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

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author luis
date Tue, 12 Jul 2016 12:33:33 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/galaxy_stubs/CrystalGenerator.xml	Tue Jul 12 12:33:33 2016 -0400
@@ -0,0 +1,324 @@
+<?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: [Structure Creation]-->
+<tool id="CrystalGenerator" name="CrystalGenerator" version="VERSION">
+  <description>creates crystals</description>
+  <macros>
+    <token name="@EXECUTABLE@">CrystalGenerator</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>CrystalGenerator
+
+#if $param_i:
+  -i $param_i
+#end if
+#if $param_o:
+  -o $param_o
+#end if
+#if $param_sg:
+  -sg
+  #if " " in str($param_sg):
+    "$param_sg"
+  #else
+    $param_sg
+  #end if
+#end if
+#if $param_axis_a:
+  -axis_a $param_axis_a
+#end if
+#if $param_axis_b:
+  -axis_b $param_axis_b
+#end if
+#if $param_axis_c:
+  -axis_c $param_axis_c
+#end if
+#if $param_angle_alpha:
+  -angle_alpha $param_angle_alpha
+#end if
+#if $param_angle_beta:
+  -angle_beta $param_angle_beta
+#end if
+#if $param_angle_gamma:
+  -angle_gamma $param_angle_gamma
+#end if
+#if $param_from_uc_a:
+  -from_uc_a $param_from_uc_a
+#end if
+#if $param_from_uc_b:
+  -from_uc_b $param_from_uc_b
+#end if
+#if $param_from_uc_c:
+  -from_uc_c $param_from_uc_c
+#end if
+#if $param_to_uc_a:
+  -to_uc_a $param_to_uc_a
+#end if
+#if $param_to_uc_b:
+  -to_uc_b $param_to_uc_b
+#end if
+#if $param_to_uc_c:
+  -to_uc_c $param_to_uc_c
+#end if
+</command>
+  <inputs>
+    <param name="param_i" type="data" format="pdb" optional="False" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="input pdb file" help="(-i) "/>
+    <param name="param_sg" type="select" optional="False" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="space group symbol in Herman-Mauguin notation" help="(-sg) ">
+      <option value="P 1">P 1</option>
+      <option value=" P 1-"> P 1-</option>
+      <option value=" P 2"> P 2</option>
+      <option value=" P 21"> P 21</option>
+      <option value=" C 2"> C 2</option>
+      <option value=" P M"> P M</option>
+      <option value=" P C"> P C</option>
+      <option value=" C M"> C M</option>
+      <option value=" C C"> C C</option>
+      <option value=" P 2/M"> P 2/M</option>
+      <option value=" P 21/M"> P 21/M</option>
+      <option value=" C 2/M"> C 2/M</option>
+      <option value=" P 2/C"> P 2/C</option>
+      <option value=" P 21/C"> P 21/C</option>
+      <option value=" C 2/C"> C 2/C</option>
+      <option value=" P 2 2 2"> P 2 2 2</option>
+      <option value=" P 2 2 21"> P 2 2 21</option>
+      <option value=" P 21 21 2"> P 21 21 2</option>
+      <option value=" P 21 21 21"> P 21 21 21</option>
+      <option value=" C 2 2 21"> C 2 2 21</option>
+      <option value=" C 2 2 2"> C 2 2 2</option>
+      <option value=" F 2 2 2"> F 2 2 2</option>
+      <option value=" I 2 2 2"> I 2 2 2</option>
+      <option value=" I 21 21 21"> I 21 21 21</option>
+      <option value=" P M M 2"> P M M 2</option>
+      <option value=" P M C 21"> P M C 21</option>
+      <option value=" P C C 2"> P C C 2</option>
+      <option value=" P M A 2"> P M A 2</option>
+      <option value=" P C A 21"> P C A 21</option>
+      <option value=" P N C 2"> P N C 2</option>
+      <option value=" P M N 21"> P M N 21</option>
+      <option value=" P B A 2"> P B A 2</option>
+      <option value=" P N A 21"> P N A 21</option>
+      <option value=" P N N 2"> P N N 2</option>
+      <option value=" C M M 2"> C M M 2</option>
+      <option value=" C M C 21"> C M C 21</option>
+      <option value=" C C C 2"> C C C 2</option>
+      <option value=" A M M 2"> A M M 2</option>
+      <option value=" A B M 2"> A B M 2</option>
+      <option value=" A M A 2"> A M A 2</option>
