Mercurial > repos > marcel > caddsuite_linux_x86_64

annotate CADDSuite-1.5/galaxyconfigs/tools/MolDepict.xml @ 15:ac342506cd4e draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
CADDSuite version 1.5
author Marcel Schumann <schumann.marcel@gmail.com>
date Tue, 24 Jul 2012 11:08:49 -0400
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
15
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
1
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
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.-->
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
3 <tool id="moldepict" name="MolDepict" version="1.5">
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
4 <description>create structure diagrams</description>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
5 <command interpreter="bash"><![CDATA[../../MolDepict
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
6 #if str( $i ) != '' and str( $i ) != 'None' :
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
7 -i "$i"
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
8 #end if
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
9 #if str( $o ) != '' and str( $o ) != 'None' :
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
10 -o "$o"
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
11 #end if
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
12 #if str( $max ) != '' and str( $max ) != 'None' :
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
13 -max "$max"
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
14 #end if
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
15 | tail -n 5
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
16 ]]></command>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
17 <inputs>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
18 <param name="i" optional="false" label="input file" type="data" format="mol2/sdf/drf"/>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
19 <param name="max" optional="true" label="Optional: maximal number of pictures (default=60, 0=unlimited)" type="text" area="true" size="1x5" value="60"/>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
20 </inputs>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
21 <outputs>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
22 <data name="o" format="pdf"/>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
23 </outputs>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
24 <help>This tool create structure diagrams for small molecules.
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
25 Supported input-formats are mol, mol2, sdf, drf.
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
26
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
27 Output of this tool is one pdf-file containing the structure diagrams for all molecules in the input-file.</help>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
28 </tool>