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annotate shovill.xml @ 6:83ead2be47b2 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit f667915d861dbf0a25cc8fd132cc956d82e73ee9"
author iuc
date Thu, 02 Jul 2020 08:58:03 -0400
parents 8d1af5db538d
children 2a9baa0c4316
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83ead2be47b2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit f667915d861dbf0a25cc8fd132cc956d82e73ee9"
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1 <tool id="shovill" name="Shovill" version="@TOOL_VERSION@+galaxy0">
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2 <description>Faster SPAdes assembly of Illumina reads</description>
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3 <macros>
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4 <token name="@TOOL_VERSION@">1.1.0</token>
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5 </macros>
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6 <requirements>
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7 <requirement type="package" version="@TOOL_VERSION@">shovill</requirement>
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8 </requirements>
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9 <version_command>shovill --version</version_command>
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10 <command detect_errors="exit_code"><![CDATA[
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11 #if str($library.lib_type) == "paired"
d9f6a00b6db7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit eb617cb0aeeb18710ecb12f5208f4e69b7659dbc"
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12 #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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13 #set r2_ext = $library.R2.extension
d9f6a00b6db7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit eb617cb0aeeb18710ecb12f5208f4e69b7659dbc"
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14 ln -s '$library.R1' fastq_r1.'$r1_ext' &&
d9f6a00b6db7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit eb617cb0aeeb18710ecb12f5208f4e69b7659dbc"
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15 ln -s '$library.R2' fastq_r2.'$r2_ext' &&
d9f6a00b6db7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit eb617cb0aeeb18710ecb12f5208f4e69b7659dbc"
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16 #else if str($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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17 #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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18 #set r2_ext = $library.input1.reverse.extension
d9f6a00b6db7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit eb617cb0aeeb18710ecb12f5208f4e69b7659dbc"
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19 ln -s '$library.input1.forward' fastq_r1.'$r1_ext' &&
d9f6a00b6db7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit eb617cb0aeeb18710ecb12f5208f4e69b7659dbc"
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20 ln -s '$library.input1.reverse' fastq_r2.'$r2_ext' &&
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21 #end if
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22
8d1af5db538d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit da99aa8018e36c84fc4cbd7c73923fc710b3b31a"
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23 ## Sets the memory used by Shovill according to the following conditions
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24 ## (1) If SHOVILL_RAM is already set, use this value
8d1af5db538d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit da99aa8018e36c84fc4cbd7c73923fc710b3b31a"
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25 ## (2) Otherwise, set based on GALAXY_MEMORY_MB
8d1af5db538d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit da99aa8018e36c84fc4cbd7c73923fc710b3b31a"
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26 ## (3) Or default to 4 GB if GALAXY_MEMORY_MB is unset
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27 GALAXY_MEMORY_GB=\$((\${GALAXY_MEMORY_MB:-4096}/1024)) &&
8d1af5db538d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit da99aa8018e36c84fc4cbd7c73923fc710b3b31a"
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28 SHOVILL_RAM=\${SHOVILL_RAM:-\${GALAXY_MEMORY_GB}} &&
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29
0
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30 shovill
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
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31 --outdir 'out'
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32 --cpus \${GALAXY_SLOTS:-1}
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33 --ram \${SHOVILL_RAM:-4}
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34 --R1 fastq_r1.'$r1_ext'
d9f6a00b6db7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit eb617cb0aeeb18710ecb12f5208f4e69b7659dbc"
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35 --R2 fastq_r2.'$r2_ext'
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36 $trim
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37 --namefmt '$adv.namefmt'
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38 --depth '$adv.depth'
196a599ec43d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
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39 #if $adv.gsize
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40 --gsize '$adv.gsize'
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41 #end if
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42 #if $adv.kmers
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43 --kmers '$adv.kmers'
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44 #end if
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45 #if $adv.opts
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46 --opts '$adv.opts'
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47 #end if
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48 $adv.nocorr
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49 --minlen $adv.minlen
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50 --mincov $adv.mincov
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51 --assembler $assembler
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52
0
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53 ]]></command>
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54 <inputs>
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55 <conditional name="library">
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56 <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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57 <option value="paired" selected="true">Paired End</option>
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58 <option value="collection">Paired Collection</option>
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59 </param>
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60 <when value="paired">
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61 <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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62 <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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63 </when>
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64 <when value="collection">
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65 <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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66 </when>
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67 </conditional>
