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comparison convert_detect_formats/rings_convert_format/glycan_convert.xml @ 0:89592faa2875 draft

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author chrisb
date Wed, 23 Mar 2016 14:35:56 -0400
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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>