Mercurial > repos > marcel > caddsuite_mac10_6
diff CADDSuite/galaxyconfigs/tools/DBExporter.xml @ 3:bb26168c5715
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author | marcel |
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date | Tue, 12 Jul 2011 10:53:07 -0400 |
parents | |
children | af446ca2d5c6 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/galaxyconfigs/tools/DBExporter.xml Tue Jul 12 10:53:07 2011 -0400 @@ -0,0 +1,97 @@ + +<!--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="dbexporter" name="DBExporter" version="0.95 (ob)"> + <description>export molecules from data base</description> + <command interpreter="bash"><![CDATA[../../DBExporter +#if str( $o ) != '' and str( $o ) != 'None' : + -o "$o" +#end if +#if str( $start_id ) != '' and str( $start_id ) != 'None' : + -start_id "$start_id" +#end if +#if str( $end_id ) != '' and str( $end_id ) != 'None' : + -end_id "$end_id" +#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( $max_mols ) != '' and str( $max_mols ) != 'None' : + -max_mols "$max_mols" +#end if +#if str( $target ) != '' and str( $target ) != 'None' : + -target "$target" +#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( $uck ) != '' and str( $uck ) != 'None' : + -uck "$uck" +#end if +#if str( $d ) != '' and str( $d ) != 'None' : + -d "$d" +#end if +#if str( $u ) != '' and str( $u ) != 'None' : + -u "$u" +#end if +#if str( $h ) != '' and str( $h ) != 'None' : + -h "$h" +#end if +#if str( $port ) != '' and str( $port ) != 'None' : + -port "$port" +#end if +#if str( $p ) != '' and str( $p ) != 'None' : + -p "$p" +#end if +#if str( $s ) != '' and str( $s ) != 'None' : + -s +#end if + | tail -n 5 +]]></command> + <inputs> + <param name="q" optional="true" label="query molecules for similarity searching" type="data" format="mol2/sdf/drf"/> + <param name="smarts_file" optional="true" label="SMARTS pattern" type="data" format="data"/> + <param name="start_id" optional="true" label="Optional: ID of the first conformation to be exported" type="text" area="true" size="1x5" value=""/> + <param name="end_id" optional="true" label="Optional: ID of the last conformation to be exported" type="text" area="true" size="1x5" value=""/> + <param name="min_logP" optional="true" label="Optional: minimal logP value" type="text" min="-10.000000" max="10.000000" area="true" size="1x5" value=""/> + <param name="max_logP" optional="true" label="Optional: maximal logP value" type="text" min="-10.000000" max="10.000000" 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="max_mols" optional="true" label="Optional: max. number of molecules to be exported" type="text" area="true" size="1x5" value=""/> + <param name="target" optional="true" label="Optional: target/dataset name whose molecules should be exported" area="true" type="text" size="1x15"/> + <param name="min_sim" optional="true" label="Optional: minimal average similarity" type="text" min="0.000000" max="1.000000" area="true" size="1x5" value=""/> + <param name="max_sim" optional="true" label="Optional: maximal similarity" type="text" min="0.000000" max="1.000000" area="true" size="1x5" value=""/> + <param name="smarts" optional="true" label="Optional: SMARTS pattern" area="true" type="text" size="1x15"/> + <param name="uck" optional="true" label="Optional: UCK key" area="true" type="text" size="1x15"/> + <param name="d" optional="false" label="database name" area="true" type="text" size="1x15"/> + <param name="u" optional="false" label="database username" area="true" type="text" size="1x15"/> + <param name="h" optional="false" label="database host" area="true" type="text" size="1x15"/> + <param name="port" optional="true" label="Optional: database port" type="text" area="true" size="1x5" value="3306"/> + <param name="p" optional="false" label="database password" area="true" type="text" size="1x15"/> + <param name="s" optional="true" label="show summary of datasets in database" type="boolean" truevalue="true" falsevalue=""/> + </inputs> + <outputs> + <data name="o" format="mol2/sdf/drf"/> + </outputs> + <help>This tool exports compounds from a database to a molecular file. Compounds can be filtered according to (among others) SMARTS expressions, logP, molecular weight, or similarity to query molecule(s) and dataset name.</help> +</tool> \ No newline at end of file