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annotate shovill.xml @ 3:865119fcb694 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
author iuc
date Tue, 13 Nov 2018 10:41:12 -0500
parents f698c7604b3b
children d9f6a00b6db7
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865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
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1 <tool id="shovill" name="Shovill" version="1.0.4">
0
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2 <description>Faster SPAdes assembly of Illumina reads</description>
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3 <requirements>
3
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4 <requirement type="package" version="1.0.4">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[
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8 shovill
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9 --outdir 'out'
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10 --cpus \${GALAXY_SLOTS:-1}
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11 --ram \${SHOVILL_RAM:-4}
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12 #if str($library.lib_type) == "paired"
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13 --R1 '$library.R1'
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14 --R2 '$library.R2'
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15 #else if str($library.lib_type) == "collection"
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16 --R1 '$library.input1.forward'
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17 --R2 '$library.input1.reverse'
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18 #end if
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19 $trim
2
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20 --namefmt '$adv.namefmt'
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21 --depth '$adv.depth'
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22 #if $adv.gsize
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23 --gsize '$adv.gsize'
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24 #end if
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25 #if $adv.kmers
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26 --kmers '$adv.kmers'
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27 #end if
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28 #if $adv.opts
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29 --opts '$adv.opts'
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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 --assembler $assembler
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35
0
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36 ]]></command>
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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">
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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"/>
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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">
1
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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"/>
0
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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 <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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54 <option value="skesa">skesa</option>
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55 <option value="megahit">megahit</option>
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56 <option value="velvet">velvet</option>
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57 <option value="spades" selected="true">Spades</option>
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58 </param>
0
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59 <section name="adv" title="Advanced options" expanded="False">
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60 <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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61 <sanitizer>
2
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62 <valid initial="string.printable">
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63 <remove value="&apos;" />
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64 </valid>
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65 <mapping initial="none">
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66 <add source="&apos;" target="&apos;&quot;&apos;&quot;&apos;" />
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67 </mapping>
0
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68 </sanitizer>
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69 </param>
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70 <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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71 <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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72 <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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73 <param name="opts" argument="--opts" type="text" value="" label="Extra SPAdes options" help="eg. --plasmid --sc ... (default: '')" />
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74 <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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75 <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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76 <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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77 </section>
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78 </inputs>
1
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79
0
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80 <outputs>
3
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81 <data name="shovill_std_log" format="txt" label="${tool.name} on ${on_string} Log file" from_work_dir="out/shovill.log" >
0
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82 <filter>log</filter>
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83 </data>
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84 <data format="fasta" name="contigs" label="${tool.name} on ${on_string}: Contigs" from_work_dir="out/contigs.fa"/>
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85 <data format="txt" name="contigs_graph" label="${tool.name} on ${on_string}: Contig Graph" from_work_dir="out/contigs.gfa"/>
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86 </outputs>
1
57d5928f456e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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87
0
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88 <tests>
3
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89 <test> <!-- Test 1: Basic test -->
0
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
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90 <param name="lib_type" value="paired" />
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91 <param name="R1" value="mutant_R1.fastq" ftype="fastqsanger" />
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
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92 <param name="R2" value="mutant_R2.fastq" ftype="fastqsanger" />
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
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93 <output name="contigs" ftype="fasta">
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94 <assert_contents>
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95 <has_text text="&gt;contig00001"/>
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
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96 </assert_contents>
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97 </output>
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98 <output name="shovill_std_log" ftype="txt" >
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
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99 <assert_contents>
3
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
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100 <has_text text="[mash]"/>
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101 <has_text text="[lighter] Processed 24960 reads"/>
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
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102 <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
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103 <has_text text="[spades] ======= SPAdes pipeline finished."/>
0
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
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104 </assert_contents>
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105 </output>
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
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106 </test>
3
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
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107 <test> <!-- Test 2: Auto everything + trim + different name format test -->
0
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108 <param name="lib_type" value="paired" />
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109 <param name="R1" value="mutant_R1.fastq" ftype="fastqsanger" />
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
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110 <param name="R2" value="mutant_R2.fastq" ftype="fastqsanger" />
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
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111 <param name="trim" value="true" />
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
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112 <section name="adv">
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113 <param name="depth" value="0"/>
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
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114 <param name="minlen" value="0"/>
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
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115 <param name="mincov" value="0"/>
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
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116 <param name="nocorr" value="false"/>
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
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117 <param name="namefmt" value="contig%03d"/>
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
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118 </section>
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119 <output name="contigs" ftype="fasta">
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
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120 <assert_contents>
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121 <has_text text="&gt;contig001"/>
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
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122 </assert_contents>
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123 </output>
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
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124 <output name="shovill_std_log" ftype="txt" >
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
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125 <assert_contents>
3
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126 <has_text text="[mash] Writing to"/>
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127 <has_text text="[trimmomatic] TrimmomaticPE: Completed successfully"/>
