Mercurial > repos > chrisb > gap_all_glycan_tools
diff convert_detect_formats/rings_convert_format/glycan_convert.xml @ 0:89592faa2875 draft
Uploaded
author | chrisb |
---|---|
date | Wed, 23 Mar 2016 14:35:56 -0400 |
parents | |
children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/convert_detect_formats/rings_convert_format/glycan_convert.xml Wed Mar 23 14:35:56 2016 -0400 @@ -0,0 +1,58 @@ +<tool id="glytools_converter_soap" name="GAP convert format (SOAP)" version="0.3"> + <description> Convert between multiple glycan formats using the RINGS SOAP service</description> + <requirements> + <requirement type="package" version="1.0">python_for_glycan_tools</requirement> + </requirements> + <command interpreter="python"><![CDATA[glycan_convert.py -i $input -f $changeformat -o $output]]></command> + <inputs> + <param format="kcf,glycoct_xml,linucs,linearcode,iupac,glydeii,txt" name="input" type="data" label="Source file"/> + <param name="changeformat" type="select" label="Format to convert to"> + <option value="KCF" selected="true"> KCF </option> + <option value="LinearCode" selected="false"> LinearCode </option> + <option value="LINUCS" selected="false"> LINUCS </option> + <option value="GlycoCT" selected="false"> Glycoct </option> + <option value="IUPAC" selected="false"> IUPAC </option> + </param> + </inputs> + <outputs> + + <data format="input" name="output" metadata_source="input"> + <change_format> + <when input="changeformat" value="KCF" format="kcf"/> + <when input="changeformat" value="GlycoCT" format="glycoct"/> + <when input="changeformat" value="LinearCode" format="linearcode"/> + <when input="changeformat" value="IUPAC" format="iupac"/> + <when input="changeformat" value="LINUCS" format="linucs"/> + </change_format> + </data> + </outputs> + + <citations> + <!-- --> + <citation type="doi">10.1089/omi.2009.0129</citation> +</citations> + + <help> <![CDATA[ +.. class:: infomark + +**What this tool does** + +This tool converts between glycan formats using the RINGS SOAP convert service. + +.. class:: infomark + +**Input** + +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) + + +.. class:: infomark + +**Output** + +Can only convert to KCF, GlycoCT (xml), LinearCode, LINUCS, IUPAC (last checked 25/02/2015). + +]]> + </help> + +</tool>