Mercurial > repos > marpiech > norwich_tools

changeset 3:171a689adee2 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 781926e52355f7805db8d9a4ccafeff397b19aa4-dirty
author marpiech
date Mon, 29 Aug 2016 06:57:00 -0400
parents 16673005d799
children 33606cbc9806
files README contributors.txt rdock.xml
diffstat 3 files changed, 82 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README	Mon Aug 29 06:57:00 2016 -0400
@@ -0,0 +1,29 @@
+# README #
+
+This README would normally document whatever steps are necessary to get your application up and running.
+
+### What is this repository for? ###
+
+* Quick summary
+* Version
+* [Learn Markdown](https://bitbucket.org/tutorials/markdowndemo)
+
+### How do I get set up? ###
+
+* Summary of set up
+* Configuration
+* Dependencies
+* Database configuration
+* How to run tests
+* Deployment instructions
+
+### Contribution guidelines ###
+
+* Writing tests
+* Code review
+* Other guidelines
+
+### Who do I talk to? ###
+
+* Repo owner or admin
+* Other community or team contact
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/contributors.txt	Mon Aug 29 06:57:00 2016 -0400
@@ -0,0 +1,2 @@
+Marcin Piechota - marpiech
+Dzesika Hoinkis - dzesikah
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rdock.xml	Mon Aug 29 06:57:00 2016 -0400
@@ -0,0 +1,51 @@
+<tool id="rdock" name="rdock" version="1.0">
+    <description>tail-to-head</description>
+    <command>
+        <![CDATA[ 
+    	cat $inputmol2 > inputmol2.mol2; cat $inputprm | sed "s|RECEPTOR_FILE.*|RECEPTOR_FILE inputmol2.mol2|g" | sed "s|REF_MOL.*|REF_MOL ligand.sd|g" > new.prm; 
+        cp -r $__tool_directory__/tools/rdock/data .;
+        mkdir data/ligands; 
+        cp $inputsd data/ligands/ligand.sd; 
+        LD_LIBRARY_PATH=$__tool_directory__/tools/rdock/lib $__tool_directory__/tools/rdock/bin/rbcavity -r new.prm -was > /tmp/rbcavity.log; 
+		LD_LIBRARY_PATH=$__tool_directory__/tools/rdock/lib $__tool_directory__/tools/rdock/bin/rbdock -r new.prm -p dock.prm -n 100 -i $inputsd -o output_docking_out > /tmp/docking_out.log;
+        PERL5LIB=$__tool_directory__/tools/rdock/lib/ LD_LIBRARY_PATH=$__tool_directory__/tools/rdock/lib $__tool_directory__/tools/rdock/bin/sdsort -n -f'SCORE' output_docking_out.sd > sorted.sd; 
+        PYTHONPATH=/usr/lib/python2.7/dist-packages/ $__tool_directory__/tools/rdock/bin/sdrmsd $inputsd sorted.sd > $output_rdock
+    	]]>
+    </command>
+    <inputs>
+        <param name="inputprm" format="prm" type="data" label="PRM file" />
+        <param name="inputmol2" format="mol2" type="data" label="MOL2 file" />
+        <param name="inputsd" format="sd" type="data" label="SD file" />
+    </inputs>
+    <outputs>
+        <data name="output_rdock" format="data" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="inputprm" value="rdock/1sj0_rdock.prm" />
+            <param name="inputmol2" value="rdock/1sj0_rdock.mol2" />
+            <param name="inputsd" value="rdock/1sj0_ligand.sd" />
+            <output name="output_rdock">
+                <assert_contents>
+                    <has_n_columns n="2" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="inputprm" value="rdock/1nem_rdock.prm" />
+            <param name="inputmol2" value="rdock/1nem_rdock.mol2" />
+            <param name="inputsd" value="rdock/1nem_lig.sd" />
+            <output name="output_rdock">
+                <assert_contents>
+                    <has_n_columns n="2" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help>
+        rDock tool
+    </help>
+    <citations>
+        <citation type="doi">doi:10.1371/journal.pcbi.1003571</citation>
+    </citations>
+</tool>