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128 <has_text text="[lighter] Processed 24960 reads:"/>
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
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diff changeset
129 <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
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130 <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
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131 <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
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132 <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
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133 <has_text text="[shovill] Done."/>
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134 </assert_contents>
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135 </output>
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
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diff changeset
136 </test>
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
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diff changeset
137 <test> <!-- Test 3: Alternate assembler #1: Megahit -->
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
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diff changeset
138 <param name="lib_type" value="paired" />
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
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diff changeset
139 <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
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diff changeset
140 <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
141 <param name="assembler" value="megahit" />
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
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diff changeset
142 <output name="contigs" ftype="fasta">
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
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diff changeset
143 <assert_contents>
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iuc
parents: 2
diff changeset
144 <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
145 </assert_contents>
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iuc
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diff changeset
146 </output>
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
147 <output name="shovill_std_log" ftype="txt" >
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148 <assert_contents>
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iuc
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diff changeset
149 <has_text text="[mash]"/>
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
150 <has_text text="[lighter] Processed 24960 reads"/>
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
151 <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
152 <has_text text="[megahit] --- [STAT]"/>
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
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diff changeset
153 </assert_contents>
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diff changeset
154 </output>
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
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diff changeset
155 </test>
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
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diff changeset
156 <test> <!-- Test 4: Alternate assembler #2: Skesa -->
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
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diff changeset
157 <param name="lib_type" value="paired" />
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
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diff changeset
158 <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
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diff changeset
159 <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
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diff changeset
160 <param name="assembler" value="skesa" />
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
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diff changeset
161 <output name="contigs" ftype="fasta">
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
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diff changeset
162 <assert_contents>
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iuc
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diff changeset
163 <has_text text="&gt;contig00001"/>
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
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diff changeset
164 </assert_contents>
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diff changeset
165 </output>
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
166 <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
167 <assert_contents>
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iuc
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diff changeset
168 <has_text text="[mash]"/>
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
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169 <has_text text="[lighter] Processed 24960 reads"/>
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
parents: 2
diff changeset
170 <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
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diff changeset
171 <has_text text="[skesa] DONE"/>
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
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diff changeset
172 </assert_contents>
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iuc
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diff changeset
173 </output>
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iuc
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diff changeset
174 </test>
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iuc
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diff changeset
175 <test> <!-- Test 5: Alternate assembler #3: Velvet -->
865119fcb694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
iuc
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diff changeset
176 <param name="lib_type" value="paired" />
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iuc
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diff changeset
177 <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
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178 <param name="R2" value="mutant_R2.fastq" ftype="fastqsanger" />
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179 <param name="assembler" value="velvet" />
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180 <output name="contigs" ftype="fasta">
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181 <assert_contents>
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182 <has_text text="&gt;contig00001"/>
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183 </assert_contents>
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184 </output>
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185 <output name="shovill_std_log" ftype="txt" >
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186 <assert_contents>
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187 <has_text text="[mash]"/>
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188 <has_text text="[lighter] Processed 24960 reads"/>
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189 <has_text text="[FLASH] FLASH v1.2.11 complete!"/>
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190 <has_text text="[velvetg] Final graph has"/>
0
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191 </assert_contents>
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192 </output>
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193 </test>
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194 </tests>
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195 <help><![CDATA[
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196 Synopsis:
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197 Faster de novo assembly pipeline for Illumina paired end reads based around Spades
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198
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199 Details and options:
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200 - Takes paired end Illumina fastq reads
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201 - Trim reads: Use Trimmomatic to remove common adaptors first (default: OFF)
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202 - Output log file: If set to "Yes", tool will return Shovill's log file as part of the output
3
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203 - Assembler: Which assembler should shovill use from: Skesa, Megahit, Velvet or Spades. Spades is the default.
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204
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205 Advanced options:
0
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206 - Name format: Format of output contig FASTA IDs in 'printf' style (default: 'contig%05d')
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207 - Depth: Sub-sample the reads to this depth. Disable with *Depth: 0* (default: 100)
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208 - Estimated genomesize: An estimate of the final genome size, it will autodetect if this is blank. (default: '')
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209 - List of kmers to use: List of K-mer sizes to use in SPAdes. Blank is AUTO. (default: '')
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210 - Extra SPAdes options: Extra SPAdes options eg. --plasmid --sc ... (default: '')
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211 - Disable post-assembly correction: Disable post assembly correction with pilon (default: ON)
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212 - Minimum contig length: Minimum length of contig to be output. 0 is AUTO (default: 0)
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213 - Minimum contig coverage: Minimum coverage to call part of a contig. 0 is AUTO (default: 2)
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214 - Spades result to correct: Spades result to correct: before_rr, contigs or scaffolds (default: 'contigs')
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215
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216 Documentation can be found at Torsten Seemann `site <https://github.com/tseemann/shovill>`_.
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217 ]]></help>
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218 <citations>
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219 <citation type="bibtex">
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220 @UNPUBLISHED{Seemann2017,
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221 author = {Seemann, Torsten},
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222 title = {Shovill: Faster SPAdes assembly of Illumina reads},
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223 year = {2017},
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224 url = {https://github.com/tseemann/shovill},
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225 }
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226 </citation>
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227 </citations>
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228 </tool>