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annotate shovill.xml @ 8:ad80238462c1 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445
author iuc
date Fri, 16 Sep 2022 14:39:43 +0000
parents 2a9baa0c4316
children ee17a294d3a3
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ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445
iuc
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1 <tool id="shovill" name="Shovill" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
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196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
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2 <description>Faster SPAdes assembly of Illumina reads</description>
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ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445
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3 <macros>
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445
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4 <token name="@TOOL_VERSION@">1.1.0</token>
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445
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5 <token name="@VERSION_SUFFIX@">1</token>
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445
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6 </macros>
7
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7 <xrefs>
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8 <xref type="bio.tools">shovill</xref>
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9 </xrefs>
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10 <requirements>
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11 <requirement type="package" version="@TOOL_VERSION@">shovill</requirement>
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196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
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12 </requirements>
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
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13 <version_command>shovill --version</version_command>
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
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14 <command detect_errors="exit_code"><![CDATA[
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15 ## NOTE: the wrapper uses cp instead of ln -s because of this problem
2a9baa0c4316 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 89d6fae4df90f4e56c0179c6bd97267f6d9c0074"
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16 ## with shovill 1.1.0: https://github.com/tseemann/shovill/issues/157
2a9baa0c4316 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 89d6fae4df90f4e56c0179c6bd97267f6d9c0074"
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17
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18 #if str($library.lib_type) == "paired"
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19 #set r1_ext = $library.R1.extension
d9f6a00b6db7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit eb617cb0aeeb18710ecb12f5208f4e69b7659dbc"
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20 #set r2_ext = $library.R2.extension
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21 #if $r1_ext == 'fastqsanger.gz' or $r1_ext == 'fastqsanger.bz2'
2a9baa0c4316 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 89d6fae4df90f4e56c0179c6bd97267f6d9c0074"
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22 cp '$library.R1' fastq_r1.'$r1_ext' &&
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ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445
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23 cp '$library.R2' fastq_r2.'$r2_ext' &&
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24 #else
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25 ln -s '$library.R1' fastq_r1.'$r1_ext' &&
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ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445
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26 ln -s '$library.R2' fastq_r2.'$r2_ext' &&
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27 #end if
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28 #else if str($library.lib_type) == "collection"
d9f6a00b6db7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit eb617cb0aeeb18710ecb12f5208f4e69b7659dbc"
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29 #set r1_ext = $library.input1.forward.extension
d9f6a00b6db7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit eb617cb0aeeb18710ecb12f5208f4e69b7659dbc"
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30 #set r2_ext = $library.input1.reverse.extension
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31 #if $r1_ext == 'fastqsanger.gz' or $r1_ext == 'fastqsanger.bz2'
2a9baa0c4316 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 89d6fae4df90f4e56c0179c6bd97267f6d9c0074"
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32 cp '$library.input1.forward' fastq_r1.'$r1_ext' &&
2a9baa0c4316 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 89d6fae4df90f4e56c0179c6bd97267f6d9c0074"
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33 cp '$library.input1.reverse' fastq_r2.'$r2_ext' &&
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34 #else
2a9baa0c4316 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 89d6fae4df90f4e56c0179c6bd97267f6d9c0074"
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35 ln -s '$library.input1.forward' fastq_r1.'$r1_ext' &&
2a9baa0c4316 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 89d6fae4df90f4e56c0179c6bd97267f6d9c0074"
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36 ln -s '$library.input1.reverse' fastq_r2.'$r2_ext' &&
2a9baa0c4316 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 89d6fae4df90f4e56c0179c6bd97267f6d9c0074"
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37 #end if
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38 #end if
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39
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40 ## Sets the memory used by Shovill according to the following conditions
8d1af5db538d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit da99aa8018e36c84fc4cbd7c73923fc710b3b31a"