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68 <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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69 <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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70 <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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71 <option value="skesa">skesa</option>
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72 <option value="megahit">megahit</option>
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73 <option value="velvet">velvet</option>
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74 <option value="spades" selected="true">Spades</option>
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75 </param>
0
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76 <section name="adv" title="Advanced options" expanded="False">
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77 <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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78 <sanitizer>
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79 <valid initial="string.printable">
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80 <remove value="&apos;" />
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81 </valid>
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82 <mapping initial="none">
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83 <add source="&apos;" target="&apos;&quot;&apos;&quot;&apos;" />
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84 </mapping>
0
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85 </sanitizer>
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86 </param>
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87 <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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88 <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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89 <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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90 <param name="opts" argument="--opts" type="text" value="" label="Extra SPAdes options" help="eg. --plasmid --sc ... (default: '')" />
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91 <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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92 <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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93 <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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94 </section>
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95 </inputs>
1
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96
0
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97 <outputs>
3
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98 <data name="shovill_std_log" format="txt" label="${tool.name} on ${on_string} Log file" from_work_dir="out/shovill.log" >
0
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99 <filter>log</filter>
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100 </data>
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101 <data format="fasta" name="contigs" label="${tool.name} on ${on_string}: Contigs" from_work_dir="out/contigs.fa"/>
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102 <data format="txt" name="contigs_graph" label="${tool.name} on ${on_string}: Contig Graph" from_work_dir="out/contigs.gfa"/>
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103 </outputs>
1
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104
0
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105 <tests>
3
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106 <test> <!-- Test 1: Basic test -->
0
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107 <param name="lib_type" value="paired" />
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108 <param name="R1" value="mutant_R1.fastq" ftype="fastqsanger" />
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109 <param name="R2" value="mutant_R2.fastq" ftype="fastqsanger" />
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110 <output name="contigs" ftype="fasta">
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111 <assert_contents>
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112 <has_text text="&gt;contig00001"/>
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113 </assert_contents>
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114 </output>
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115 <output name="shovill_std_log" ftype="txt" >
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116 <assert_contents>
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117 <has_text text="Read stats: total_bp = 300000"/>
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118 <has_text text="[lighter] Processed 820 reads"/>
3
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119 <has_text text="[FLASH] FLASH v1.2.11 complete!"/>
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120 <has_text text="[spades] ======= SPAdes pipeline finished."/>
0
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121 </assert_contents>
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122 </output>
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123 </test>
3
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124 <test> <!-- Test 2: Auto everything + trim + different name format test -->
0
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125 <param name="lib_type" value="paired" />
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126 <param name="R1" value="mutant_R1.fastq" ftype="fastqsanger" />
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127 <param name="R2" value="mutant_R2.fastq" ftype="fastqsanger" />
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128 <param name="trim" value="true" />
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129 <section name="adv">
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130 <param name="depth" value="0"/>
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131 <param name="minlen" value="0"/>
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132 <param name="mincov" value="0"/>
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133 <param name="nocorr" value="false"/>
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134 <param name="namefmt" value="contig%03d"/>
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135 </section>
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136 <output name="contigs" ftype="fasta">
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137 <assert_contents>
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138 <has_text text="&gt;contig001"/>
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139 </assert_contents>
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140 </output>
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141 <output name="shovill_std_log" ftype="txt" >
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142 <assert_contents>
3
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143 <has_text text="[trimmomatic] TrimmomaticPE: Completed successfully"/>
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144 <has_text text="[lighter] Processed"/>
3
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145 <has_text text="[FLASH] FLASH v1.2.11 complete!"/>
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146 <has_text text="[spades] ======= SPAdes pipeline finished."/>
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147 <has_text text="[bwa+samtools-sort] [samclip] Done."/>
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148 <has_text text="[pilon] Mean total coverage:"/>
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149 <has_text text="[shovill] Done."/>
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150 </assert_contents>
