diff spring_model.xml @ 39:172398348efd draft

"planemo upload commit 26b4018c88041ee0ca7c2976e0a012015173d7b6-dirty"

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+++ b/spring_model.xml	Fri Jan 22 15:50:27 2021 +0000
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+<tool id="spring_model" name="SPRING Model" version="0.1.0" python_template_version="3.5" license="MIT">
+    <description>complex structures</description>
+    <requirements>
+        <requirement type="package" version="1.78">biopython</requirement>
+        <requirement type="package" version="20170708">tmalign</requirement>
+        <requirement type="package" version="3.06">pulchra</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        python3 '$__tool_directory__/spring_model.py' -a '$a' -b '$b' -i '$index' -d '$database' -c '$cross' -o '$output'
+    ]]></command>
+    <inputs>
+        <param format="text" name="a" type="data" label="First HHR target file" help="Threading result for target sequence using HHsearch."/>
+        <param format="text" name="b" type="data" label="Second HHR target file" help="Threading result for target sequence using HHsearch."/>
+        <param format="ffindex" name="index" type="data" label="PDB Index" help="PDB Database Index file (ffindex)."/>
+        <param format="ffdata" name="database" type="data" label="PDB Database" help="PDB Database files (ffdata)."/>
+        <param format="tabular" name="cross" type="data" label="Cross Reference" help="SPRING PDB Cross Reference as produced by SPRING Cross tool."/>
+    </inputs>
+    <outputs>
+        <data format="pdb" name="output" label="SPRING Model Structure"/>
+    </outputs>
+    <help><![CDATA[
+Creates protein complex model from HHsearch threading results.
+    ]]></help>
+    <tests>
+        <test>
+            <param name="a" value="model/ACE2_HUMAN.hhr" />
+            <param name="b" value="model/SPIKE_SARS2.hhr" />
+            <param name="index" value="model/pdb_structures.ffindex" />
+            <param name="database" value="model/pdb_structures.ffdata" />
+            <param name="cross" value="model/crossreference.txt" />
+            <output name="output" file="model/sp|Q9BYF1|ACE2_HUMAN.sp|P0DTC2|SPIKE_SARS2.pdb"/>
+        </test>
+    </tests>
+    <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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