diff spring_model_all.xml @ 39:172398348efd draft

"planemo upload commit 26b4018c88041ee0ca7c2976e0a012015173d7b6-dirty"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/spring_model_all.xml	Fri Jan 22 15:50:27 2021 +0000
@@ -0,0 +1,51 @@
+<tool id="spring_model_all" name="SPRING Model-All" 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 '$__tool_directory__/spring_model_all.py' -p '$pairs' -ih '$index_hhr' -dh '$database_hhr' -i '$index_pdb' -d '$database_pdb' -c '$crossreference' -o 'models' -g '$log'
+    ]]></command>
+    <inputs>
+        <param format="tabular" name="pairs" type="data" label="Interacting Pairs" help="Tabular 2-column file containing putative protein interaction pairs."/>
+        <param format="ffindex" name="index_hhr" type="data" label="HHR Index" help="HHR Database Index file (ffindex)."/>
+        <param format="ffdata" name="database_hhr" type="data" label="HHR Database" help="HHR Database files (ffdata)."/>
+        <param format="ffindex" name="index_pdb" type="data" label="PDB Index" help="PDB Database Index file (ffindex)."/>
+        <param format="ffdata" name="database_pdb" type="data" label="PDB Database" help="PDB Database files (ffdata)."/>
+        <param format="tabular" name="crossreference" type="data" label="Cross Reference" help="SPRING PDB Cross Reference as produced by SPRING Cross tool."/>
+    </inputs>
+    <outputs>
+        <collection type="list" label="SPRING Model Structures" name="models">
+            <discover_datasets pattern="__name_and_ext__" directory="models" />
+        </collection>
+        <data format="tabular" name="log" label="SPRING Model Log"/>
+    </outputs>
+    <help><![CDATA[
+Creates protein complex model from HHsearch threading results.
+    ]]></help>
+    <tests>
+        <test>
+            <param name="pairs" value="model/pairs.txt" />
+            <param name="index_hhr" value="model/hhr.ffindex" />
+            <param name="database_hhr" value="model/hhr.ffdata" />
+            <param name="index_pdb" value="model/pdb_structures.ffindex" />
+            <param name="database_pdb" value="model/pdb_structures.ffdata" />
+            <param name="crossreference" value="model/crossreference.txt" />
+            <output name="log" file="model/log.txt"/>
+        </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>
\ No newline at end of file