diff spring_map.xml @ 37:0be0af9e695d draft

"planemo upload commit c716195a2cc1ed30ff8c4936621091296a93b2fc"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/spring_map.xml	Wed Nov 25 14:35:35 2020 +0000
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+<tool id="spring_map" name="SPRING Map" version="0.1.0" python_template_version="3.5" license="MIT">
+    <description>with BLAST</description>
+    <requirements>
+        <requirement type="package" version="2.10.1">blast</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        python3 '$__tool_directory__/spring_map.py' -l '$list' -i '$index' -d '$database' -c '$cross' -o '$output' -g '$log' -t temp
+    ]]></command>
+    <inputs>
+        <param format="tabular" name="list" type="data" label="PDB Chain Identifiers" help="List of PDB chains [PDB_CHAIN]."/>
+        <param format="tabular" name="index" type="data" label="PDB Database Index" help="Database Index file (ffindex)."/>
+        <param format="data" name="database" type="data" label="PDB Database" help="Database Data file (ffdata)."/>
+        <param format="tabular" name="cross" type="data" label="Unmapped Cross Reference" help="SPRING PDB Cross Reference (unmapped)."/>
+    </inputs>
+    <outputs>
+        <data format="tabular" name="output" label="SPRING Map Cross Reference"/>
+        <data format="txt" name="log" label="SPRING Map Log"/>
+    </outputs>
+    <help><![CDATA[
+Creates a 3rd column for the SPRING cross reference containing the chain identifier of the binding partners homologue.
+    ]]></help>
+    <tests>
+        <test>
+            <param name="list" value="cross/chains.tabular" />
+            <param name="index" value="cross/pdb.ffindex" />
+            <param name="database" value="cross/pdb.ffdata" />
+            <param name="cross" value="cross/reference.tabular" />
+            <output name="output" file="map/mapped.reference.tabular"/>
+        </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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