view galaxy_stubs/SLICK.xml @ 2:605370bc1def draft default tip

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<?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="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="input receptor file" help="(-rec) "/>
    <param name="param_lig" type="data" format="" optional="False" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="input ligand file" help="(-lig) "/>
    <param name="param_cr" type="data" format="" optional="True" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="charge rules" help="(-cr) "/>
    <param name="param_pr" type="data" format="" optional="True" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="radius rules for the polar solvation" help="(-pr) "/>
    <param name="param_lj" type="data" format="" optional="True" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="use FILE for LJ parameters" help="(-lj) "/>
    <param name="param_op" type="data" format="ini" optional="True" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" 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>