Mercurial > repos > iuc > valet

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
author iuc
date Thu, 16 Nov 2017 08:54:24 -0500
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4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
iuc
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1 <tool id="valet" name="VALET" version="@WRAPPER_VERSION@.0">
4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
iuc
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2 <description>to detect mis-assemblies in metagenomic assemblies</description>
4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
iuc
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3 <macros>
4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
iuc
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4 <token name="@WRAPPER_VERSION@">1.0</token>
4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
iuc
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5 <token name="@INPUT_@">
4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
iuc
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6 1.0
4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
iuc
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7 </token>
4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
iuc
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8 <xml name="insert_size">
4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
iuc
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9 <param argument="--minins" type="integer" min="0" value="0" label="Min insert sizes for mate pairs" />
4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
iuc
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10 <param argument="--maxins" type="integer" min="0" value="500" label="Max insert sizes for mate pairs" />
4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
iuc
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11 </xml>
4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
iuc
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12 <xml name="orientation">
4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
iuc
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13 <param argument="--orientation" type="select" label="Orientation of the mates" >
4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
iuc
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14 <option value="fr">fr: mate 1 appears upstream of the reverse complement of mate 2 or mate 2 appears upstream of the reverse
4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
iuc
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15 complement of mate 1</option>
4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
iuc
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16 <option value="rf">rf: reverse-complemented mate 1 is upstream and forward-oriented mate 2 is downstream</option>
4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
iuc
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17 <option value="ff">ff: both upstream mate 1 and downstream mate 2 are forward-oriented</option>
4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
iuc
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18 </param>
4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
iuc
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19 </xml>
4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
iuc
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20 </macros>
4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
iuc
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21 <requirements>
4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
iuc
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22 <requirement type="package" version="@WRAPPER_VERSION@">valet</requirement>
4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
iuc
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23 </requirements>
4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
iuc
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24 <version_command>echo @WRAPPER_VERSION@</version_command>
4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
iuc
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25 <command detect_errors="exit_code">
4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
iuc
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26 <![CDATA[
4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
iuc
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27 valet.py
4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
iuc
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28 #set assembly_fasta = []
4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
iuc
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29 #set assembly_names = []
4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
iuc
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30 #for $repeat in $assembly
4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
iuc
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31 $assembly_fasta.append(str($repeat.assembly_fasta))
4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
iuc
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32 $assembly_names.append(str($repeat.assembly_names))
4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
iuc
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33 #end for
4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
iuc
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34 --assembly-fasta ${','.join($assembly_fasta)}
4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
iuc
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35 --assembly-names ${','.join($assembly_names)}
4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
iuc
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36 #if $input_reads.type == 'single'
4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
iuc
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37 $input_reads.single_input_reads.type
4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
iuc
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38 --reads '$input_reads.single_input_reads.reads'
4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
iuc
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39 #else if $input_reads.type == 'paired'
4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
iuc
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40 #set mate_1 = []
4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
iuc
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41 #set mate_2 = []
4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
iuc
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42 #set minins = []
4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
iuc
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43 #set maxins = []
4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
iuc
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44 #for $repeat in $input_reads.paired_input_reads.paired_reads
4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
iuc
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45 $mate_1.append(str($repeat.mate_1))
4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
iuc
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46 $mate_2.append(str($repeat.mate_2))
4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
iuc
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47 $minins.append(str($repeat.minins))
4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
iuc
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48 $maxins.append(str($repeat.maxins))
4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
iuc
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49 #end for
4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
iuc
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50 --1 ${','.join($mate_1)}
4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
iuc
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51 --2 ${','.join($mate_2)}
4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
iuc
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52 --minins ${','.join($minins)}
4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
iuc
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53 --maxins ${','.join($maxins)}
4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
iuc
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54 $input_reads.paired_input_reads.type
4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
iuc
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55 --orientation '$input_reads.orientation'
4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
iuc
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56 #else if $input_reads.type == 'paired_collection'
4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
iuc
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57 #set mate_1 = []
4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
iuc
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58 #set mate_2 = []
4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
iuc
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59 #set minins = []
4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
iuc
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60 #set maxins = []
4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
iuc
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61 #for $repeat in $input_reads.paired_coll_input_reads.paired_collection_reads
4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
iuc
