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

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<?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>