0
|
1 <tool id="glytools_converter_soap" name="GAP convert format (SOAP)" version="0.3">
|
|
2 <description> Convert between multiple glycan formats using the RINGS SOAP service</description>
|
|
3 <requirements>
|
|
4 <requirement type="package" version="1.0">python_for_glycan_tools</requirement>
|
|
5 </requirements>
|
|
6 <command interpreter="python"><![CDATA[glycan_convert.py -i $input -f $changeformat -o $output]]></command>
|
|
7 <inputs>
|
|
8 <param format="kcf,glycoct_xml,linucs,linearcode,iupac,glydeii,txt" name="input" type="data" label="Source file"/>
|
|
9 <param name="changeformat" type="select" label="Format to convert to">
|
|
10 <option value="KCF" selected="true"> KCF </option>
|
|
11 <option value="LinearCode" selected="false"> LinearCode </option>
|
|
12 <option value="LINUCS" selected="false"> LINUCS </option>
|
|
13 <option value="GlycoCT" selected="false"> Glycoct </option>
|
|
14 <option value="IUPAC" selected="false"> IUPAC </option>
|
|
15 </param>
|
|
16 </inputs>
|
|
17 <outputs>
|
|
18
|
|
19 <data format="input" name="output" metadata_source="input">
|
|
20 <change_format>
|
|
21 <when input="changeformat" value="KCF" format="kcf"/>
|
|
22 <when input="changeformat" value="GlycoCT" format="glycoct"/>
|
|
23 <when input="changeformat" value="LinearCode" format="linearcode"/>
|
|
24 <when input="changeformat" value="IUPAC" format="iupac"/>
|
|
25 <when input="changeformat" value="LINUCS" format="linucs"/>
|
|
26 </change_format>
|
|
27 </data>
|
|
28 </outputs>
|
|
29
|
|
30 <citations>
|
|
31 <!-- -->
|
|
32 <citation type="doi">10.1089/omi.2009.0129</citation>
|
|
33 </citations>
|
|
34
|
|
35 <help> <![CDATA[
|
|
36 .. class:: infomark
|
|
37
|
|
38 **What this tool does**
|
|
39
|
|
40 This tool converts between glycan formats using the RINGS SOAP convert service.
|
|
41
|
|
42 .. class:: infomark
|
|
43
|
|
44 **Input**
|
|
45
|
|
46 Any glycan dataset *except* for GlycoCT{condensed}, WURCS, MDL Mol and LINUCS (LINUCS only converts to LINUCS with this tools and the other formats do not convert)
|
|
47
|
|
48
|
|
49 .. class:: infomark
|
|
50
|
|
51 **Output**
|
|
52
|
|
53 Can only convert to KCF, GlycoCT (xml), LinearCode, LINUCS, IUPAC (last checked 25/02/2015).
|
|
54
|
|
55 ]]>
|
|
56 </help>
|
|
57
|
|
58 </tool>
|