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62 $mate_1.append(str($repeat.input.forward))
4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
iuc
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63 $mate_2.append(str($repeat.input.reverse))
4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
iuc
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64 $minins.append(str($repeat.minins))
4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
iuc
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65 $maxins.append(str($repeat.maxins))
4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
iuc
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66 #end for
4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
iuc
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67 --1 ${','.join($mate_1)}
4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
iuc
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68 --2 ${','.join($mate_2)}
4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
iuc
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69 --minins ${','.join($minins)}
4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
iuc
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70 --maxins ${','.join($maxins)}
4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
iuc
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71 $input_reads.paired_coll_input_reads.type
4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
iuc
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72 --orientation '$input_reads.orientation'
4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
iuc
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73 #end if
4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
iuc
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74 --output-dir output
4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
iuc
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75 --window-size '$window_size'
4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
iuc
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76 --threads \${GALAXY_SLOTS:-4}
4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
iuc
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77 --max-alignments '$max_alignments'
4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
iuc
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78 --min-coverage '$min_coverage'
4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
iuc
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79 --coverage-multiplier '$coverage_multiplier'
4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
iuc
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80 --min-suspicious '$min_suspicious'
4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
iuc
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81 --suspicious-flank-size '$suspicious_flank_size'
4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
iuc
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82 --min-contig-length '$min_contig_length'
4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
iuc
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83 --ignore-ends '$ignore_ends'
4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
iuc
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84 --breakpoint-bin '$breakpoint_bin'
4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
iuc
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85 #if $orf_file
4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
iuc
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86 --orf-file '$orf_file'
4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
iuc
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87 #end if
4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
iuc
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88 #if $coverage_file
4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
iuc
parents:
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89 --coverage-file '$coverage_file'
4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
iuc
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90 #end if
4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
iuc
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91 --kmer '$kmer'
4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
iuc
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92 --skip-reapr
4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
iuc
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93 #for $repeat in $assembly
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94 && mv output/${repeat.assembly_names}/summary.bed output/${repeat.assembly_names}_summary.bed
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95 && mv output/${repeat.assembly_names}/summary.tsv output/${repeat.assembly_names}_summary.tsv
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96 && mv output/${repeat.assembly_names}/suspicious.bed output/${repeat.assembly_names}_suspicious.bed
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97 #end for
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98 ]]></command>
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99 <inputs>
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100 <repeat name="assembly" title="Candidate assemblies">
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101 <param name="assembly_fasta" argument="--assembly-fasta" type="data" format="fasta" label="Candidate assembly file" />
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102 <param name="assembly_names" argument="--assembly-names" type="text" value="" label="Name of the assembly">
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103 <validator type="empty_field" message="A name is required"/>
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104 </param>
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105 </repeat>
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106 <conditional name="input_reads">
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107 <param name="type" type="select" label="Type of input reads used for the assembly">
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108 <option value="single">Single</option>
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109 <option value="paired">Paired</option>
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110 <option value="paired_collection">Paired-collection</option>
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111 </param>
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112 <when value="single">
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113 <conditional name="single_input_reads">
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114 <param name="type" type="select" label="Input format">
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115 <option value="--fasta">Fasta</option>
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116 <option value="--fastq">FastQ</option>
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117 </param>
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118 <when value="--fasta">
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119 <param argument="--reads" type="data" format="fasta" label="Assembly input reads" />
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120 </when>
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121 <when value="--fastq">
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122 <param argument="--reads" type="data" format="fastq" label="Assembly input reads" />
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123 </when>
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124 </conditional>
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125 </when>
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126 <when value="paired">
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127 <conditional name="paired_input_reads">
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128 <param name="type" type="select" label="Input format">
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129 <option value="--fasta">Fasta</option>
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130 <option value="--fastq">FastQ</option>
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131 </param>
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132 <when value="--fasta">
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133 <repeat name="paired_reads" title="Mate pair reads">
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134 <param name="mate_1" argument="--1" type="data" format="fasta" label="Assembly input first mate reads" />
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135 <param name="mate_2" argument="--2" type="data" format="fasta" label="Assembly input second mate reads" />
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136 <expand macro="insert_size"/>
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137 </repeat>
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138 </when>
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139 <when value="--fastq">
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140 <repeat name="paired_reads" title="Mate pair reads">
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141 <param name="mate_1" argument="--1" type="data" format="fastq" label="Assembly input first mate reads" />
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142 <param name="mate_2" argument="--2" type="data" format="fastq" label="Assembly input second mate reads" />
