Mercurial > repos > davidvanzessen > igblast_human

comparison igblastn.xml @ 63:7997fea1f16a draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author davidvanzessen
date Thu, 06 Nov 2014 03:31:15 -0500
parents a700a552f031
children
comparison
equal deleted inserted replaced
62:a700a552f031 63:7997fea1f16a
1 <tool id="igblastn" name="igBLASTn" version="0.1.0"> 1 <tool id="igblastn" name="igBLASTn" version="0.1.0">
2 <description> </description> 2 <description> </description>
3 <command interpreter="bash"> 3 <command interpreter="python">
4 igblastn.sh $input $output 4 igblast_post.py --input $input --output $output
5 </command> 5 </command>
6 <inputs> 6 <inputs>
7 <param name="input" type="data" format="fasta" label="Fasta file"/> 7 <param name="input" type="data" format="fasta" label="Fasta file"/>
8 </inputs> 8 </inputs>
9 <outputs> 9 <outputs>
10 <data name="output" format="text" label="${input.name}-igBLASTn Report"/> 10 <data name="output" format="tabular" type="data" label="${input.name}-igBLASTn Report"/>
11 <!--<data name="log" format="text" label="log"/>--> 11 <!--<data name="log" format="text" label="log"/>-->
12 </outputs> 12 </outputs>
13 <requirements>
14 <requirement type="package" version="1.0.0">igBlastn</requirement>
15 </requirements>
13 <help> 16 <help>
14 Step 1 of the Immune Repertoire tools, generates a report to be parsed with the "igparse" tool. 17 ============
18 iReport
19 ============
20
21 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.
22
23 **NOTE**
24
25 .. class:: warningmark
26
27 - 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.
28
29 **USAGE**
30
31 .. class:: infomark
32
33 - 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.
34
35
36 **INPUT**
37
38 This tool accepts FASTA files as input:
39
40 ::
41
42 >lcl|FLN1FA002RWEZA.1|
43 ggctggagtgggtttcatacattagtagtaatagtggtgccatatactacgcagactctgtgaagggccgattcaccatc
44 tccagaaacaatgccaaggactcactgtatctgcaaatgaacagcctgagagccgaggacacggctgtgtattactgtgc
45 gagagcgatcccccggtattactatgatactagtggcccaaacgactactggggccagggaaccctggtcaccgtctcct
46 cag
47 >lcl|FLN1FA001BLION.1|
48 aggcttgagtggatgggatggatcaacgctggcaatggtaacacaaaatattcacagaagttccagggcagagtcaccat
49 taccagggacacatccgcgagcacagcctacatggagctgagcagcctgagatctgaagacacggctgtgtattactgtg
50 cgagagtgggcagcagctggtctgatgcttttgattatctggggccaagggacaatggtcaccgtctcctcag
51
52 **OUTPUT**
53
54 The following data is used for ARGalaxy
55
56 +-----------------+----------------------------------------------+
57 | Column name | Column contents |
58 +-----------------+----------------------------------------------+
59 | ID | The Sequence ID provided by the sequencer. |
60 +-----------------+----------------------------------------------+
61 | VDJ Frame | In-frame/Out-frame |
62 +-----------------+----------------------------------------------+
63 | Top V Gene | The best matching V gene found. |
64 +-----------------+----------------------------------------------+
65 | Top D Gene | The best matching D gene found. |
66 +-----------------+----------------------------------------------+
67 | Top J Gene | The best matching J gene found. |
68 +-----------------+----------------------------------------------+
69 | CDR3 Seq | The CDR3 region. |
70 +-----------------+----------------------------------------------+
71 | CDR3 Length | The length of the CDR3 region. |
72 +-----------------+----------------------------------------------+
73 | CDR3 Seq DNA | The CDR3 sequence region. |
74 +-----------------+----------------------------------------------+
75 | CDR3 Length DNA | The length of the CDR3 sequence region. |
76 +-----------------+----------------------------------------------+
77 | Functionality | If sequence is productive/unproductive |
78 +-----------------+----------------------------------------------+
79
80
15 </help> 81 </help>
16 </tool> 82 </tool>