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41 ## (1) If SHOVILL_RAM is already set, use this value
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42 ## (2) Otherwise, set based on GALAXY_MEMORY_MB
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43 ## (3) Or default to 4 GB if GALAXY_MEMORY_MB is unset
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44 GALAXY_MEMORY_GB=\$((\${GALAXY_MEMORY_MB:-4096}/1024)) &&
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45 SHOVILL_RAM=\${SHOVILL_RAM:-\${GALAXY_MEMORY_GB}} &&
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ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445
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46
0
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47 shovill
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48 --outdir 'out'
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49 --cpus \${GALAXY_SLOTS:-1}
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50 --ram \${SHOVILL_RAM:-4}
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51 --R1 'fastq_r1.$(r1_ext)'
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445
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52 --R2 'fastq_r2.$(r2_ext)'
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53 $trim
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54 --namefmt '$adv.namefmt'
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55 --depth '$adv.depth'
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56 #if $adv.gsize
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57 --gsize '$adv.gsize'
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58 #end if
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
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59 #if $adv.kmers
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60 --kmers '$adv.kmers'
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61 #end if
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62 #if $adv.opts
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63 --opts '$adv.opts'
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64 #end if
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65 --minlen $adv.minlen
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66 --mincov $adv.mincov
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67 --assembler $assembler
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68 #if $adv.keep_files.nocorr == 'no_correction'
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69 --nocorr
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70 #else
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71 $adv.keep_files.keepfiles
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72 #end if
0
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73 ]]></command>
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74 <inputs>
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75 <conditional name="library">
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76 <param name="lib_type" type="select" label="Input reads type, collection or single library" help="Select 'paired end' for a single library or 'collection' for a paired end collection">
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
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77 <option value="paired" selected="true">Paired End</option>
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78 <option value="collection">Paired Collection</option>
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79 </param>
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80 <when value="paired">
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81 <param name="R1" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="Forward reads (R1)" help="The file of forward reads in FASTQ format"/>
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
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82 <param name="R2" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="Reverse reads (R2)" help="The file of reverse reads in FASTQ format"/>
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
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83 </when>
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84 <when value="collection">
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85 <param name="input1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" type="data_collection" collection_type="paired" label="Paired collection" help="See help section for an explanation of dataset collections"/>
0
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86 </when>
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87 </conditional>
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88 <param name="trim" argument="--trim" type="boolean" truevalue="--trim" falsevalue="" label="Trim reads" help="Use Trimmomatic to remove common adaptors first (default: OFF)" />
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89 <param name="assembler" argument="--assembler" type="select" label="Assembler to use" help="Which assembler would you like shovill to use, default is Spades">
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90 <option value="skesa">skesa</option>
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91 <option value="megahit">megahit</option>
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92 <option value="velvet">velvet</option>
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93 <option value="spades" selected="true">Spades</option>
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94 </param>
0
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95 <section name="adv" title="Advanced options" expanded="False">
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96 <param name="namefmt" argument="--namefmt" type="text" value="contig%05d" label="Contig name format" help="Format of contig FASTA IDs in 'printf' style (default: 'contig%05d')" >
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97 <sanitizer>
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98 <valid initial="string.printable">
