annotate CADDSuite/galaxyconfigs/tools/InputReader.xml @ 5:b7a89b15646f

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<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.-->
<tool id="inputreader" name="InputReader" version="0.95">
    <description>generate QSAR data set</description>
    <command interpreter="bash"><![CDATA[../../InputReader 
#if str( $i ) != ''  and str( $i ) != 'None' :
   -i "$i"
#end if
#if str( $o ) != ''  and str( $o ) != 'None' :
   -o "$o"
#end if
#if str( $act ) != ''  and str( $act ) != 'None' :
   -act "$act"
#end if
#if str( $csv ) != ''  and str( $csv ) != 'None' :
   -csv "$csv"
#end if
#if str( $csv_nr ) != ''  and str( $csv_nr ) != 'None' :
   -csv_nr "$csv_nr"
#end if
#if str( $csv_sep ) != ''  and str( $csv_sep ) != 'None' :
   -csv_sep "$csv_sep"
#end if
#if str( $sdp ) != ''  and str( $sdp ) != 'None' :
   -sdp
#end if
#if str( $no_cd ) != ''  and str( $no_cd ) != 'None' :
   -no_cd
#end if
#if str( $no_cr ) != ''  and str( $no_cr ) != 'None' :
   -no_cr
#end if
#if str( $csv_cl ) != ''  and str( $csv_cl ) != 'None' :
   -csv_cl
#end if
#if str( $csv_dl ) != ''  and str( $csv_dl ) != 'None' :
   -csv_dl
#end if
 | tail -n 5
]]></command>
    <inputs>
        <param name="i" optional="false" label="input sd-file" type="data" format="sdf"/>
        <param name="csv" optional="true" label="input csv-file w/ additional descriptors" type="data" format="csv"/>
        <param name="act" optional="true" label="Optional: sd-property containing response values" area="true" type="text" size="1x15"/>
        <param name="csv_nr" optional="true" label="Optional: no. of response variables in csv-file" type="text" area="true" size="1x5" value=""/>
        <param name="csv_sep" optional="true" label="Optional: separator symbol in csv-file" type="text" area="true" size="1x5" value=""/>
        <param name="sdp" optional="true" label="use sd-properties as additional descriptors" type="boolean" truevalue="true" falsevalue=""/>
        <param name="no_cd" optional="true" label="do not center descriptors" type="boolean" truevalue="true" falsevalue=""/>
        <param name="no_cr" optional="true" label="do not center response values" type="boolean" truevalue="true" falsevalue=""/>
        <param name="csv_cl" optional="true" label="csv-file has compound (row) labels" type="boolean" truevalue="true" falsevalue=""/>
        <param name="csv_dl" optional="true" label="csv-file has descriptor (column) labels" type="boolean" truevalue="true" falsevalue=""/>
    </inputs>
    <outputs>
        <data name="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>