Mercurial > repos > bgruening > autodock_vina_prepare_box

diff prepare_box.xml @ 2:73c2c9774c2d draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
author bgruening
date Wed, 02 Oct 2019 12:49:11 -0400
parents 4f7c5cad3377
children 908880455b2d
line wrap: on
line diff
--- a/prepare_box.xml	Tue May 07 13:31:59 2019 -0400
+++ b/prepare_box.xml	Wed Oct 02 12:49:11 2019 -0400
@@ -6,18 +6,20 @@
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         python '$__tool_directory__/calc_vina_box_params.py'
-        --ligand '$input1'
-        --config '$output1'
+        --ligand '$ligand'
+        --config '$output'
         --bufx '$bufx'
         --bufy '$bufy'
         --bufz '$bufz'
-        --exh '$exh'
+        #if $exh:
+            --exh '$exh'
+        #end if
         #if $seed_value:
             --seed '$seed_value'
         #end if
     ]]></command>
     <inputs>
-        <param type="data" name="input1" format="mol" label="Input ligand"
+        <param type="data" name="ligand" format="mol" label="Input ligand"
             help="The input ligand (mol file)"/>
         <param name="bufx" type="float" value="0" label="x-axis buffer"
             help="Buffer in the x direction (in angs.)"/>
@@ -25,24 +27,30 @@
             help="Buffer in the y direction (in angs.)"/>
         <param name="bufz" type="float" value="0" label="z-axis buffer"
             help="Buffer in the z direction (in angs.)"/>
-        <param name="exh" type="integer" value="0" label="Exhaustiveness"
-            help="Number of poses to return from docking job"/>
-        <!-- <param name="seed" type="boolean" label="Specify random seed for simulation reproducibility?"/> -->
+        <param name="exh" type="integer" optional="true" label="Exhaustiveness (optional)"
+            help="Exhaustiveness of global search (optional, default = 8)"/>
         <param type="integer" name="seed_value" optional="true" label="Random seed (optional)" 
             help="Choose a seed value; if none is selected, a seed will be chosen randomly"/>
     </inputs>
     <outputs>
-        <data name="output1" format="txt" />
+        <data name="output" format="txt" />
     </outputs>
     <tests>
         <test>
-            <param name="input1" value="NUDT5A-x0114_2.mol" />
+            <param name="ligand" value="NUDT5A-x0114_2.mol" />
+            <param name="bufx" value="1" />
+            <param name="bufy" value="2" />
+            <param name="bufz" value="3" />
+            <output name="output" file="box_params_1.txt" />
+        </test>
+        <test>
+            <param name="ligand" value="NUDT5A-x0114_2.mol" />
             <param name="bufx" value="1" />
             <param name="bufy" value="2" />
             <param name="bufz" value="3" />
             <param name="exh" value="10" />
             <param name="seed_value" value="1" />
-            <output name="output1" file="box_params.txt" />
+            <output name="output" file="box_params_2.txt" />
         </test>
     </tests>
     <help>