# HG changeset patch
# User marpiech
# Date 1472469260 14400
# Node ID fda6e327fac844870cf51b7e1cf038606c8e60c1
# Parent  33606cbc9806d045b99c7ba98dd2ddb52d6bfecf
planemo upload

diff -r 33606cbc9806 -r fda6e327fac8 sample.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sample.xml	Mon Aug 29 07:14:20 2016 -0400
@@ -0,0 +1,11 @@
+<tool id="sam_filter_1" name="SAM Filter">
+	<command interpreter="python">
+		
+	</command>
+	<inputs>
+		
+	</inputs>
+	<outputs>
+	
+	</outputs>
+</tool>
diff -r 33606cbc9806 -r fda6e327fac8 smina.xml
--- a/smina.xml	Mon Aug 29 07:05:34 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,146 +0,0 @@
-<tool id="smina" name="smina" version="0.1.0">
-    <stdio>
-        <exit_code range="1:" />
-    </stdio>
-    <command>
-        <![CDATA[ 
-        cat $receptor > receptor.pdbqt;
-        cat $ligand > ligand.pdbqt;
-        $__tool_directory__/tools/smina/smina.static 
-                                                    --receptor receptor.pdbqt 
-                                                    --ligand ligand.pdbqt 
-
-                                                    #if $flex
-                                                    --flex $flex
-                                                    #end if
-                                                    #if $flexres
-                                                    --flexres $flexres
-                                                    #end if
-                                                    #if $flexdist_ligand
-                                                    --flexdist_ligand $flexdist_ligand
-                                                    #end if
-                                                    #if $flexdist
-                                                    --flexdist $flexdist
-                                                    #end if
-
-                                                    --center_x $center_x 
-                                                    --center_y $center_y
-                                                    --center_z $center_z 
-                                                    --size_x $size_x
-                                                    --size_y $size_y
-                                                    --size_z $size_z
-
-                                                    #if $autobox_ligand
-                                                    --autobox_ligand $autobox_ligand 
-                                                    #end if 
-                                                    #if $autobox_add 
-                                                    --autobox_add $autobox_add
-                                                    #end if
-                                                    #if $no_lig=="true"
-                                                    --no_lig
-                                                    #end if 
-
-                                                    --scoring $scoring 
-                                                    #if $custom_scoring
-                                                    --custom_scoring $custom_scoring
-                                                    #end if
-                                                    #if $custom_atoms
-                                                    --custom_atoms $custom_atoms 
-                                                    #end if
-                                                    #if $score_only=="true"
-                                                    --score_only 
-                                                    #end if
-                                                    #if $local_only=="true"
-                                                    --local_only 
-                                                    #end if
-                                                    #if $minimize=="true"
-                                                    --minimize 
-                                                    #end if 
-                                                    #if $randomize_only=="true"    
-                                                    --randomize_only  
-                                                    #end if 
-                                                    #if $minimize_iters  
-                                                    --minimize_iters $minimize_iters 
-                                                    #end if
-
-                                                    --seed 1000 > $output;
-                                                    cat $output > /tmp/ouput
-    ]]>
-    </command>
-    <inputs>
-        <param name="receptor" type="data" format="pdbqt" label="receptor: rigid part of the receptore" />
-        <param name="ligand" type="data" format="data" label="ligand: ligand(s)" />
-
-        <param name="flex" type="data" format="pdbqt" label="flex: flexible side chains, if any" optional="true" />
-        <param name="flexres" type="text" label="flexres: flexible side chains specified by comma separated list of chain:resid" optional="true" />
-        <param name="flexdist_ligand" type="data" format="data" label="flexdist_ligand: Ligand to use for flexdist" optional="true" />
-        <param name="flexdist" type="float" label="flexdist: set all side chains within specified distance to flexdist_ligand to flexible" optional="true" />
-
-        <param name="center_x" type="float" value="0" label="center_x: X coordinate of the center" />
-        <param name="center_y" type="float" value="0" label="center_y: Y coordinate of the center" />
-        <param name="center_z" type="float" value="0" label="center_z: Z coordinate of the center" />
-        <param name="size_x" type="integer" value="1" label="size_x: size in the X dimension" />
-        <param name="size_y" type="integer" value="1" label="size_y: size in the Y dimension" />
-        <param name="size_z" type="integer" value="1" label="size_z: size in the Z dimension" />
-
-        <param name="autobox_ligand" type="data" format="data" label="autobox_ligand: Ligand to use for autobox" optional="true" />
-        <param name="autobox_add" type="float" value="4" label="autobox_add: Amount of buffer space to add to auto-generated box text(default +4 on all six sides)" optional="true" />
-        <param name="no_lig" type="select" label="no_lig: no ligand; for sampling/minimizing flexible residues (Type true if you want to use it)" optional="true">
-            <option value="false" selected="true">Don't use this option</option>
-            <option value="true">Use this option</option>
-        </param>
-
-        <param name="scoring" type="select" label="scoring: specify alternative builtin scoring function" optional="true">
-            <option value="default" selected="true">default</option>
-            <option value="ad4_scoring">ad4_scoring</option>
-            <option value="dkoes_fast">dkoes_fast</option>
-            <option value="dkoes_scoring">dkoes_scoring</option>
-            <option value="dkoes_scoring_old">dkoes_scoring_old</option>
-            <option value="vina">vina</option>
-            <option value="vinardo">vinardo</option>
-        </param>
-        <param name="custom_scoring" type="data" format="data" label="custom_scoring: custom scoring function file" optional="true" />
-        <param name="custom_atoms" type="data" format="data" label="custom_atoms: custom atom type parameters file" optional="true" />
-        <param name="score_only" type="select" label="score_only: score provided ligand pose" optional="true">
-            <option value="false" selected="true">Don't use this option</option>
-            <option value="true">Use this option</option>
-            </param>
-        <param name="local_only" type="select" label="local_only: local search only using autobox (you probably want to use --minimize)" optional="true">
-            <option value="false" selected="true">Don't use this option</option>
-            <option value="true">Use this option</option>
-        </param>
-        <param name="minimize" type="select" label="minimize: energy minimization" optional="true">
-            <option value="false" selected="true">Don't use this option</option>
-            <option value="true">Use this option</option>
-        </param>
-        <param name="randomize_only" type="select" label="randomize_only: generate random poses, attempting to avoid clashes" optional="true">
-            <option value="false" selected="true">Don't use this option</option>
-            <option value="true">Use this option</option>
-        </param>
-        <param name="minimize_iters" type="integer" label="minimize_iters: number iterations of steepest descent; default scales with rotors and usually isn't sufficient for convergence" optional="true" />
-    </inputs>
-    <outputs>
-        <data name="output" format="data" />
-    </outputs>
-    <tests>
-        <test>
-            <param name="receptor" value="smina/protein.pdbqt" />
-            <param name="ligand" value="smina/ligand.pdbqt" />
-            <param name="center_x" value="11" />
-            <param name="center_y" value="90.5" />
-            <param name="center_z" value="57.5" />
-            <param name="size_x" value="22" />
-            <param name="size_y" value="24" />
-            <param name="size_z" value="28" />
-            <output name="output" file="smina/output_smina" />
-        </test>
-    </tests>
-    <help>
-        "Smina help"
-    </help>
-    <citations>
-        <citation type="bibtex">
-            @misc{renameTODO, author = {LastTODO, FirstTODO}, year = {TODO}, title = {TODO}, url = {https://sourceforge.net/projects/smina/}, }
-        </citation>
-    </citations>
-</tool>