Mercurial > repos > chrisb > gap_all_glycan_tools
comparison manipulate/rename_kcf/rename_kcf.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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-1:000000000000 | 0:89592faa2875 |
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1 <tool id="glytools_rename_KCF" name="GAP Rename KCF" version="0.3"> | |
2 <description>rename the ENTRY tag in KCF file</description> | |
3 <requirements> | |
4 <requirement type="package" version="1.0">python_for_glycan_tools</requirement> | |
5 </requirements> | |
6 <command interpreter="python"><![CDATA[ rename_kcf.py -i $input -o $kcfoutput -p $prefix -c $counter]]></command> | |
7 <inputs> | |
8 <param format="kcf" name="input" type="data" label="KCF source file"/> | |
9 <param name="prefix" type="text" value="GLY" optional="false" label="Prefix for renaming ENTRY" help="Type in a prefix for renaming entry"/> | |
10 <param name="counter" type="integer" value="0" min="0" max="10000" optional="false" label="Integer start counter for renaming ENTRY"/> | |
11 </inputs> | |
12 <outputs> | |
13 <data format="kcf" name="kcfoutput" label="Renamed KCF $input.name"/> | |
14 </outputs> | |
15 | |
16 <citations> | |
17 <!-- --> | |
18 <citation type="doi">10.1002/0471250953.bi0112s38</citation> | |
19 </citations> | |
20 | |
21 <help> <![CDATA[ | |
22 .. class:: infomark | |
23 | |
24 **What this tool does** | |
25 | |
26 This tool reads KCF glycans and sequentially renames them as GLY{$COUNT}. Why? Sometimes entry names have illegal chars e.g. "-" or sometimes they are linearcode. Which seems great but linearcode is too long and has too many illegals chars in it, meaning that other tools along the pipeline start to fail. | |
27 | |
28 .. class:: infomark | |
29 | |
30 **Input** | |
31 | |
32 *KCF* | |
33 | |
34 .. class:: infomark | |
35 | |
36 **Output** | |
37 | |
38 *KCF* | |
39 | |
40 ]]> | |
41 </help> | |
42 | |
43 </tool> |