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comparison igblastn.xml @ 0:afe85eb6572e draft

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author davidvanzessen
date Mon, 29 Aug 2016 05:41:20 -0400
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1 <tool id="igblastn" name="igBLASTn" version="0.1.0">
2 <description> </description>
3 <command interpreter="bash">
4 igblast/igblast.sh $input $species $locus $output
5 </command>
6 <inputs>
7 <param name="input" type="data" format="fasta" label="Fasta file"/>
8 <param name="species" type="select" label="Species">
9 <option value="human">Homo sapiens</option>
10 <option value="mouse">Mus musculus</option>
11 <option value="rat">Rattus norvegicus</option>
12 <option value="rabbit">Oryctolagus cuniculus</option>
13 <option value="rhesus_monkey">Macaca mulatta</option>
14 </param>
15 <param name="locus" type="select" label="Locus">
16 <option value="TRA">TRA</option>
17 <option value="TRB">TRB</option>
18 <option value="TRG">TRG</option>
19 <option value="TRD">TRD</option>
20 <option value="IGH">IGH</option>
21 <option value="IGK">IGK</option>
22 <option value="IGL">IGL</option>
23 </param>
24 </inputs>
25 <outputs>
26 <data name="output" format="tabular" type="data" label="${input.name}-igBLASTn aligned"/>
27 <!--<data name="log" format="text" label="log"/>-->
28 </outputs>
29 <requirements>
30 <requirement type="package" version="0.6">igblastwrp</requirement>
31 </requirements>
32 <help>
33 ============
34 iReport
35 ============
36
37 This tool uses the online igBLAST website hosted by NCBI to blast a FASTA file, it retrieves the result and generates a convenient tabular format for further processing.
38
39 **NOTE**
40
41 .. class:: warningmark
42
43 - Everything goes through the servers of NCBI, so if you have sensitive data that that isn't allowed to leave your local network, this isn't the tool the use.
44
45 **USAGE**
46
47 .. class:: infomark
48
49 - This tool uses a free service provided by NCBI, and although there doesn't seem to be any restrictions on usage, avoid unnecessary usage to lighten the load on NCBI's servers.
50
51
52 **INPUT**
53
54 This tool accepts FASTA files as input:
55
56 ::
57
58 >lcl|FLN1FA002RWEZA.1|
59 ggctggagtgggtttcatacattagtagtaatagtggtgccatatactacgcagactctgtgaagggccgattcaccatc
60 tccagaaacaatgccaaggactcactgtatctgcaaatgaacagcctgagagccgaggacacggctgtgtattactgtgc
61 gagagcgatcccccggtattactatgatactagtggcccaaacgactactggggccagggaaccctggtcaccgtctcct
62 cag
63 >lcl|FLN1FA001BLION.1|
64 aggcttgagtggatgggatggatcaacgctggcaatggtaacacaaaatattcacagaagttccagggcagagtcaccat
65 taccagggacacatccgcgagcacagcctacatggagctgagcagcctgagatctgaagacacggctgtgtattactgtg
66 cgagagtgggcagcagctggtctgatgcttttgattatctggggccaagggacaatggtcaccgtctcctcag
67
68 **OUTPUT**
69
70 The following data is used for ARGalaxy
71
72 +-----------------+----------------------------------------------+
73 | Column name | Column contents |
74 +-----------------+----------------------------------------------+
75 | ID | The Sequence ID provided by the sequencer. |
76 +-----------------+----------------------------------------------+
77 | VDJ Frame | In-frame/Out-frame |
78 +-----------------+----------------------------------------------+
79 | Top V Gene | The best matching V gene found. |
80 +-----------------+----------------------------------------------+
81 | Top D Gene | The best matching D gene found. |
82 +-----------------+----------------------------------------------+
83 | Top J Gene | The best matching J gene found. |
84 +-----------------+----------------------------------------------+
85 | CDR3 Seq | The CDR3 region. |
86 +-----------------+----------------------------------------------+
87 | CDR3 Length | The length of the CDR3 region. |
88 +-----------------+----------------------------------------------+
89 | CDR3 Seq DNA | The CDR3 sequence region. |
90 +-----------------+----------------------------------------------+
91 | CDR3 Length DNA | The length of the CDR3 sequence region. |
92 +-----------------+----------------------------------------------+
93 | Functionality | If sequence is productive/unproductive |
94 +-----------------+----------------------------------------------+
95
96
97 </help>
98 </tool>