter operation</description>
+    <code file="spring_minz.py"/>
+    <command detect_errors="exit_code"><![CDATA[
+        mkdir -p inputs &&
+        #for input in $inputs:
+            link '${str(input)}' 'inputs/${input.name}' &&
+            echo '${input.name}' >> 'input_list' &&
+        #end for &&
+        python3 '$__tool_directory__/spring_minz.py' -m '$minscore' -t '$target' -c '$crossreference' -o '$output' -l input_list -i inputs
+    ]]></command>
+    <inputs>
+        <param format="data" name="target" type="data" label="Target Sequence" help="Homology search results of query sequence `hhr`. (-t)"/>
+        <param format="data" name="inputs" type="data_collection" collection_type="list" label="Input Sequences" help="Homology search results of target sequences `hhr`. (-i)"/>
+        <param format="data" name="crossreference" type="data" label="Cross Reference" help="Cross reference of interacting proteins pairs. (-c)"/>
+        <param name="minscore" type="integer" label="min-Z score threshold" value="10" min="1" max="100" help="Matching complex templates with a score lower than this threshold will be excluded. (-c)"/>
+    </inputs>
+    <outputs>
+        <data format="txt" name="output" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="target" value="NP_000282.1.hhr"/>
+            <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" />
+                </collection>
+            </param>
+            <param name="crossreference" value="index.txt"/>
+            <output name="output" file="result.txt"/>
+        </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.
+    ]]></help>
+    <citations>
+        <citation type="bibtex">
+@misc{githubhh-suite,
+author = {Guerler, Govindarajoo, Zhang},
+year = {2013},
+title = {Mapping Monomeric Threading to Protein-Protein Structure Prediction},
+publisher = {ACS Publications},
+journal = {Journal of Chemical Information and Modeling},
+url = {https://pubs.acs.org/doi/10.1021/ci300579r},
+}
+        </citation>
+    </citations>
+</tool>
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