Mercurial > repos > chrisb > gap_all_glycan_tools
comparison convert_detect_formats/rings_convert_format/glycan_convert.xml @ 0:89592faa2875 draft
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author | chrisb |
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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> |