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143 <expand macro="insert_size"/>
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144 </repeat>
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145 </when>
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146 </conditional>
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147 <expand macro="orientation"/>
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148 </when>
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149 <when value="paired_collection">
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150 <conditional name="paired_coll_input_reads">
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151 <param name="type" type="select" label="Input format">
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152 <option value="--fasta">Fasta</option>
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153 <option value="--fastq">FastQ</option>
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154 </param>
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155 <when value="--fasta">
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156 <repeat name="paired_collection_reads" title="Mate paired read collections">
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157 <param name="input" format="fasta" type="data_collection" collection_type="paired" label="Assembly input reads" />
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158 <expand macro="insert_size"/>
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159 </repeat>
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160 </when>
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161 <when value="--fastq">
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162 <repeat name="paired_collection_reads" title="Mate paired read collections">
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163 <param name="input" format="fastq" type="data_collection" collection_type="paired" label="Assembly input reads" />
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164 <expand macro="insert_size"/>
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165 </repeat>
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166 </when>
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167 </conditional>
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168 <expand macro="orientation"/>
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169 </when>
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170 </conditional>
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171 <param name="window_size" argument="--window-size" type="integer" min="0" value="501" label="Sliding window size when determining misassemblies" />
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172 <param name="max_alignments" argument="--max-alignments" type="integer" min="0" value="10000" label="Bowtie2 parameter to set the max number of alignments" />
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173 <param name="min_coverage" argument="--min-coverage" type="integer" min="0" value="0" label="Minimum average coverage to run misassembly detection" />
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174 <param name="coverage_multiplier" argument="--coverage-multiplier" type="float" min="0" value="0" label="When binning by coverage, the new high = high + high * multiplier" />
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175 <param name="min_suspicious" argument="--min-suspicious" type="integer" min="0" value="2" label="Minimum number of overlapping flagged miassemblies to mark region as suspicious" />
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176 <param name="suspicious_flank_size" argument="--suspicious-flank-size" type="integer" min="0" value="2000" label="Mark region as suspicious if multiple signatures occur within this window size" />
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177 <param name="min_contig_length" argument="--min-contig-length" type="integer" min="0" value="1000" label="Ignore contigs smaller than this length" />
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178 <param name="ignore_ends" argument="--ignore-ends" type="integer" min="0" value="0" label="Ignore flagged regions within b bps from the ends of the contigs" />
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179 <param name="breakpoint_bin" argument="--breakpoint-bin" type="integer" min="0" value="50" label="Bin sized used to find breakpoints" />
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180 <param name="kmer" argument="--kmer" type="integer" min="0" value="15" label="Kmer length used for abundance estimation" />
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181 <param name="coverage_file" argument="--coverage-file" type="data" format="tabular,txt" optional="true" label="Assembly created per-contig coverage file" />
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182 <param name="orf_file" argument="--orf-file" type="data" format="gff,gtf" optional="true" label="File containing ORFs" />
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183 </inputs>
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184 <outputs>
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185 <collection name="flagged" type="list" label="${tool.name} on ${on_string}: Flagged regions">
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186 <discover_datasets pattern="(?P&lt;designation&gt;.+)_summary.bed" format="bed" directory="output"/>
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187 </collection>
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188 <collection name="suspicious" type="list" label="${tool.name} on ${on_string}: Suspicious regions">
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189 <discover_datasets pattern="(?P&lt;designation&gt;.+)_suspicious.bed" format="bed" directory="output"/>
4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
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190 </collection>
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191 <collection name="summary" type="list" label="${tool.name} on ${on_string}: Summary">
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192 <discover_datasets pattern="(?P&lt;designation&gt;.+)_summary.tsv" format="tabular" directory="output"/>
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193 </collection>
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194 <data name="comparison_plot" format="pdf" from_work_dir="output/comparison_plots.pdf" label="${tool.name} on ${on_string}: Comparison plot" />
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195 </outputs>
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196 <tests>
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197 <test>
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198 <repeat name="assembly">
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199 <param name="assembly_fasta" value="c_rudii_reference.fna"/>
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200 <param name="assembly_names" value="reference"/>
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201 </repeat>
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202 <repeat name="assembly">
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203 <param name="assembly_fasta" value="c_rudii_dup.fna"/>
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204 <param name="assembly_names" value="duplication"/>
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205 </repeat>
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206 <repeat name="assembly">
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207 <param name="assembly_fasta" value="c_rudii_relocation.fna"/>
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208 <param name="assembly_names" value="relocation"/>
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209 </repeat>
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210 <repeat name="assembly">
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211 <param name="assembly_fasta" value="c_rudii_reloc_dup.fna"/>
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212 <param name="assembly_names" value="reloc-dup"/>
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213 </repeat>
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214 <conditional name="input_reads">
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215 <param name="type" value="paired"/>
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216 <conditional name="paired_input_reads">
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217 <param name="type" value="--fastq"/>
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218 <repeat name="paired_reads">
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219 <param name="mate_1" value="lib1.1.fastq" />
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220 <param name="mate_2" value="lib1.2.fastq" />
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221 <param name="minins" value="0"/>
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222 <param name="maxins" value="500" />
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223 </repeat>
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224 </conditional>
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225 <param name="orientation" value="fr" />
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226 </conditional>
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227 <param name="window_size" value="501"/>
