Mercurial > repos > luis > ball
diff galaxy_stubs/SLICK.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/SLICK.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: [Scoring]--> +<tool id="SLICK" name="SLICK" version="1.1.0"> + <description>scoring protein-carbohydrate interactions</description> + <macros> + <token name="@EXECUTABLE@">SLICK</token> + <import>macros.xml</import> + </macros> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>SLICK + +#if $param_rec: + -rec $param_rec +#end if +#if $param_lig: + -lig $param_lig +#end if +#if $param_cr: + -cr $param_cr +#end if +#if $param_pr: + -pr $param_pr +#end if +#if $param_lj: + -lj $param_lj +#end if +#if $param_op: + -op $param_op +#end if +#if $param_v: + -v $param_v +#end if +#if $param_s: + -s $param_s +#end if +#if $param_t: + -t $param_t +#end if +#if $param_E: + -E $param_E +#end if +#if $param_S: + -S $param_S +#end if +#if $param_u: + -u $param_u +#end if +#if $param_n: + -n $param_n +#end if +#if $param_N: + -N $param_N +#end if +#if $param_log: + -log $param_log +#end if +</command> + <inputs> + <param name="param_rec" type="data" format="" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="input receptor file" help="(-rec) "/> + <param name="param_lig" type="data" format="" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="input ligand file" help="(-lig) "/> + <param name="param_cr" type="data" format="" optional="True" value="<class 'CTDopts.CTDopts._Null'>" label="charge rules" help="(-cr) "/> + <param name="param_pr" type="data" format="" optional="True" value="<class 'CTDopts.CTDopts._Null'>" label="radius rules for the polar solvation" help="(-pr) "/> + <param name="param_lj" type="data" format="" optional="True" value="<class 'CTDopts.CTDopts._Null'>" label="use FILE for LJ parameters" help="(-lj) "/> + <param name="param_op" type="data" format="ini" optional="True" value="<class 'CTDopts.CTDopts._Null'>" label="read options from FILE (command line overrides!)" help="(-op) "/> + <param name="param_v" type="integer" value="0" label="verbosity to level" help="(-v) "/> + <param name="param_s" type="float" value="0.0" label="scaling factor for receptor charges" help="(-s) "/> + <param name="param_t" type="float" value="0.0" label="scaling factor for ligand charges" help="(-t) "/> + <param name="param_E" type="integer" min="0" max="1" optional="True" value="0" label="compute only SLICKEnergy" help="(-E) "/> + <param name="param_S" type="integer" min="0" max="1" optional="True" value="0" label="compute only SLICKScore" help="(-S) "/> + <param name="param_u" type="integer" min="0" max="1" optional="True" value="0" label="unite atoms" help="(-u) "/> + <param name="param_n" type="integer" min="0" max="1" optional="True" value="0" label="read radius rules for the nonpolar solvation from FILE" help="(-n) "/> + <param name="param_N" type="integer" min="0" max="1" optional="True" value="0" label="scale nonpolar radii by FACTOR" help="(-N) "/> + <param name="param_log" type="integer" min="0" max="1" optional="True" value="0" label="write log file" help="(-log) "/> + </inputs> + <expand macro="advanced_options"/> + <outputs> + <data name="param_stdout" format="text" label="Output from stdout"/> + </outputs> + <help>This tool calculates the SLICKEnergy / SLICK Score for protein-carbohydrate complexes. + +</help> +</tool>