+      <option value=" A B A 2"> A B A 2</option>
+      <option value=" F M M 2"> F M M 2</option>
+      <option value=" F D D 2"> F D D 2</option>
+      <option value=" I M M 2"> I M M 2</option>
+      <option value=" I B A 2"> I B A 2</option>
+      <option value=" I M A 2"> I M A 2</option>
+      <option value=" P M M M"> P M M M</option>
+      <option value=" P N N N"> P N N N</option>
+      <option value=" P C C M"> P C C M</option>
+      <option value=" P B A N"> P B A N</option>
+      <option value=" P M M A"> P M M A</option>
+      <option value=" P N N A"> P N N A</option>
+      <option value=" P M N A"> P M N A</option>
+      <option value=" P C C A"> P C C A</option>
+      <option value=" P B A M"> P B A M</option>
+      <option value=" P C C N"> P C C N</option>
+      <option value=" P B C M"> P B C M</option>
+      <option value=" P N N M"> P N N M</option>
+      <option value=" P M M N"> P M M N</option>
+      <option value=" P B C N"> P B C N</option>
+      <option value=" P B C A"> P B C A</option>
+      <option value=" P N M A"> P N M A</option>
+      <option value=" C M C M"> C M C M</option>
+      <option value=" C M C A"> C M C A</option>
+      <option value=" C M M M"> C M M M</option>
+      <option value=" C C C M"> C C C M</option>
+      <option value=" C M M A"> C M M A</option>
+      <option value=" C C C A"> C C C A</option>
+      <option value=" F M M M"> F M M M</option>
+      <option value=" F D D D"> F D D D</option>
+      <option value=" I M M M"> I M M M</option>
+      <option value=" I B A M"> I B A M</option>
+      <option value=" I B C A"> I B C A</option>
+      <option value=" I M M A"> I M M A</option>
+      <option value=" P 4"> P 4</option>
+      <option value=" P 41"> P 41</option>
+      <option value=" P 42"> P 42</option>
+      <option value=" P 43"> P 43</option>
+      <option value=" I 4"> I 4</option>
+      <option value=" I 41"> I 41</option>
+      <option value=" P -4"> P -4</option>
+      <option value=" I -4"> I -4</option>
+      <option value=" P 4/M"> P 4/M</option>
+      <option value=" P 42/M"> P 42/M</option>
+      <option value=" P 4/N"> P 4/N</option>
+      <option value=" P 42/N"> P 42/N</option>
+      <option value=" I 4/M"> I 4/M</option>
+      <option value=" I 41/A"> I 41/A</option>
+      <option value=" P 4 2 2"> P 4 2 2</option>
+      <option value=" P 4 21 2"> P 4 21 2</option>
+      <option value=" P 41 2 2"> P 41 2 2</option>
+      <option value=" P 41 21 2"> P 41 21 2</option>
+      <option value=" P 42 2 2"> P 42 2 2</option>
+      <option value=" P 42 21 2"> P 42 21 2</option>
+      <option value=" P 43 2 2"> P 43 2 2</option>
+      <option value=" P 43 21 2"> P 43 21 2</option>
+      <option value=" I 4 2 2"> I 4 2 2</option>
+      <option value=" I 41 2 2"> I 41 2 2</option>
+      <option value=" P 4 M M"> P 4 M M</option>
+      <option value=" P 4 B M"> P 4 B M</option>
+      <option value=" P 42 C M"> P 42 C M</option>
+      <option value=" P 42 N M"> P 42 N M</option>
+      <option value=" P 4 C C"> P 4 C C</option>
+      <option value=" P 4 N C"> P 4 N C</option>
+      <option value=" P 42 M C"> P 42 M C</option>
+      <option value=" P 42 B C"> P 42 B C</option>
+      <option value=" I 4 M M"> I 4 M M</option>
+      <option value=" I 4 C M"> I 4 C M</option>
+      <option value=" I 41 M D"> I 41 M D</option>
+      <option value=" I 41 C D"> I 41 C D</option>
+      <option value=" P -4 2 M"> P -4 2 M</option>
+      <option value=" P -4 2 C"> P -4 2 C</option>
+      <option value=" P -4 21 M"> P -4 21 M</option>
+      <option value=" P -4 21 C"> P -4 21 C</option>
+      <option value=" P -4 M 2"> P -4 M 2</option>
+      <option value=" P -4 C 2"> P -4 C 2</option>
+      <option value=" P -4 B 2"> P -4 B 2</option>
