annotate CADDSuite/galaxyconfigs/tools/MolFilter.xml @ 0:bac3c274238f

Migrated tool version 0.93 from old tool shed archive to new tool shed repository

<!--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="0.9">
    <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( $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
-quiet 
 | tail -n 5
]]></command>
    <inputs>
        <param name="i" label="input molecule-file" optional="false" type="data" format="mol2/sdf/drf"/>
        <param name="q" label="query molecules for similarity searching" optional="true" type="data" format="txt"/>
        <param name="smarts_file" label="SMARTS pattern" optional="true" type="data" format="data"/>
        <param name="min_logP" label="minimal logP value" optional="true" type="text" area="true" size="1x5" value=""/>
        <param name="max_logP" label="maximal logP value" optional="true" type="text" area="true" size="1x5" value=""/>
        <param name="min_MW" label="minimal molecular weight" optional="true" type="text" area="true" size="1x5" value=""/>
        <param name="max_MW" label="maximal molecular weight" optional="true" type="text" area="true" size="1x5" value=""/>
        <param name="min_sim" label="minimal average similarity" optional="true" type="text" area="true" size="1x5" value=""/>
        <param name="max_sim" label="maximal similarity" optional="true" type="text" area="true" size="1x5" value=""/>
        <param name="smarts" label="SMARTS pattern" optional="true" area="true" type="text" size="1x15"/>
    </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>