Mercurial > repos > marpiech > norwich_tools

changeset 1:5c9f84736e6e draft

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planemo upload
author marpiech
date Mon, 29 Aug 2016 06:28:40 -0400
parents bc03dbb6eb37
children 16673005d799
files README contributors.txt rdock.xml
diffstat 3 files changed, 0 insertions(+), 82 deletions(-) [+]
line wrap: on
line diff
--- a/README	Mon Aug 29 03:38:13 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,29 +0,0 @@
-# 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
--- a/contributors.txt	Mon Aug 29 03:38:13 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
-Marcin Piechota - marpiech
-Dzesika Hoinkis - dzesikah
--- a/rdock.xml	Mon Aug 29 03:38:13 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,51 +0,0 @@
-<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>