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comparison manipulate/extend_linearcode/lc_extend.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_lc_extend" name="GAP Permute Linearcode" version="0.3">
2 <description> and append or extend fragments on fuzzy linear code </description>
3 <requirements>
4 <requirement type="package" version="1.0">python_for_glycan_tools</requirement>
5 </requirements>
6 <command interpreter="python"><![CDATA[lc_extend.py -i $input -o $output -l $logfile $appendorextend ]]></command>
7 <inputs>
8 <param format="linearcode" name="input" type="data" label="Linear Code source file"/>
9 <param name="appendorextend" type="select" label="Behaviour">
10 <option value="" selected="true"> Default append behaviour</option>
11 <option value="-e">Create all possible linearcode combinations (not recommended)</option>
12 </param>
13 </inputs>
14 <outputs>
15 <data format="linearcode" name="output" label="LC permutations of $input.name"/>
16 <data format="txt" name="logfile" label="debugging log file of $input.name"/>
17 </outputs>
18 <help> <![CDATA[
19 .. class:: infomark
20
21 **What this tool does**
22
23 This tool provides all permutations of linear code with uncertain leaves i.e. that is it converts fuzzy glycans to unfuzzy glycans.
24
25 .. class:: infomark
26
27 **Inputs**
28
29 This tool requires *LinearCode* format.
30
31 ----
32
33 .. class:: infomark
34
35 **Example**
36
37 Query sequence::
38
39 (Ma2Ma3(Ma3(Ma6)Ma6)Mb4GNb4GN,M)
40 (A??GN??Ma3(GN??Ma6)Mb4GNb4(Fa6)GN)
41
42 Default Output sequence::
43
44 ((M??)X??)(Ma2Ma3(Ma3)(Ma6)Ma6)Mb4GNb4GN
45 (A??GN??Ma3(GN??Ma6)Mb4GNb4(Fa6)GN)
46
47 Extended Output sequence (not recommended)::
48
49 M??Ma2Ma3(Ma3(Ma6)Ma6)Mb4GNb4GN
50 Ma2Ma3(M??Ma3(Ma6)Ma6)Mb4GNb4GN
51 Ma2Ma3(Ma3(M??Ma6)Ma6)Mb4GNb4GN
52 (A??GN??Ma3(GN??Ma6)Mb4GNb4(Fa6)GN)
53
54 ]]>
55
56 </help>
57
58 </tool>