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annotate shovill.xml @ 0:196a599ec43d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
author iuc
date Wed, 25 Oct 2017 03:39:03 -0400
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196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
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1 <tool id="shovill" name="Shovill" version="0.8.0">
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>
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
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3 <requirements>
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4 <requirement type="package" version="0.8.0">shovill</requirement>
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5 </requirements>
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6 <version_command>shovill --version</version_command>
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7 <command detect_errors="exit_code"><![CDATA[
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
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8 shovill
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
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9 --outdir 'out'
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
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10 --cpus \${GALAXY_SLOTS:-1}
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
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11 --ram \${SHOVILL_RAM:-4}
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
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12 #if str($library.lib_type) == "paired"
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
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13 --R1 '$library.R1'
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
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14 --R2 '$library.R2'
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
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15 #else if str($library.lib_type) == "collection"
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
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16 --R1 '$library.input1.forward'
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
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17 --R2 '$library.input1.reverse'
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18 #end if
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19 $trim
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20 --namefmt "$adv.namefmt"
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
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21 --depth '$adv.depth'
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
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22 #if $adv.gsize
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23 --gsize '$adv.gsize'
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
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24 #end if
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25 #if $adv.kmers
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
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26 --kmers '$adv.kmers'
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27 #end if
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28 #if $adv.opts
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
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29 --opts '$adv.opts'
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
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30 #end if
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31 $adv.nocorr
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32 --minlen $adv.minlen
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
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33 --mincov $adv.mincov
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34 --asm $adv.asm
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35
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36 ]]></command>
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
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37 <inputs>
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38 <conditional name="library">
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39 <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">
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40 <option value="paired" selected="true">Paired End</option>
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41 <option value="collection">Paired Collection</option>
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42 </param>
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43 <when value="paired">
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
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44 <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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45 <param name="R2" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="Reverse reads (R2)" help="The file of reverse reads in FASTQ format"/>
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46 </when>
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47 <when value="collection">
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48 <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"/>
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49 </when>
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50 </conditional>
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51 <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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52 <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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53 <section name="adv" title="Advanced options" expanded="False">
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54 <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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55 <sanitizer>
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56 <valid initial="string.printable" />
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57 </sanitizer>
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58 </param>
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59 <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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60 <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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61 <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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62 <param name="opts" argument="--opts" type="text" value="" label="Extra SPAdes options" help="eg. --plasmid --sc ... (default: '')" />
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63 <param name="nocorr" argument="--nocorr" type="boolean" truevalue="--nocorr" falsevalue="" checked="True" label="Disable post-assembly correction" help="Disable post assembly correction with pilon (default: ON)" />
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64 <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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65 <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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66 <param name="asm" argument="--asm" type="select" label="Spades result to correct" help="Which SPAdes output to correct for: before_rr, contigs or scaffolds. (default: 'contigs')">
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67 <option value="before_rr">before_rr</option>
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68 <option value="contigs" selected="true">contigs</option>
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69 <option value="scaffolds">scaffolds</option>
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70 </param>
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71 </section>
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72 </inputs>
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73
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74 <outputs>
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75 <data name="shovill_std_log" format="txt" label="${tool.name} on ${on_string} Log file" from_work_dir="out/00-shovill.log" >
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76 <filter>log</filter>
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77 </data>
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78 <data format="fasta" name="contigs" label="${tool.name} on ${on_string}: Contigs" from_work_dir="out/contigs.fa"/>
