diff galaxy_stubs/CalculateEnergy.xml @ 2:605370bc1def draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/galaxy_stubs/CalculateEnergy.xml	Tue Jul 12 12:33:33 2016 -0400
@@ -0,0 +1,64 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
+<!--Proposed Tool Section: [ForceFields]-->
+<tool id="CalculateEnergy" name="CalculateEnergy" version="1.1.0">
+  <description>calculate free energy of a protein </description>
+  <macros>
+    <token name="@EXECUTABLE@">CalculateEnergy</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>CalculateEnergy
+
+#if $param_pdb:
+  -pdb $param_pdb
+#end if
+#if $param_force_field:
+  -force_field
+  #if " " in str($param_force_field):
+    "$param_force_field"
+  #else
+    $param_force_field
+  #end if
+#end if
+#if $param_non_bond_cutoff:
+  -non_bond_cutoff $param_non_bond_cutoff
+#end if
+#if $param_elec_stat_cuton:
+  -elec_stat_cuton $param_elec_stat_cuton
+#end if
+#if $param_elec_stat_cutoff:
+  -elec_stat_cutoff $param_elec_stat_cutoff
+#end if
+#if $param_dist_dep_dielec:
+  -dist_dep_dielec $param_dist_dep_dielec
+#end if
+#if $param_overwrite_types:
+  -overwrite_types $param_overwrite_types
+#end if
+#if $param_overwrite_charges:
+  -overwrite_charges $param_overwrite_charges
+#end if
+</command>
+  <inputs>
+    <param name="param_pdb" type="data" format="pdb" optional="False" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="input pdb file" help="(-pdb) "/>
+    <param name="param_force_field" type="select" optional="True" value="AMBER" label="force field (AMBER, MMFF94)" help="(-force_field) ">
+      <option value="AMBER">AMBER</option>
+      <option value=" MMFF94"> MMFF94</option>
+    </param>
+    <param name="param_non_bond_cutoff" type="float" value="20.0" label="cutoff radius in calculations of nonbonded interactions" help="(-non_bond_cutoff) "/>
+    <param name="param_elec_stat_cuton" type="float" value="13.0" label="electrostatic cuton" help="(-elec_stat_cuton) "/>
+    <param name="param_elec_stat_cutoff" type="float" value="15.0" label="electrostatic cutoff" help="(-elec_stat_cutoff) "/>
+    <param name="param_dist_dep_dielec" type="integer" min="0" max="1" optional="True" value="0" label="apply distance dependent dielectric constant" help="(-dist_dep_dielec) "/>
+    <param name="param_overwrite_types" type="integer" min="0" max="1" optional="True" value="0" label="overwrite even non-empty type names" help="(-overwrite_types) "/>
+    <param name="param_overwrite_charges" type="integer" min="0" max="1" optional="True" value="0" label="overwrite even non-zero charges" help="(-overwrite_charges) "/>
+  </inputs>
+  <expand macro="advanced_options"/>
+  <outputs>
+    <data name="param_stdout" format="text" label="Output from stdout"/>
+  </outputs>
+  <help>This tool computes the free energy of a pdb file using a specified force field (-force_field) and force field parameters (-non_bond_cutoff, -elec_stat_cuton ... ).
+
+</help>
+</tool>