+      <option value=" P -4 N 2"> P -4 N 2</option>
+      <option value=" I -4 M 2"> I -4 M 2</option>
+      <option value=" I -4 C 2"> I -4 C 2</option>
+      <option value=" I -4 2 M"> I -4 2 M</option>
+      <option value=" I -4 2 D"> I -4 2 D</option>
+      <option value=" P 4/M M M"> P 4/M M M</option>
+      <option value=" P 4/M C C"> P 4/M C C</option>
+      <option value=" P 4/N B M"> P 4/N B M</option>
+      <option value=" P 4/N N C"> P 4/N N C</option>
+      <option value=" P 4/M B M"> P 4/M B M</option>
+      <option value=" P 4/M N C"> P 4/M N C</option>
+      <option value=" P 4/N M M"> P 4/N M M</option>
+      <option value=" P 4/N C C"> P 4/N C C</option>
+      <option value=" P 42/M M C"> P 42/M M C</option>
+      <option value=" P 42/M C M"> P 42/M C M</option>
+      <option value=" P 42/N B C"> P 42/N B C</option>
+      <option value=" P 42/N N M"> P 42/N N M</option>
+      <option value=" P 42/M B C"> P 42/M B C</option>
+      <option value=" P 42/M N M"> P 42/M N M</option>
+      <option value=" P 42/N M C"> P 42/N M C</option>
+      <option value=" P 42/N C M"> P 42/N C M</option>
+      <option value=" I 4/M M M"> I 4/M M M</option>
+      <option value=" I 4/M C M"> I 4/M C M</option>
+      <option value=" I 41/A M D"> I 41/A M D</option>
+      <option value=" I 41/A C D"> I 41/A C D</option>
+      <option value=" P 3"> P 3</option>
+      <option value=" P 31"> P 31</option>
+      <option value=" P 32"> P 32</option>
+      <option value=" R 3"> R 3</option>
+      <option value=" P -3"> P -3</option>
+      <option value=" R -3"> R -3</option>
+      <option value=" P 3 1 2"> P 3 1 2</option>
+      <option value=" P 3 2 1"> P 3 2 1</option>
+      <option value=" P 31 1 2"> P 31 1 2</option>
+      <option value=" P 31 2 1"> P 31 2 1</option>
+      <option value=" P 32 1 2"> P 32 1 2</option>
+      <option value=" P 32 2 1"> P 32 2 1</option>
+      <option value=" R 3 2"> R 3 2</option>
+      <option value=" P 3 M 1"> P 3 M 1</option>
+      <option value=" P 3 1 M"> P 3 1 M</option>
+      <option value=" P 3 C 1"> P 3 C 1</option>
+      <option value=" P 3 1 C"> P 3 1 C</option>
+      <option value=" R 3 M"> R 3 M</option>
+      <option value=" R 3 C"> R 3 C</option>
+      <option value=" P -3 1 M"> P -3 1 M</option>
+      <option value=" P -3 1 C"> P -3 1 C</option>
+      <option value=" P -3 M 1"> P -3 M 1</option>
+      <option value=" P -3 C 1"> P -3 C 1</option>
+      <option value=" R -3 M"> R -3 M</option>
+      <option value=" R -3 C"> R -3 C</option>
+      <option value=" P 6"> P 6</option>
+      <option value=" P 61"> P 61</option>
+      <option value=" P 65"> P 65</option>
+      <option value=" P 62"> P 62</option>
+      <option value=" P 64"> P 64</option>
+      <option value=" P 63"> P 63</option>
+      <option value=" P -6"> P -6</option>
+      <option value=" P 6/M"> P 6/M</option>
+      <option value=" P 63/M"> P 63/M</option>
+      <option value=" P 6 2 2"> P 6 2 2</option>
+      <option value=" P 61 2 2"> P 61 2 2</option>
+      <option value=" P 65 2 2"> P 65 2 2</option>
+      <option value=" P 62 2 2"> P 62 2 2</option>
+      <option value=" P 64 2 2"> P 64 2 2</option>
+      <option value=" P 63 2 2"> P 63 2 2</option>
+      <option value=" P 6 M M"> P 6 M M</option>
+      <option value=" P 6 C C"> P 6 C C</option>
+      <option value=" P 63 C M"> P 63 C M</option>
+      <option value=" P 63 M C"> P 63 M C</option>
+      <option value=" P -6 M 2"> P -6 M 2</option>
+      <option value=" P -6 C 2"> P -6 C 2</option>
+      <option value=" P -6 2 M"> P -6 2 M</option>
+      <option value=" P -6 2 C"> P -6 2 C</option>
+      <option value=" P 6/M M M"> P 6/M M M</option>
+      <option value=" P 6/M C C"> P 6/M C C</option>