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79 <data format="txt" name="contigs_graph" label="${tool.name} on ${on_string}: Contig Graph" from_work_dir="out/contigs.gfa"/>
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80 </outputs>
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81
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82 <tests>
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83 <test> <!-- Test 0: Basic test -->
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84 <param name="lib_type" value="paired" />
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85 <param name="R1" value="mutant_R1.fastq" ftype="fastqsanger" />
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86 <param name="R2" value="mutant_R2.fastq" ftype="fastqsanger" />
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87 <output name="contigs" ftype="fasta">
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88 <assert_contents>
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89 <has_text text="&gt;contig00001"/>
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90 </assert_contents>
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91 </output>
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92 <output name="shovill_std_log" ftype="txt" >
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93 <assert_contents>
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94 <has_text text="Running: seqtk"/>
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95 <has_text text="Running: kmc"/>
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96 <has_text text="Running: lighter"/>
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97 <has_text text="User supplied --nocorr"/>
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98 <has_text text="Running: flash"/>
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99 <has_text text="Running: spades"/>
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100 <has_text text="Done."/>
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101 </assert_contents>
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102 </output>
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103 </test>
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104 <test> <!-- Test 1: Auto everything + trim + different name format test -->
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105 <param name="lib_type" value="paired" />
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106 <param name="R1" value="mutant_R1.fastq" ftype="fastqsanger" />
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107 <param name="R2" value="mutant_R2.fastq" ftype="fastqsanger" />
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108 <param name="trim" value="true" />
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109 <section name="adv">
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110 <param name="depth" value="0"/>
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111 <param name="minlen" value="0"/>
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112 <param name="mincov" value="0"/>
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113 <param name="nocorr" value="false"/>
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114 <param name="namefmt" value="contig%03d"/>
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115 </section>
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116 <output name="contigs" ftype="fasta">
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117 <assert_contents>
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118 <has_text text="&gt;contig001"/>
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119 </assert_contents>
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120 </output>
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121 <output name="shovill_std_log" ftype="txt" >
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122 <assert_contents>
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123 <has_text text="Running: seqtk"/>
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124 <has_text text="Running: kmc"/>
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125 <has_text text="Running: trimmomatic"/>
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126 <has_text text="Running: lighter"/>
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127 <has_text text="Running: flash"/>
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128 <has_text text="Running: spades"/>
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129 <has_text text="Running: bwa index"/>
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130 <has_text text="Running: (bwa mem"/>
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131 <has_text text="Running: _JAVA"/>
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132 <has_text text="Done."/>
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133 </assert_contents>
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134 </output>
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135 </test>
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136 </tests>
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137 <help><![CDATA[
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138 Synopsis:
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139 Faster de novo assembly pipeline for Illumina paired end reads based around Spades
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140
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141 Details and options:
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142 - Takes paired end Illumina fastq reads
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143 - Trim reads: Use Trimmomatic to remove common adaptors first (default: OFF)
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144 - Output log file: If set to "Yes", tool will return Shovill's log file as part of the output
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145
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146 Advanced options:
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147 - Name format: Format of output contig FASTA IDs in 'printf' style (default: 'contig%05d')
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148 - Depth: Sub-sample the reads to this depth. Disable with *Depth: 0* (default: 100)
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149 - Estimated genomesize: An estimate of the final genome size, it will autodetect if this is blank. (default: '')
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150 - List of kmers to use: List of K-mer sizes to use in SPAdes. Blank is AUTO. (default: '')
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151 - Extra SPAdes options: Extra SPAdes options eg. --plasmid --sc ... (default: '')
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152 - Disable post-assembly correction: Disable post assembly correction with pilon (default: ON)
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153 - Minimum contig length: Minimum length of contig to be output. 0 is AUTO (default: 0)
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154 - Minimum contig coverage: Minimum coverage to call part of a contig. 0 is AUTO (default: 2)
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155 - Spades result to correct: Spades result to correct: before_rr, contigs or scaffolds (default: 'contigs')
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156
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157 Documentation can be found at Torsten Seemann `site <https://github.com/tseemann/shovill>`_.
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158 ]]></help>
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159 <citations>
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160 <citation type="bibtex">
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161 @UNPUBLISHED{Seemann2017,
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162 author = {Seemann, Torsten},
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163 title = {Shovill: Faster SPAdes assembly of Illumina reads},
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164 year = {2017},
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165 url = {https://github.com/tseemann/shovill},
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166 }
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167 </citation>
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168 </citations>
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169 </tool>