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99 <remove value="&apos;" />
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100 </valid>
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101 <mapping initial="none">
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102 <add source="&apos;" target="&apos;&quot;&apos;&quot;&apos;" />
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103 </mapping>
0
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104 </sanitizer>
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105 </param>
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106 <param name="depth" argument="--depth" type="integer" value="100" label="Depth" help="Sub-sample --R1/--R2 to this depth. Disable with --depth 0 (default: 100)" />
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107 <param name="gsize" argument="--gsize" type="text" value="" label="Estimated genome size" help="An estimate of the final genome size, it will autodetect if this is blank. (default: '')" />
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108 <param name="kmers" argument="--kmers" type="text" value="" label="List of kmer sizes to use" help="List of K-mer sizes to use in SPAdes. Blank is AUTO. default: ''" />
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109 <param name="opts" argument="--opts" type="text" value="" label="Extra SPAdes options" help="eg. --plasmid --sc ... (default: '')" />
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110 <conditional name="keep_files">
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111 <param name="nocorr" argument="--nocorr" type="select" label="Disable post-assembly correction" help="Disable post assembly correction with pilon (default: ON)">
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112 <option value="no_correction" selected="true">No corrections</option>
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113 <option value="yes_correction">Post assembly corrections</option>
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114 </param>
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115 <when value="no_correction"/>
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116 <when value="yes_correction">
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117 <param name="keepfiles" argument="--keepfiles" type="boolean" truevalue="--keepfiles" checked="False" falsevalue="" label="Keep bam files" help="Keep bam files only if post-assembly correction is enable"/>
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118 </when>
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119 </conditional>
0
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120 <param name="minlen" argument="--minlen" type="integer" value="0" label="Minimum contig length" help="Minimum length of contig to be output. 0 is AUTO (default: 0)" />
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121 <param name="mincov" argument="--mincov" type="integer" value="2" label="Minimum contig coverage" help="Minimum coverage to call part of a contig. 0 is AUTO (default: 2)" />
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122 </section>
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123 <param name="log" type="boolean" label="Output log file?" checked="true" help="Return the Shovill log file as part of the output. Default is on" />
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124
0
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125 </inputs>
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126 <outputs>
3
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127 <data name="shovill_std_log" format="txt" label="${tool.name} on ${on_string} Log file" from_work_dir="out/shovill.log" >
8
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128 <filter>log == True</filter>
0
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129 </data>
8
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130 <data name="contigs" format="fasta" label="${tool.name} on ${on_string}: Contigs" from_work_dir="out/contigs.fa"/>
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131 <data name="contigs_graph" format="txt" label="${tool.name} on ${on_string}: Contig Graph" from_work_dir="out/contigs.gfa"/>
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132 <data name="bamfiles" format="unsorted.bam" from_work_dir="out/shovill.bam" label="Bam file for ${tool.name} on ${on_string}">
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133 <filter> adv['keep_files']['nocorr'] == 'yes_correction' and adv['keep_files']['keepfiles'] == True </filter>
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134 </data>
0
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135 </outputs>
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136 <tests>
8
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137 <test expect_num_outputs="3"> <!-- Test 1: Basic test -->
0
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138 <param name="lib_type" value="paired" />
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139 <param name="R1" value="mutant_R1.fastq" ftype="fastqsanger" />
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140 <param name="R2" value="mutant_R2.fastq" ftype="fastqsanger" />
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141 <output name="contigs" ftype="fasta">
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142 <assert_contents>
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143 <has_text text="&gt;contig00001"/>
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144 </assert_contents>
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145 </output>
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146 <output name="shovill_std_log" ftype="txt" >
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147 <assert_contents>
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148 <has_text text="Read stats: total_bp = 300000"/>
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149 <has_text text="[lighter] Processed 820 reads"/>
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150 <has_text text="[FLASH] FLASH v1.2.11 complete!"/>
