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annotate CADDSuite-1.5/galaxyconfigs/tools/Converter.xml @ 7:bfab27640f5e draft

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CADDSuite version 1.5
author Marcel Schumann <schumann.marcel@gmail.com>
date Tue, 24 Jul 2012 11:13:59 -0400
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1
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2 <!--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.-->
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3 <tool id="converter" name="Converter" version="1.5">
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4 <description>interconvert molecular file-formats</description>
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5 <command interpreter="bash"><![CDATA[../../Converter
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6 #if str( $i ) != '' and str( $i ) != 'None' :
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7 -i "$i"
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8 #end if
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9 #if str( $o ) != '' and str( $o ) != 'None' :
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10 -o "$o"
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11 #end if
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12 #if str( $f ) != '' and str( $f ) != 'None' :
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13 -f "$f"
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14 #end if
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15 #if str( $rm ) != '' and str( $rm ) != 'None' :
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16 -rm
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17 #end if
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18 | tail -n 5
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19 ]]></command>
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20 <inputs>
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21 <param name="i" optional="false" label="input file" type="data" format="mol2/sdf/drf"/>
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22 <param name="f" optional="true" label="output format" type="select">
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23 <option value="mol2">mol2</option>
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24 <option value="sdf">sdf</option>
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25 <option value="drf">drf</option>
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26 <option value="pdb">pdb</option>
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27 <option value="ac">ac</option>
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28 <option value="ent">ent</option>
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29 <option value="brk">brk</option>
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30 <option value="hin">hin</option>
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31 <option value="mol">mol</option>
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32 <option value="xyz">xyz</option>
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33 <option value="mol2.gz">mol2.gz</option>
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34 <option value="sdf.gz">sdf.gz</option>
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35 <option value="drf.gz">drf.gz</option>
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36 <option value="pdb.gz">pdb.gz</option>
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37 <option value="ac.gz">ac.gz</option>
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38 <option value="ent.gz">ent.gz</option>
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39 <option value="brk.gz">brk.gz</option>
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40 <option value="hin.gz">hin.gz</option>
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41 <option value="mol.gz">mol.gz</option>
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42 <option value="xyz.gz">xyz.gz</option>
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43 </param>
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44 <param name="rm" optional="true" label="remove input file when finished" type="boolean" truevalue="true" falsevalue=""/>
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45 </inputs>
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46 <outputs>
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47 <data name="o" format="mol2/sdf/drf">
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48 <change_format>
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49 <when input="f" value="mol2" format="mol2"/>
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50 <when input="f" value="sdf" format="sdf"/>
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51 <when input="f" value="drf" format="drf"/>
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52 <when input="f" value="pdb" format="pdb"/>
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53 <when input="f" value="ac" format="ac"/>
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54 <when input="f" value="ent" format="ent"/>
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55 <when input="f" value="brk" format="brk"/>
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56 <when input="f" value="hin" format="hin"/>
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57 <when input="f" value="mol" format="mol"/>
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58 <when input="f" value="xyz" format="xyz"/>
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59 <when input="f" value="mol2.gz" format="mol2.gz"/>
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60 <when input="f" value="sdf.gz" format="sdf.gz"/>
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61 <when input="f" value="drf.gz" format="drf.gz"/>
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62 <when input="f" value="pdb.gz" format="pdb.gz"/>
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63 <when input="f" value="ac.gz" format="ac.gz"/>
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64 <when input="f" value="ent.gz" format="ent.gz"/>
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65 <when input="f" value="brk.gz" format="brk.gz"/>
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66 <when input="f" value="hin.gz" format="hin.gz"/>
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67 <when input="f" value="mol.gz" format="mol.gz"/>
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68 <when input="f" value="xyz.gz" format="xyz.gz"/>
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69 </change_format>
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70 </data>
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71 </outputs>
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72 <help>This tool can be used to convert between different molecular file-formats.
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73 Supported formats are mol2, sdf, drf, pdb, ac, ent, brk, hin, mol, xyz, mol2.gz, sdf.gz, drf.gz, pdb.gz, ac.gz, ent.gz, brk.gz, hin.gz, mol.gz, xyz.gz.</help>
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74 </tool>