Mercurial > repos > nml > smalt_index
comparison smalt_index.xml @ 0:4b79af35baf9 draft default tip
planemo upload for repository https://sourceforge.net/projects/smalt/ commit 008f4667b70be22e9ddf496738b3f74bb942ed28
| author | nml |
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| date | Tue, 19 Sep 2017 16:38:57 -0400 |
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| -1:000000000000 | 0:4b79af35baf9 |
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| 1 <tool id="smalt_index" name="smalt index" version="1.2.0"> | |
| 2 <description>Index a reference </description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="0.7.6">smalt</requirement> | |
| 5 </requirements> | |
| 6 <stdio> | |
| 7 <exit_code range="1:" level="fatal" description="Unknown error" /> | |
| 8 </stdio> | |
| 9 <command> | |
| 10 smalt index | |
| 11 #if $k: | |
| 12 -k "$k" | |
| 13 #end if | |
| 14 | |
| 15 #if $s: | |
| 16 -s "$s" | |
| 17 #end if | |
| 18 'temp' "$reference" | |
| 19 </command> | |
| 20 <inputs> | |
| 21 <param name="reference" type="data" format="fasta" label="Fasta reference file"/> | |
| 22 <param name="k" type="integer" value="13" label="K-mer size" help="Specifies the word length. [wordlen] is an integer within the limits. between 3 and 20. The default word length is 13" max="20" min="3"/> | |
| 23 <param name="s" type="integer" optional="true" label="Step size" help="Specifies how many bases are skipped between indexed words."/> | |
| 24 </inputs> | |
| 25 <outputs> | |
| 26 <data name="output" label="SMI" from_work_dir="temp.smi" format="binary"/> | |
| 27 <data name="output2" label="SMA" from_work_dir="temp.sma" format="binary"/> | |
| 28 </outputs> | |
| 29 <tests> | |
| 30 <test> | |
| 31 <param name="reference" value="ref.fasta"/> | |
| 32 <output name="output" file="output.smi"/> | |
| 33 <output name="output2" file="output.sma"/> | |
| 34 </test> | |
| 35 </tests> | |
| 36 <help> | |
| 37 | |
| 38 **What it does** | |
| 39 | |
| 40 Generates an index of k-mer words for the genomic reference sequences. The words are of fixed length <wordlen> and are sampled at equidistant steps <stepsiz> bases apart. The reference sequences are provided in a single file <reference_file> in FASTA or FASTQ format. Two binary files are output. The file <index_name>.sma contains the reference sequences in compressed form. The file <index_name>.smi contains the k-mer word index. | |
| 41 | |
| 42 | |
| 43 ------ | |
| 44 | |
| 45 Please cite the website "http://www.sanger.ac.uk/resources/software/smalt/". | |
| 46 | |
| 47 ------ | |
| 48 | |
| 49 -k <wordlen> | |
| 50 Specifies the word length. <wordlen> is an integer within the limits | |
| 51 3 < wordlen <= 20. The default word length is 13. | |
| 52 | |
| 53 -s <stepsiz> | |
| 54 Specifies how many bases are skipped between indexed words. With '-s 1' | |
| 55 every k-mer word along the reference sequences is indexed. With '-s 2' | |
| 56 every other word is indexed etc. By default the step size is set equal | |
| 57 to the word length (tiling words). | |
| 58 | |
| 59 | |
| 60 </help> | |
| 61 </tool> | |
| 62 |