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annotate primer_search.xml @ 0:1f4836da4a14 draft default tip

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planemo upload for repository https://github.com/bvalot/galaxy commit d57c24d4b2c0c741d572af9ca0d09f8b82689640
author bvalot
date Tue, 14 Jun 2022 08:52:22 +0000
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1f4836da4a14 planemo upload for repository https://github.com/bvalot/galaxy commit d57c24d4b2c0c741d572af9ca0d09f8b82689640
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1 <tool id="primer_search_wrapper" name="Primer Search" version="0.1">
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2 <description></description>
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3 <requirements>
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4 <requirement type="package" version="1.28">gassst</requirement>
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5 <requirement type="package" version="1.78">biopython</requirement>
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6 </requirements>
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7 <stdio>
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8 <exit_code range="1:" level="fatal" />
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9 </stdio>
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10 <version_command>$__tool_directory__/primer_search.py -v</version_command>
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11 <command>
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12 $__tool_directory__/primer_search.py -o $output
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13 #if str($error)
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14 -e $error
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15 #end if
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16 #if str($min)
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17 -m $min
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18 #end if
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19 #if str($max)
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20 -M $max
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21 #end if
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22 #if $keep
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23 -k
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24 #end if
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25 #if $remove
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26 -r
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27 #end if
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28 $forward $reverse $database 2> $logfile
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29 </command>
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30 <inputs>
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31 <param name="database" type="data" format="fasta" label="Database to search on fasta" help="FASTA format" />
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32 <param name="forward" type="text" value="" optional="false" size="50"
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33 label="Forward primer sequence"
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34 help="DNA sequence, letters corresponding to multiple nucleotide allowed" />
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35 <param name="reverse" type="text" value="" optional="false" size="50"
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36 label="Reverse primer sequence"
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37 help="DNA sequence, letters corresponding to multiple nucleotide allowed" />
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38 <param name="error" type="integer" value="1" optional="true"
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39 label="Maximun error allowed on match" help="Number of mismatch allowed for each primer" />
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40 <param name="min" type="integer" value="100" optional="true"
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41 label="Min len amplicon size" help="Only amplicon with this minimun length were reported" />
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42 <param name="max" type="integer" value="1500" optional="true"
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43 label="Max len amplicon size" help="Only amplicon with this maximun length were reported" />
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44 <param name="keep" type="boolean" checked="false"
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45 label="If set, Keep description instead of report PCR position" />
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46 <param name="remove" type="boolean" checked="false"
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47 label="If set, remove primer sequance from reported amplicons" />
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48 </inputs>
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49 <outputs>
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50 <data name="logfile" format="txt" label="${tool.name} on ${on_string}: log" />
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51 <data name="output" format="fasta" label="${tool.name} on ${on_string}: fasta" />
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52 </outputs>
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53 <tests>
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54 <test expect_num_outputs="2">
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55 <param name="database" value="input.fasta" />
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56 <param name="forward" value="ACCTGGTGTACGCCTCGCTGAC" />
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57 <param name="reverse" value="GACATAGATGCCCTGCCCCTTGAT" />
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58 <param name="error" value="2" />
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59 <output name="output" file="pcr.fasta" ftype="fasta" />
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60 </test>
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61 </tests>
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62 <help>
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63 **What it does**
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64
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65 Search primer on database and return amplicons on fasta format.
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66
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67 **License and citation**
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68
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69 This Galaxy tool is Copyright © 2018 `B. Valot` and is released under the `GPL3 license`.
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70
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71 This tool uses Gassst, which is licensed separately.
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72 Please cite: Rizk G. and Dominique Lavenier D. (2010) GASSST: global alignment short sequence search tool. *Bioinformatics* 26(20), 2534-2540.
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73 http://www.irisa.fr/symbiose/projects/gassst/
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74 </help>
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75 <citations>
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76 <citation type="doi">10.1093/bioinformatics/btq485</citation>
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77 </citations>
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78 </tool>