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author nml
date Fri, 06 Apr 2018 14:29:17 -0400
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1 <tool id="pseudogenome" name="Create pseudo genome" version="1.0.0">
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2 <description>from a fasta file in order of appearance</description>
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3 <requirements>
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4 <requirement type="package" version="1.6.924">perl-bioperl</requirement>
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5 <requirement type="package" version="1.04">perl-readonly</requirement>
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6 <requirement type="package" version="2.49">perl-getopt-long</requirement>
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7 <requirement type="package" version="1.25">perl-ipc-system-simple</requirement>
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8 </requirements>
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9 <command detect_errors="exit_code"><![CDATA[
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10 perl '$__tool_directory__/pseudogenome.pl' -i '$input'
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11
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12 #if $stitch.howto == "jcvi":
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13 -s
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14 #else
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15 -n '$stitch.number' -c '$stitch.glue'
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16 #end if
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17
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18 -o '$output'
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19 ]]></command>
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20 <inputs>
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21 <param name="input" type="data" format="fasta" label="Multi contig fasta file" optional="false"/>
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22
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23 <conditional name="stitch">
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24 <param name="howto" type="select" label="How do you want to merge contigs?">
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25 <option selected="true" value="jcvi">JCVI Linker</option>
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26 <option value="custom">Custom options</option>
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27 </param>
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28 <when value="jcvi">
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29 </when>
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30 <when value="custom">
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31 <param name="number" type="integer" value="10" label="Number of filler base pairs" optional="false"/>
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32 <param name="glue" type="text" value="N" label="Character inserted between contigs" optional="false"/>
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33 </when>
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34 </conditional>
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35 </inputs>
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36 <outputs>
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37 <data format="fasta" name="output"/>
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38 </outputs>
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39 <tests>
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40 <test>
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41 <param name="input" value="input.fasta"/>
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42 <output name="output" value="output.fasta"/>
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43 </test>
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44 <test>
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45 <param name="input" value="input.fasta"/>
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46 <param name="howto" value="custom"/>
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47 <param name="number" value="50"/>
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48 <param name="glue" value="X"/>
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49 <output name="output" value="custom.fasta"/>
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50 </test>
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51 </tests>
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52 <help>
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53
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54 What it does
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55 ============
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56 This tool takes in a mult-contig fasta file and converts it into a pseudo genome.
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57
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58
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59
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60 JCVI Linker
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61 ============
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62
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63 Linker is a 36 base pair sequence which places start and
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64 stop codons in all 6 reading frames to prevent gene for being predicted across contigs.
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65
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66 Sequence below:
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67
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68 "NNNNNCACACACTTAATTAATTAAGTGTGTGNNNNN"
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69
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70 </help>
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71 <citations>
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72 </citations>
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73 </tool>