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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/galaxy_stubs/InputReader.xml	Tue Jul 12 12:33:33 2016 -0400
@@ -0,0 +1,85 @@
+<?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: [QuEasy (QSAR)]-->
+<tool id="InputReader" name="InputReader" version="1.1.0">
+  <description>generate QSAR data set     </description>
+  <macros>
+    <token name="@EXECUTABLE@">InputReader</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>InputReader
+
+#if $param_i:
+  -i $param_i
+#end if
+#if $param_o:
+  -o $param_o
+#end if
+#if $param_act:
+  -act     "$param_act"
+#end if
+#if $param_csv:
+  -csv $param_csv
+#end if
+#if $param_csv_nr:
+  -csv_nr $param_csv_nr
+#end if
+#if $param_csv_sep:
+  -csv_sep $param_csv_sep
+#end if
+#if $param_sdp:
+  -sdp $param_sdp
+#end if
+#if $param_no_cd:
+  -no_cd $param_no_cd
+#end if
+#if $param_no_cr:
+  -no_cr $param_no_cr
+#end if
+#if $param_csv_cl:
+  -csv_cl $param_csv_cl
+#end if
+#if $param_csv_dl:
+  -csv_dl $param_csv_dl
+#end if
+</command>
+  <inputs>
+    <param name="param_i" type="data" format="sdf" optional="False" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="input sd-file" help="(-i) "/>
+    <param name="param_act" type="text" size="30" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="sd-property containing response values" help="(-act) ">
+      <sanitizer>
+        <valid initial="string.printable">
+          <remove value="'"/>
+          <remove value="&quot;"/>
+        </valid>
+      </sanitizer>
+    </param>
+    <param name="param_csv" type="data" format="csv" optional="True" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="input csv-file w/ additional descriptors" help="(-csv) "/>
+    <param name="param_csv_nr" type="integer" value="0" label="no. of response variables in csv-file" help="(-csv_nr) "/>
+    <param name="param_csv_sep" type="integer" value="0" label="separator symbol in csv-file" help="(-csv_sep) "/>
+    <param name="param_sdp" type="integer" min="0" max="1" optional="True" value="0" label="use sd-properties as additional descriptors" help="(-sdp) "/>
+    <param name="param_no_cd" type="integer" min="0" max="1" optional="True" value="0" label="do not center descriptors" help="(-no_cd) "/>
+    <param name="param_no_cr" type="integer" min="0" max="1" optional="True" value="0" label="do not center response values" help="(-no_cr) "/>
+    <param name="param_csv_cl" type="integer" min="0" max="1" optional="True" value="0" label="csv-file has compound (row) labels" help="(-csv_cl) "/>
+    <param name="param_csv_dl" type="integer" min="0" max="1" optional="True" value="0" label="csv-file has descriptor (column) labels" help="(-csv_dl) "/>
+  </inputs>
+  <expand macro="advanced_options"/>
+  <outputs>
+    <data name="param_o" format="dat"/>
+  </outputs>
+  <help>This tool reads input from sd-files and generate features for QSAR analysis.
+Activity data (response values) for a training set are taken from sd-properties of the input file; the name of this property can be specified by option '-act'.
+The following number of features will be automatically created for each molecule in your sd-file:
+
+    * 40 atom and bond count descriptors
+    * 2 connectivity indices (Balaban and Zagreb index)
+    * 4 partial charge descriptors
+    * 14 surface descriptors
+    * 133 topological descriptors (functional group counts)
+
+If desired, you can also read additional descriptors from a csv-file; in this case you need to specify the file with the above options.
+Output of this tool is a data file that can be used by other QuEasy tools (e.g. ModelCreator).
+
+</help>
+</tool>