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228 <param name="max_alignments" value="10000"/>
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229 <param name="min_coverage" value="0" />
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230 <param name="coverage_multiplier" value="0"/>
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231 <param name="min_suspicious" value="2" />
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232 <param name="suspicious_flank_size" value="2000" />
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233 <param name="min_contig_length" value="1000"/>
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234 <param name="ignore_ends" value="0"/>
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235 <param name="breakpoint_bin" value="50" />
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236 <param name="kmer" value="15" />
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237 <param name="coverage_file" value="carsonella_asm.cvg" />
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238 <output_collection name="flagged" type="list">
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239 <element name="reference" ftype="bed" file="flagged_reference.bed"/>
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240 <element name="duplication" ftype="bed" file="flagged_duplication.bed"/>
4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
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241 <element name="relocation" ftype="bed" file="flagged_relocation.bed"/>
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242 <element name="reloc-dup" ftype="bed" file="flagged_reloc-dup.bed"/>
4872c51a696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet commit 30ecbd2ebd336d7002ca11abd69d600a24986156
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243 </output_collection>
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244 <output_collection name="suspicious" type="list">
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245 <element name="reference" ftype="bed" file="suspicious_reference.bed"/>
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246 <element name="duplication" ftype="bed" file="suspicious_duplication.bed"/>
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247 <element name="relocation" ftype="bed" file="suspicious_relocation.bed"/>
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248 <element name="reloc-dup" ftype="bed" file="suspicious_reloc-dup.bed"/>
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249 </output_collection>
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250 <output_collection name="summary" type="list">
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251 <element name="reference" ftype="tabular" file="summary_reference.tabular"/>
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252 <element name="duplication" ftype="tabular" file="summary_duplication.tabular"/>
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253 <element name="relocation" ftype="tabular" file="summary_relocation.tabular"/>
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254 <element name="reloc-dup" ftype="tabular" file="summary_reloc-dup.tabular"/>
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255 </output_collection>
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256 <output name="comparison_plot" file="test1_comparison_plot.pdf" compare="sim_size"/>
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257 </test>
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258 <test>
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259 <repeat name="assembly">
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260 <param name="assembly_fasta" value="c_rudii_dup.fna"/>
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261 <param name="assembly_names" value="duplication"/>
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262 </repeat>
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263 <conditional name="input_reads">
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264 <param name="type" value="paired_collection"/>
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265 <conditional name="paired_coll_input_reads">
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266 <param name="type" value="--fastq"/>
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267 <repeat name="paired_collection_reads">
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268 <param name="input">
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269 <collection type="paired">
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270 <element name="forward" value="lib1.1.fastq" ftype="fastq" />
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271 <element name="reverse" value="lib1.2.fastq" ftype="fastq" />
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272 </collection>
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273 </param>
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274 <param name="minins" value="0"/>
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275 <param name="maxins" value="500" />
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276 </repeat>
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277 </conditional>
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278 <param name="orientation" value="fr" />
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279 </conditional>
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280 <param name="window_size" value="501"/>
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281 <param name="max_alignments" value="10000"/>
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282 <param name="min_coverage" value="0" />
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283 <param name="coverage_multiplier" value="0"/>
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284 <param name="min_suspicious" value="2" />
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285 <param name="suspicious_flank_size" value="2000" />
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286 <param name="min_contig_length" value="1000"/>
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287 <param name="ignore_ends" value="0"/>
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288 <param name="breakpoint_bin" value="50" />
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289 <param name="kmer" value="15" />
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290 <output_collection name="flagged" type="list">
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291 <element name="duplication" ftype="bed" file="flagged_duplication.bed"/>
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292 </output_collection>
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293 <output_collection name="suspicious" type="list">
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294 <element name="duplication" ftype="bed" file="suspicious_duplication.bed"/>
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295 </output_collection>
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296 <output_collection name="summary" type="list">
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297 <element name="duplication" ftype="tabular" file="summary_duplication.tabular"/>
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298 </output_collection>
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299 <output name="comparison_plot" file="test2_comparison_plot.pdf" compare="sim_size"/>
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300 </test>
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301 </tests>
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302 <help><![CDATA[
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303 **What it does**
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304
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305 VALET is a de novo pipeline for detecting all types of mis-assemblies in metagenomic data sets.
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306
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307 Its primarily adapts the approaches developed in the context of isolate genomes. To avoid false positives and false
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308 negatives because of uneven depth of coverage, VALET bins contig by coverage before applying these methods.
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309
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310 Possible break points in the assembly are found by examining regions, where a large number of parts of the reads are
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311 unable to align. To identify break points, VALET uses the first and last third of each unaligned read, called sister
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312 reads. The sister reads are aligned independently to the reference genome, and then regions where the sister reads
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313 align to nonadjacent segments of the genome are flagged as mis-assemblies.
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314
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315 For more details about the tool, please check: https://github.com/marbl/VALET
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316 ]]></help>
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317 <citations/>
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318 </tool>