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1 <tool id="igblastn" name="igBLASTn" version="0.1.0">
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2 <description> </description>
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3 <command interpreter="python">
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4 igblast_post.py --input $input --output $output
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5 </command>
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6 <inputs>
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7 <param name="input" type="data" format="fasta" label="Fasta file"/>
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8 </inputs>
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9 <outputs>
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10 <data name="output" format="tabular" type="data" label="${input.name}-igBLASTn Report"/>
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11 <!--<data name="log" format="text" label="log"/>-->
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12 </outputs>
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13 <requirements>
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14 <requirement type="package" version="1.0.0">igBlastn</requirement>
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15 </requirements>
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16 <help>
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17 ============
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18 iReport
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19 ============
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20
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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.
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22
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23 **NOTE**
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24
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25 .. class:: warningmark
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26
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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.
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28
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29 **USAGE**
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30
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31 .. class:: infomark
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32
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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.
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34
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35
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36 **INPUT**
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37
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38 This tool accepts FASTA files as input:
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39
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40 ::
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41
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42 >lcl|FLN1FA002RWEZA.1|
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43 ggctggagtgggtttcatacattagtagtaatagtggtgccatatactacgcagactctgtgaagggccgattcaccatc
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44 tccagaaacaatgccaaggactcactgtatctgcaaatgaacagcctgagagccgaggacacggctgtgtattactgtgc
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45 gagagcgatcccccggtattactatgatactagtggcccaaacgactactggggccagggaaccctggtcaccgtctcct
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46 cag
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47 >lcl|FLN1FA001BLION.1|
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48 aggcttgagtggatgggatggatcaacgctggcaatggtaacacaaaatattcacagaagttccagggcagagtcaccat
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49 taccagggacacatccgcgagcacagcctacatggagctgagcagcctgagatctgaagacacggctgtgtattactgtg
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50 cgagagtgggcagcagctggtctgatgcttttgattatctggggccaagggacaatggtcaccgtctcctcag
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51
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52 **OUTPUT**
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53
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54 The following data is used for ARGalaxy
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55
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56 +-----------------+----------------------------------------------+
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57 | Column name | Column contents |
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58 +-----------------+----------------------------------------------+
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59 | ID | The Sequence ID provided by the sequencer. |
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60 +-----------------+----------------------------------------------+
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61 | VDJ Frame | In-frame/Out-frame |
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62 +-----------------+----------------------------------------------+
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63 | Top V Gene | The best matching V gene found. |
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64 +-----------------+----------------------------------------------+
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65 | Top D Gene | The best matching D gene found. |
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66 +-----------------+----------------------------------------------+
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67 | Top J Gene | The best matching J gene found. |
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68 +-----------------+----------------------------------------------+
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69 | CDR3 Seq | The CDR3 region. |
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70 +-----------------+----------------------------------------------+
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71 | CDR3 Length | The length of the CDR3 region. |
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72 +-----------------+----------------------------------------------+
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73 | CDR3 Seq DNA | The CDR3 sequence region. |
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74 +-----------------+----------------------------------------------+
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75 | CDR3 Length DNA | The length of the CDR3 sequence region. |
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76 +-----------------+----------------------------------------------+
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77 | Functionality | If sequence is productive/unproductive |
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78 +-----------------+----------------------------------------------+
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79
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80
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81 </help>
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82 </tool>
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