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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/galaxy_stubs/BondOrderAssigner.xml	Tue Jul 12 12:33:33 2016 -0400
@@ -0,0 +1,86 @@
+<?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: [Preparation]-->
+<tool id="BondOrderAssigner" name="BondOrderAssigner" version="1.1.0">
+  <description>computes bond order assignments for a ligand </description>
+  <macros>
+    <token name="@EXECUTABLE@">BondOrderAssigner</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>BondOrderAssigner
+
+#if $param_i:
+  -i $param_i
+#end if
+#if $param_o:
+  -o $param_o
+#end if
+#if $param_max_sol:
+  -max_sol $param_max_sol
+#end if
+#if $param_scr_pen:
+  -scr_pen
+  #if " " in str($param_scr_pen):
+    "$param_scr_pen"
+  #else
+    $param_scr_pen
+  #end if
+#end if
+#if $param_non_opt:
+  -non_opt $param_non_opt
+#end if
+#if $adv_opts.adv_opts_selector=='advanced':
+    #if $adv_opts.param_o_id:
+  -o_id     "$adv_opts.param_o_id"
+#end if
+    #if $adv_opts.param_o_dir:
+  -o_dir     "$adv_opts.param_o_dir"
+#end if
+#end if
+</command>
+  <inputs>
+    <param name="param_i" type="data" format="mol2" optional="False" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="input mol2-file" help="(-i) "/>
+    <param name="param_max_sol" type="integer" min="0" max="100" optional="True" value="25" label="maximal number of assignments solutions to compute" help="(-max_sol) "/>
+    <param name="param_scr_pen" type="select" optional="True" value="Antechamber" label="penalty table (Antechamber, BALL)" help="(-scr_pen) ">
+      <option value="Antechamber">Antechamber</option>
+      <option value=" BALL"> BALL</option>
+    </param>
+    <param name="param_non_opt" type="integer" min="0" max="1" optional="True" value="0" label="compute sub-optimal assignments as well" help="(-non_opt) "/>
+    <expand macro="advanced_options">
+      <param name="param_o_id" type="text" size="30" value="$o.id" label="output id" help="(-o_id) ">
+        <sanitizer>
+          <valid initial="string.printable">
+            <remove value="'"/>
+            <remove value="&quot;"/>
+          </valid>
+        </sanitizer>
+      </param>
+      <param name="param_o_dir" type="text" size="30" value="$__new_file_path__" label="output directory for 2nd to last solution" help="(-o_dir) ">
+        <sanitizer>
+          <valid initial="string.printable">
+            <remove value="'"/>
+            <remove value="&quot;"/>
+          </valid>
+        </sanitizer>
+      </param>
+    </expand>
+  </inputs>
+  <outputs>
+    <data name="param_o" format="mol2"/>
+  </outputs>
+  <help>This tool computes optimal and sub-optimal bond order assignments based on an atomic penalty function for a given ligand in mol2 file format.
+
+Optional parameters are the maximal number of solutions to be computed ('-max_sol'), the penalty table specifiying the atomic penalty rules ('-scr_pen'),and a flag indicating if sub-optimal solutions should be computed as well ('-non_opt').
+
+Output of this tool is a number of mol2 files each containing one bond order assignment.
+
+To upload an input file please use the upload tool (Get Data -&gt; Upload File).
+
+**Further information and help** can be found in our wiki https://github.com/BALL-Project/ball/wiki/BOAConstructor_Help.
+
+Please cite the following: Dehof, A.K., Rurainski, A., Bui, Q.B.A., Boecker, S., Lenhof, H.-P. &amp; Hildebrandt, A. (2011). Automated Bond Order Assignment as an Optimization Problem. Bioinformatics, 2011
+
+</help>
+</tool>