+      <option value=" P 63/M C M"> P 63/M C M</option>
+      <option value=" P 63/M M C"> P 63/M M C</option>
+      <option value=" P 2 3"> P 2 3</option>
+      <option value=" F 2 3"> F 2 3</option>
+      <option value=" I 2 3"> I 2 3</option>
+      <option value=" P 21 3"> P 21 3</option>
+      <option value=" I 21 3"> I 21 3</option>
+      <option value=" P M -3"> P M -3</option>
+      <option value=" P N -3"> P N -3</option>
+      <option value=" F M -3"> F M -3</option>
+      <option value=" F D -3"> F D -3</option>
+      <option value=" I M -3"> I M -3</option>
+      <option value=" P A -3"> P A -3</option>
+      <option value=" I A -3"> I A -3</option>
+      <option value=" P 4 3 2"> P 4 3 2</option>
+      <option value=" P 42 3 2"> P 42 3 2</option>
+      <option value=" F 4 3 2"> F 4 3 2</option>
+      <option value=" F 41 3 2"> F 41 3 2</option>
+      <option value=" I 4 3 2"> I 4 3 2</option>
+      <option value=" P 43 3 2"> P 43 3 2</option>
+      <option value=" P 41 3 2"> P 41 3 2</option>
+      <option value=" I 41 3 2"> I 41 3 2</option>
+      <option value=" P -4 3 M"> P -4 3 M</option>
+      <option value=" F 4 -3 M"> F 4 -3 M</option>
+      <option value=" I -4 3 M"> I -4 3 M</option>
+      <option value=" P -4 3 N"> P -4 3 N</option>
+      <option value=" F -4 3 C"> F -4 3 C</option>
+      <option value=" I -4 3 D"> I -4 3 D</option>
+      <option value=" P M -3 M"> P M -3 M</option>
+      <option value=" P N -3 N"> P N -3 N</option>
+      <option value=" P M -3 N"> P M -3 N</option>
+      <option value=" P N -3 M"> P N -3 M</option>
+      <option value=" F M -3 M"> F M -3 M</option>
+      <option value=" F M -3 C"> F M -3 C</option>
+      <option value=" F D -3 M"> F D -3 M</option>
+      <option value=" F D -3 C"> F D -3 C</option>
+      <option value=" I M -3 M"> I M -3 M</option>
+      <option value=" I A -3 D"> I A -3 D</option>
+      <option value=" B 2"> B 2</option>
+      <option value=" P 1 1 21"> P 1 1 21</option>
+      <option value=" P 2 21 21"> P 2 21 21</option>
+      <option value=" P 21 2 21"> P 21 2 21</option>
+      <option value=" I 1 2 1"> I 1 2 1</option>
+    </param>
+    <param name="param_axis_a" type="float" value="0.0" label="cell axis a" help="(-axis_a) "/>
+    <param name="param_axis_b" type="float" value="0.0" label="cell axis" help="(-axis_b) "/>
+    <param name="param_axis_c" type="float" value="0.0" label="cell axis c" help="(-axis_c) "/>
+    <param name="param_angle_alpha" type="float" min="0.0" max="359.0" optional="True" value="0.0" label="cell angle alpha" help="(-angle_alpha) "/>
+    <param name="param_angle_beta" type="float" min="0.0" max="359.0" optional="True" value="0.0" label="cell angle beta" help="(-angle_beta) "/>
+    <param name="param_angle_gamma" type="float" min="0.0" max="359.0" optional="True" value="0.0" label="cell angle gamma" help="(-angle_gamma) "/>
+    <param name="param_from_uc_a" type="integer" min="0" max="9" optional="False" value="0" label="from unit cell index a" help="(-from_uc_a) "/>
+    <param name="param_from_uc_b" type="integer" min="0" max="9" optional="False" value="0" label="from unit cell index" help="(-from_uc_b) "/>
+    <param name="param_from_uc_c" type="integer" min="0" max="9" optional="False" value="0" label="from unit cell index c" help="(-from_uc_c) "/>
+    <param name="param_to_uc_a" type="integer" value="0" label="to unit cell index a" help="(-to_uc_a) "/>
+    <param name="param_to_uc_b" type="integer" value="0" label="to unit cell index" help="(-to_uc_b) "/>
+    <param name="param_to_uc_c" type="integer" value="0" label="to unit cell index c" help="(-to_uc_c) "/>
+  </inputs>
+  <expand macro="advanced_options"/>
+  <outputs>
+    <data name="param_o" format="pdb"/>
+  </outputs>
+  <help>TODO: Manual
+
+</help>
+</tool>