Mercurial > repos > luis > ball
diff galaxy_stubs/MolFilter.xml @ 2:605370bc1def draft default tip
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author | luis |
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date | Tue, 12 Jul 2016 12:33:33 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxy_stubs/MolFilter.xml Tue Jul 12 12:33:33 2016 -0400 @@ -0,0 +1,84 @@ +<?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: [Preparation]--> +<tool id="MolFilter" name="MolFilter" version="0.9"> + <description>filter molecule files </description> + <macros> + <token name="@EXECUTABLE@">MolFilter</token> + <import>macros.xml</import> + </macros> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>MolFilter + +#if $param_i: + -i $param_i +#end if +#if $param_min_logP: + -min_logP $param_min_logP +#end if +#if $param_max_logP: + -max_logP $param_max_logP +#end if +#if $param_min_MW: + -min_MW $param_min_MW +#end if +#if $param_max_MW: + -max_MW $param_max_MW +#end if +#if $param_q: + -q $param_q +#end if +#if $param_min_sim: + -min_sim $param_min_sim +#end if +#if $param_max_sim: + -max_sim $param_max_sim +#end if +#if $param_smarts: + -smarts "$param_smarts" +#end if +#if $param_smarts_file: + -smarts_file $param_smarts_file +#end if +#if $param_o: + -o $param_o +#end if +#if $param_quiet: + -quiet $param_quiet +#end if +#if $param_rm: + -rm $param_rm +#end if +</command> + <inputs> + <param name="param_i" type="data" format="mol2,sdf,drf" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="input molecule-file" help="(-i) "/> + <param name="param_min_logP" type="float" value="0.0" label="minimal logP value" help="(-min_logP) "/> + <param name="param_max_logP" type="float" value="20.0" label="maximal logP value" help="(-max_logP) "/> + <param name="param_min_MW" type="float" value="0.0" label="minimal molecular weight" help="(-min_MW) "/> + <param name="param_max_MW" type="float" value="10000000000.0" label="maximal molecular weight" help="(-max_MW) "/> + <param name="param_q" type="data" format="txt" optional="True" value="<class 'CTDopts.CTDopts._Null'>" label="query molecules for similarity searching" help="(-q) "/> + <param name="param_min_sim" type="float" value="0.0" label="minimal average similarity" help="(-min_sim) "/> + <param name="param_max_sim" type="float" value="1.0" label="maximal similarity" help="(-max_sim) "/> + <param name="param_smarts" type="text" size="30" value="<class 'CTDopts.CTDopts._Null'>" label="SMARTS pattern" help="(-smarts) "> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + <param name="param_smarts_file" type="data" format="txt" optional="True" value="<class 'CTDopts.CTDopts._Null'>" label="SMARTS pattern" help="(-smarts_file) "/> + <param name="param_quiet" type="integer" min="0" max="1" optional="True" value="0" label="by quiet, i.e. do not show progress information" help="(-quiet) "/> + <param name="param_rm" type="integer" min="0" max="1" optional="True" value="0" label="remove input file when finished" help="(-rm) "/> + </inputs> + <expand macro="advanced_options"/> + <outputs> + <data name="param_o" metadata_source="param_i" format="input"/> + </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>