comparison CADDSuite-1.6/galaxyconfigs/tools/MolFilter.xml @ 8:dbb480e39d95 draft

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8:dbb480e39d95

<!--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="molfilter" name="MolFilter" version="1.6">
    <description>filter molecule files</description>
    <command interpreter="bash"><![CDATA[../../MolFilter 
#if str( $i ) != ''  and str( $i ) != 'None' :
   -i "$i"
#end if
#if str( $min_logP ) != ''  and str( $min_logP ) != 'None' :
   -min_logP "$min_logP"
#end if
#if str( $max_logP ) != ''  and str( $max_logP ) != 'None' :
   -max_logP "$max_logP"
#end if
#if str( $min_MW ) != ''  and str( $min_MW ) != 'None' :
   -min_MW "$min_MW"
#end if
#if str( $max_MW ) != ''  and str( $max_MW ) != 'None' :
   -max_MW "$max_MW"
#end if
#if str( $q ) != ''  and str( $q ) != 'None' :
   -q "$q"
#end if
#if str( $min_sim ) != ''  and str( $min_sim ) != 'None' :
   -min_sim "$min_sim"
#end if
#if str( $max_sim ) != ''  and str( $max_sim ) != 'None' :
   -max_sim "$max_sim"
#end if
#if str( $min_div ) != ''  and str( $min_div ) != 'None' :
   -min_div "$min_div"
#end if
#if str( $smarts ) != ''  and str( $smarts ) != 'None' :
   -smarts "$smarts"
#end if
#if str( $smarts_file ) != ''  and str( $smarts_file ) != 'None' :
   -smarts_file "$smarts_file"
#end if
#if str( $o ) != ''  and str( $o ) != 'None' :
   -o "$o"
#end if
#if str( $pairs ) != ''  and str( $pairs ) != 'None' :
   -pairs
#end if
-quiet 
#if str( $rm ) != ''  and str( $rm ) != 'None' :
   -rm
#end if
 | tail -n 5
]]></command>
    <inputs>
        <param name="i" optional="false" label="input molecule-file" type="data" format="mol2/sdf/drf"/>
        <param name="q" optional="true" label="query molecules for similarity searching" type="data" format="txt"/>
        <param name="smarts_file" optional="true" label="SMARTS pattern" type="data" format="txt"/>
        <param name="min_logP" optional="true" label="Optional: minimal logP value" type="text" area="true" size="1x5" value=""/>
        <param name="max_logP" optional="true" label="Optional: maximal logP value" type="text" area="true" size="1x5" value=""/>
        <param name="min_MW" optional="true" label="Optional: minimal molecular weight" type="text" area="true" size="1x5" value=""/>
        <param name="max_MW" optional="true" label="Optional: maximal molecular weight" type="text" area="true" size="1x5" value=""/>
        <param name="min_sim" optional="true" label="Optional: minimal similarity to a query molecule" type="text" area="true" size="1x5" value=""/>
        <param name="max_sim" optional="true" label="Optional: maximal similarity to a query molecule" type="text" area="true" size="1x5" value=""/>
        <param name="min_div" optional="true" label="Optional: min. pairwise diversity between hits" type="text" area="true" size="1x5" value=""/>
        <param name="smarts" optional="true" label="Optional: SMARTS pattern" area="true" type="text" size="1x15"/>
        <param name="pairs" optional="true" label="output result of sim. search as pairs of input-, query-molecule" type="boolean" truevalue="true" falsevalue=""/>
        <param name="rm" optional="true" label="remove input file when finished" type="boolean" truevalue="true" falsevalue=""/>
    </inputs>
    <outputs>
        <data name="o" format="mol2/sdf/drf" format_source="i"/>
    </outputs>
    <help>MolFilter can filter molecules from a molecule input file according to SMARTS expressions, logP, molecular weight, or similarity to query molecule(s).

Output of this tool is a molecule file that contains all compounds that fulfilled the specified search criteria.</help>
</tool>