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planemo upload for repository https://sourceforge.net/projects/smalt/ commit 008f4667b70be22e9ddf496738b3f74bb942ed28
author nml
date Tue, 19 Sep 2017 16:38:57 -0400
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4b79af35baf9 planemo upload for repository https://sourceforge.net/projects/smalt/ commit 008f4667b70be22e9ddf496738b3f74bb942ed28
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1 <tool id="smalt_index" name="smalt index" version="1.2.0">
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2 <description>Index a reference </description>
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3 <requirements>
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4 <requirement type="package" version="0.7.6">smalt</requirement>
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5 </requirements>
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6 <stdio>
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7 <exit_code range="1:" level="fatal" description="Unknown error" />
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8 </stdio>
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9 <command>
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10 smalt index
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11 #if $k:
4b79af35baf9 planemo upload for repository https://sourceforge.net/projects/smalt/ commit 008f4667b70be22e9ddf496738b3f74bb942ed28
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12 -k "$k"
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13 #end if
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15 #if $s:
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16 -s "$s"
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17 #end if
4b79af35baf9 planemo upload for repository https://sourceforge.net/projects/smalt/ commit 008f4667b70be22e9ddf496738b3f74bb942ed28
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18 'temp' "$reference"
4b79af35baf9 planemo upload for repository https://sourceforge.net/projects/smalt/ commit 008f4667b70be22e9ddf496738b3f74bb942ed28
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19 </command>
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20 <inputs>
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21 <param name="reference" type="data" format="fasta" label="Fasta reference file"/>
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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"/>
4b79af35baf9 planemo upload for repository https://sourceforge.net/projects/smalt/ commit 008f4667b70be22e9ddf496738b3f74bb942ed28
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23 <param name="s" type="integer" optional="true" label="Step size" help="Specifies how many bases are skipped between indexed words."/>
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24 </inputs>
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25 <outputs>
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26 <data name="output" label="SMI" from_work_dir="temp.smi" format="binary"/>
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27 <data name="output2" label="SMA" from_work_dir="temp.sma" format="binary"/>
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28 </outputs>
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29 <tests>
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30 <test>
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31 <param name="reference" value="ref.fasta"/>
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32 <output name="output" file="output.smi"/>
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33 <output name="output2" file="output.sma"/>
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34 </test>
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35 </tests>
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36 <help>
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4b79af35baf9 planemo upload for repository https://sourceforge.net/projects/smalt/ commit 008f4667b70be22e9ddf496738b3f74bb942ed28
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38 **What it does**
4b79af35baf9 planemo upload for repository https://sourceforge.net/projects/smalt/ commit 008f4667b70be22e9ddf496738b3f74bb942ed28
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40 Generates an index of k-mer words for the genomic reference sequences. The words are of fixed length &#060;wordlen&#062; and are sampled at equidistant steps &#060;stepsiz&#062; bases apart. The reference sequences are provided in a single file &#060;reference_file&#062; in FASTA or FASTQ format. Two binary files are output. The file &#060;index_name&#062;.sma contains the reference sequences in compressed form. The file &#060;index_name&#062;.smi contains the k-mer word index.
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43 ------
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45 Please cite the website "http://www.sanger.ac.uk/resources/software/smalt/".
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47 ------
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49 -k &#060;wordlen&#062;
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50 Specifies the word length. &#060;wordlen&#062; is an integer within the limits
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51 3 &#060; wordlen &#060;= 20. The default word length is 13.
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52
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53 -s &#060;stepsiz&#062;
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54 Specifies how many bases are skipped between indexed words. With '-s 1'
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55 every k-mer word along the reference sequences is indexed. With '-s 2'
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56 every other word is indexed etc. By default the step size is set equal
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57 to the word length (tiling words).
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60 </help>
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61 </tool>
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62