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151 <has_text text="[spades] ======= SPAdes pipeline finished."/>
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152 </assert_contents>
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153 </output>
0
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154 </test>
8
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155 <test expect_num_outputs="3"> <!-- Test 2: Auto everything + trim + different name format test -->
0
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156 <param name="lib_type" value="paired" />
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157 <param name="R1" value="mutant_R1.fastq" ftype="fastqsanger" />
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158 <param name="R2" value="mutant_R2.fastq" ftype="fastqsanger" />
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159 <param name="trim" value="true" />
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160 <section name="adv">
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161 <param name="depth" value="0"/>
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162 <param name="minlen" value="0"/>
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163 <param name="mincov" value="0"/>
8
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164 <conditional name="keep_files">
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165 <param name="nocorr" value="yes_correction"/>
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166 </conditional>
0
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167 <param name="namefmt" value="contig%03d"/>
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168 </section>
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169 <output name="contigs" ftype="fasta">
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170 <assert_contents>
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171 <has_text text="&gt;contig001"/>
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
172 </assert_contents>
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
173 </output>
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
174 <output name="shovill_std_log" ftype="txt" >
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
175 <assert_contents>
3
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
176 <has_text text="[trimmomatic] TrimmomaticPE: Completed successfully"/>
6
83ead2be47b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit f667915d861dbf0a25cc8fd132cc956d82e73ee9"
iuc
parents: 5
diff changeset
177 <has_text text="[lighter] Processed"/>
3
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
178 <has_text text="[FLASH] FLASH v1.2.11 complete!"/>
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
179 <has_text text="[spades] ======= SPAdes pipeline finished."/>
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
180 <has_text text="[bwa+samtools-sort] [samclip] Done."/>
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
181 <has_text text="[pilon] Mean total coverage:"/>
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
182 <has_text text="[shovill] Done."/>
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
183 </assert_contents>
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
184 </output>
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
185 </test>
8
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445
iuc
parents: 7
diff changeset
186 <test expect_num_outputs="3"> <!-- Test 3: Alternate assembler #1: Megahit -->
3
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
187 <param name="lib_type" value="paired" />
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
188 <param name="R1" value="mutant_R1.fastq" ftype="fastqsanger" />
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
189 <param name="R2" value="mutant_R2.fastq" ftype="fastqsanger" />
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
190 <param name="assembler" value="megahit" />
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
191 <output name="contigs" ftype="fasta">
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
192 <assert_contents>
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
193 <has_text text="&gt;contig00001"/>
8
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445
iuc
parents: 7
diff changeset
194 </assert_contents>
3
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
195 </output>
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
196 <output name="shovill_std_log" ftype="txt" >
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
197 <assert_contents>
6
83ead2be47b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit f667915d861dbf0a25cc8fd132cc956d82e73ee9"
iuc
parents: 5
diff changeset
198 <has_text text="[lighter] Processed"/>
3
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
199 <has_text text="[FLASH] FLASH v1.2.11 complete!"/>
4
d9f6a00b6db7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit eb617cb0aeeb18710ecb12f5208f4e69b7659dbc"
iuc
parents: 3
diff changeset
200 <has_text_matching expression="\[megahit\] .* ALL DONE"/>
6
83ead2be47b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit f667915d861dbf0a25cc8fd132cc956d82e73ee9"
iuc
parents: 5
diff changeset
201 <has_text text="[shovill] Done."/>
3
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
202 </assert_contents>
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
203 </output>
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
204 </test>
8
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445
iuc
parents: 7
diff changeset
205 <test expect_num_outputs="3"> <!-- Test 4: Alternate assembler #2: Skesa -->
3
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
206 <param name="lib_type" value="paired" />
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
207 <param name="R1" value="mutant_R1.fastq" ftype="fastqsanger" />
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
208 <param name="R2" value="mutant_R2.fastq" ftype="fastqsanger" />
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
209 <param name="assembler" value="skesa" />
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
210 <output name="contigs" ftype="fasta">
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
