annotate CADDSuite-1.5/galaxyconfigs/tools/Converter.xml @ 16:1a24aef40d01 draft

Deleted selected files
author marcel
date Tue, 24 Jul 2012 11:10:07 -0400
parents ac342506cd4e
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="converter" name="Converter" version="1.5">
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
4 <description>interconvert molecular file-formats</description>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
5 <command interpreter="bash"><![CDATA[../../Converter
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( $f ) != '' and str( $f ) != 'None' :
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
13 -f "$f"
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 #if str( $rm ) != '' and str( $rm ) != 'None' :
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
16 -rm
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
17 #end if
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
18 | tail -n 5
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
19 ]]></command>
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 <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
22 <param name="f" optional="true" label="output format" type="select">
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
23 <option value="mol2">mol2</option>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
24 <option value="sdf">sdf</option>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
25 <option value="drf">drf</option>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
26 <option value="pdb">pdb</option>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
27 <option value="ac">ac</option>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
28 <option value="ent">ent</option>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
29 <option value="brk">brk</option>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
30 <option value="hin">hin</option>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
31 <option value="mol">mol</option>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
32 <option value="xyz">xyz</option>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
33 <option value="mol2.gz">mol2.gz</option>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
34 <option value="sdf.gz">sdf.gz</option>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
35 <option value="drf.gz">drf.gz</option>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
36 <option value="pdb.gz">pdb.gz</option>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
37 <option value="ac.gz">ac.gz</option>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
38 <option value="ent.gz">ent.gz</option>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
39 <option value="brk.gz">brk.gz</option>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
40 <option value="hin.gz">hin.gz</option>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
41 <option value="mol.gz">mol.gz</option>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
42 <option value="xyz.gz">xyz.gz</option>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
43 </param>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
44 <param name="rm" optional="true" label="remove input file when finished" type="boolean" truevalue="true" falsevalue=""/>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
45 </inputs>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
46 <outputs>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
47 <data name="o" format="mol2/sdf/drf">
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
48 <change_format>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
49 <when input="f" value="mol2" format="mol2"/>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
50 <when input="f" value="sdf" format="sdf"/>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
51 <when input="f" value="drf" format="drf"/>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
52 <when input="f" value="pdb" format="pdb"/>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
53 <when input="f" value="ac" format="ac"/>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
54 <when input="f" value="ent" format="ent"/>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
55 <when input="f" value="brk" format="brk"/>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
56 <when input="f" value="hin" format="hin"/>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
57 <when input="f" value="mol" format="mol"/>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
58 <when input="f" value="xyz" format="xyz"/>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
59 <when input="f" value="mol2.gz" format="mol2.gz"/>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
60 <when input="f" value="sdf.gz" format="sdf.gz"/>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
61 <when input="f" value="drf.gz" format="drf.gz"/>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
62 <when input="f" value="pdb.gz" format="pdb.gz"/>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
63 <when input="f" value="ac.gz" format="ac.gz"/>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
64 <when input="f" value="ent.gz" format="ent.gz"/>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
65 <when input="f" value="brk.gz" format="brk.gz"/>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
66 <when input="f" value="hin.gz" format="hin.gz"/>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
67 <when input="f" value="mol.gz" format="mol.gz"/>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
68 <when input="f" value="xyz.gz" format="xyz.gz"/>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
69 </change_format>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
70 </data>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
71 </outputs>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
72 <help>This tool can be used to convert between different molecular file-formats.
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
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>
ac342506cd4e CADDSuite version 1.5
Marcel Schumann <schumann.marcel@gmail.com>
parents:
diff changeset
74 </tool>