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1 <tool id="jmoleditor" name="JMol Editor" tool_type="data_source">
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2 <description>A Chemical Structure Editor</description>
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3 <command interpreter="python">jmoleditor.py $output</command>
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4 <inputs action="http://localhost:8000/Jmoleditor/editor.htm" check_values="false" method="GET">
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5 <param name="GALAXY_URL" type="baseurl" value="/tool_runner" />
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6 <param name="URL" type="hidden" value="http://localhost:8000/Jmoleditor/editor.htm" />
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7 <param name="tool_id" type="hidden" value="jmoleditor" />
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8 </inputs>
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9 <request_param_translation>
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10 <request_param galaxy_name="URL_method" remote_name="URL_method" missing="post" />
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11 <request_param galaxy_name="URL" remote_name="URL" missing="" />
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12 <request_param galaxy_name="galaxyData" remote_name="galaxyData" missing="?" />
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13 <request_param galaxy_name="data_type" remote_name="data_type" missing="txt" />
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14 <request_param galaxy_name="output_label" remote_name="data_type" missing="txt" >
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15 <value_translation>
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16 <value galaxy_value="Molecule" remote_value="sdf" />
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17 <value galaxy_value="SMILES" remote_value="smi" />
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18 </value_translation>
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19 </request_param>
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20 </request_param_translation>
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21 <uihints minwidth="800"/>
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22 <outputs>
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23 <data name="output" format="smi" label='imported ${output_label} file'>
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24 <change_format>
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25 <when input="output_label" value="SMILES" format="smi"/>
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26 </change_format>
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27 </data>
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28 </outputs>
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29 <options sanitize="False" refresh="True"/>
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30 <help>
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31
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32 .. class:: infomark
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33
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34 **What this tool does**
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35
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36 Paint a structure and load it into your Galaxy history.
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37
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38 -----
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39
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40 .. class:: infomark
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41
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42 **Cite**
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43
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44 Jmol_: an open-source Java viewer for chemical structures in 3D
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45
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46 .. _Jmol: http://jmol.sourceforge.net/
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47
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48 </help>
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49 </tool>
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50
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51
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