211 <assert_contents>
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
212 <has_text text="&gt;contig00001"/>
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
213 </assert_contents>
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
214 </output>
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
215 <output name="shovill_std_log" ftype="txt" >
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
216 <assert_contents>
6
83ead2be47b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit f667915d861dbf0a25cc8fd132cc956d82e73ee9"
iuc
parents: 5
diff changeset
217 <has_text text="[lighter] Processed"/>
3
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
218 <has_text text="[FLASH] FLASH v1.2.11 complete!"/>
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
219 <has_text text="[skesa] DONE"/>
6
83ead2be47b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit f667915d861dbf0a25cc8fd132cc956d82e73ee9"
iuc
parents: 5
diff changeset
220 <has_text text="[shovill] Done."/>
3
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
221 </assert_contents>
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
222 </output>
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
223 </test>
8
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445
iuc
parents: 7
diff changeset
224 <test expect_num_outputs="3"> <!-- Test 5: Alternate assembler #3: Velvet -->
3
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
225 <param name="lib_type" value="paired" />
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
226 <param name="R1" value="mutant_R1.fastq" ftype="fastqsanger" />
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
227 <param name="R2" value="mutant_R2.fastq" ftype="fastqsanger" />
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
228 <param name="assembler" value="velvet" />
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
229 <output name="contigs" ftype="fasta">
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
230 <assert_contents>
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
231 <has_text text="&gt;contig00001"/>
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
232 </assert_contents>
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
233 </output>
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
234 <output name="shovill_std_log" ftype="txt" >
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
235 <assert_contents>
6
83ead2be47b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit f667915d861dbf0a25cc8fd132cc956d82e73ee9"
iuc
parents: 5
diff changeset
236 <has_text text="[lighter] Processed"/>
3
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
237 <has_text text="[FLASH] FLASH v1.2.11 complete!"/>
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
238 <has_text text="[velvetg] Final graph has"/>
6
83ead2be47b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit f667915d861dbf0a25cc8fd132cc956d82e73ee9"
iuc
parents: 5
diff changeset
239 <has_text text="[shovill] Done."/>
0
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
240 </assert_contents>
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
241 </output>
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
iuc
parents:
diff changeset
242 </test>
8
ad80238462c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445
iuc
parents: 7
diff changeset
243 <test expect_num_outputs="3"> <!-- Test 6: Gzipped input with trimming -->
4
d9f6a00b6db7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit eb617cb0aeeb18710ecb12f5208f4e69b7659dbc"
iuc
parents: 3
diff changeset
244 <param name="lib_type" value="paired" />
7
2a9baa0c4316 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 89d6fae4df90f4e56c0179c6bd97267f6d9c0074"
iuc
parents: 6
diff changeset
245 <param name="R1" value="mutant_R1.fastq.gz" ftype="fastqsanger.gz" />
2a9baa0c4316 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 89d6fae4df90f4e56c0179c6bd97267f6d9c0074"
iuc
parents: 6
diff changeset
246 <param name="R2" value="mutant_R2.fastq.gz" ftype="fastqsanger.gz" />
4
d9f6a00b6db7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit eb617cb0aeeb18710ecb12f5208f4e69b7659dbc"
iuc
parents: 3
diff changeset
247 <param name="trim" value="true" />
d9f6a00b6db7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit eb617cb0aeeb18710ecb12f5208f4e69b7659dbc"
iuc
parents: 3
diff changeset
248 <output name="contigs" ftype="fasta">
d9f6a00b6db7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit eb617cb0aeeb18710ecb12f5208f4e69b7659dbc"
iuc
parents: 3
diff changeset
249 <assert_contents>
d9f6a00b6db7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit eb617cb0aeeb18710ecb12f5208f4e69b7659dbc"
iuc
parents: 3
diff changeset
250 <has_text text="&gt;contig00001"/>
d9f6a00b6db7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit eb617cb0aeeb18710ecb12f5208f4e69b7659dbc"
iuc
parents: 3
diff changeset
251 </assert_contents>
d9f6a00b6db7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit eb617cb0aeeb18710ecb12f5208f4e69b7659dbc"
iuc
parents: 3
diff changeset
252 </output>
d9f6a00b6db7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit eb617cb0aeeb18710ecb12f5208f4e69b7659dbc"
iuc
parents: 3
diff changeset
253 <output name="shovill_std_log" ftype="txt" >
d9f6a00b6db7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit eb617cb0aeeb18710ecb12f5208f4e69b7659dbc"
iuc
parents: 3
diff changeset
254 <assert_contents>
6
83ead2be47b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit f667915d861dbf0a25cc8fd132cc956d82e73ee9"
iuc
parents: 5
diff changeset
255 <has_text text="[lighter] Processed"/>
4
d9f6a00b6db7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit eb617cb0aeeb18710ecb12f5208f4e69b7659dbc"
iuc
parents: 3
diff changeset
256 <has_text text="[FLASH] FLASH v1.2.11 complete!"/>
d9f6a00b6db7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit eb617cb0aeeb18710ecb12f5208f4e69b7659dbc"
iuc
parents: 3
diff changeset
257 <has_text text="[spades] ======= SPAdes pipeline finished."/>
6
83ead2be47b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit f667915d861dbf0a25cc8fd132cc956d82e73ee9"
iuc
parents: 5
diff changeset
258 <has_text text="[shovill] Done."/>
4
d9f6a00b6db7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit eb617cb0aeeb18710ecb12f5208f4e69b7659dbc"
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259 </assert_contents>
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260 </output>
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261 </test>
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262 <test expect_num_outputs="4"> <!-- Test 7: Add keepfiles option -->
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263 <param name="lib_type" value="paired" />
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264 <param name="R1" value="mutant_R1.fastq.gz" ftype="fastqsanger.gz" />
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265 <param name="R2" value="mutant_R2.fastq.gz" ftype="fastqsanger.gz" />
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266 <param name="trim" value="true" />
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267 <section name="adv">
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268 <conditional name="keep_files">
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269 <param name="nocorr" value="yes_correction" />
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270 <param name="keepfiles" value="True" />
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271 </conditional>
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272 <param name="log" value="true"/>
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273 </section>
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274 <output name="contigs" ftype="fasta">
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275 <assert_contents>
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276 <has_text text="&gt;contig00001"/>
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277 </assert_contents>
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278 </output>
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279 <output name="bamfiles" ftype="unsorted.bam">
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280 <assert_contents>
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281 <has_size value="36359" delta="1000" />
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282 </assert_contents>
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283 </output>
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284 </test>
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285 </tests>
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286 <help><![CDATA[
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287 Synopsis:
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288 Faster de novo assembly pipeline for Illumina paired end reads based around Spades
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289
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290 Details and options:
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291 - Takes paired end Illumina fastq reads
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292 - Trim reads: Use Trimmomatic to remove common adaptors first (default: OFF)
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293 - Output log file: If set to "Yes", tool will return Shovill's log file as part of the output
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294 - Assembler: Which assembler should shovill use from: Skesa, Megahit, Velvet or Spades. Spades is the default.
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295
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296 Advanced options:
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297 - Name format: Format of output contig FASTA IDs in 'printf' style (default: 'contig%05d')
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298 - Depth: Sub-sample the reads to this depth. Disable with *Depth: 0* (default: 100)
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299 - Estimated genomesize: An estimate of the final genome size, it will autodetect if this is blank. (default: '')
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300 - List of kmers to use: List of K-mer sizes to use in SPAdes. Blank is AUTO. (default: '')
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301 - Extra SPAdes options: Extra SPAdes options eg. --plasmid --sc ... (default: '')
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302 - Disable post-assembly correction: Disable post assembly correction with pilon (default: ON)
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303 - Keep the bam files : Enable to keep mapped files from bwa in the post assembly correction (default: OFF)
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304 - Minimum contig length: Minimum length of contig to be output. 0 is AUTO (default: 0)
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305 - Minimum contig coverage: Minimum coverage to call part of a contig. 0 is AUTO (default: 2)
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306 - Spades result to correct: Spades result to correct: before_rr, contigs or scaffolds (default: 'contigs')
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307
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308 Documentation can be found at Torsten Seemann `site <https://github.com/tseemann/shovill>`_.
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309 ]]></help>
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310 <citations>
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311 <citation type="bibtex">
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312 @UNPUBLISHED{Seemann2017,
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313 author = {Seemann, Torsten},
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314 title = {Shovill: Faster SPAdes assembly of Illumina reads},
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315 year = {2017},
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316 url = {https://github.com/tseemann/shovill},
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317 }
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318 </citation>
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319 </citations>
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320 </tool>