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151 </output>
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152 </test>
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153 <test> <!-- Test 3: Alternate assembler #1: Megahit -->
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154 <param name="lib_type" value="paired" />
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155 <param name="R1" value="mutant_R1.fastq" ftype="fastqsanger" />
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156 <param name="R2" value="mutant_R2.fastq" ftype="fastqsanger" />
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157 <param name="assembler" value="megahit" />
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158 <output name="contigs" ftype="fasta">
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159 <assert_contents>
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160 <has_text text="&gt;contig00001"/>
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161 </assert_contents>
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162 </output>
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163 <output name="shovill_std_log" ftype="txt" >
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164 <assert_contents>
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165 <has_text text="[lighter] Processed"/>
3
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166 <has_text text="[FLASH] FLASH v1.2.11 complete!"/>
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167 <has_text_matching expression="\[megahit\] .* ALL DONE"/>
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168 <has_text text="[shovill] Done."/>
3
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169 </assert_contents>
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170 </output>
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171 </test>
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172 <test> <!-- Test 4: Alternate assembler #2: Skesa -->
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173 <param name="lib_type" value="paired" />
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174 <param name="R1" value="mutant_R1.fastq" ftype="fastqsanger" />
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175 <param name="R2" value="mutant_R2.fastq" ftype="fastqsanger" />
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176 <param name="assembler" value="skesa" />
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177 <output name="contigs" ftype="fasta">
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178 <assert_contents>
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179 <has_text text="&gt;contig00001"/>
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180 </assert_contents>
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181 </output>
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182 <output name="shovill_std_log" ftype="txt" >
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183 <assert_contents>
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184 <has_text text="[lighter] Processed"/>
3
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185 <has_text text="[FLASH] FLASH v1.2.11 complete!"/>
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186 <has_text text="[skesa] DONE"/>
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187 <has_text text="[shovill] Done."/>
3
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188 </assert_contents>
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189 </output>
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190 </test>
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191 <test> <!-- Test 5: Alternate assembler #3: Velvet -->
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192 <param name="lib_type" value="paired" />
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193 <param name="R1" value="mutant_R1.fastq" ftype="fastqsanger" />
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194 <param name="R2" value="mutant_R2.fastq" ftype="fastqsanger" />
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195 <param name="assembler" value="velvet" />
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196 <output name="contigs" ftype="fasta">
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197 <assert_contents>
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198 <has_text text="&gt;contig00001"/>
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199 </assert_contents>
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200 </output>
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201 <output name="shovill_std_log" ftype="txt" >
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202 <assert_contents>
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203 <has_text text="[lighter] Processed"/>
3
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204 <has_text text="[FLASH] FLASH v1.2.11 complete!"/>
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205 <has_text text="[velvetg] Final graph has"/>
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206 <has_text text="[shovill] Done."/>
0
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207 </assert_contents>
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208 </output>
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209 </test>
4
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210 <test> <!-- Test 6: Gzipped input with trimming -->
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211 <param name="lib_type" value="paired" />
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212 <param name="R1" value="mutant_R1.fastq.gz" ftype="fastqsanger" />
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213 <param name="R2" value="mutant_R2.fastq.gz" ftype="fastqsanger" />
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214 <param name="trim" value="true" />
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215 <output name="contigs" ftype="fasta">
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216 <assert_contents>
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217 <has_text text="&gt;contig00001"/>
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218 </assert_contents>
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219 </output>
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220 <output name="shovill_std_log" ftype="txt" >
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221 <assert_contents>
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222 <has_text text="[lighter] Processed"/>
4
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223 <has_text text="[FLASH] FLASH v1.2.11 complete!"/>
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224 <has_text text="[spades] ======= SPAdes pipeline finished."/>
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225 <has_text text="[shovill] Done."/>
4
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226 </assert_contents>
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227 </output>
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228 </test>
0
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229 </tests>
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230 <help><![CDATA[
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231 Synopsis:
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232 Faster de novo assembly pipeline for Illumina paired end reads based around Spades
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233
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234 Details and options:
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235 - Takes paired end Illumina fastq reads
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236 - Trim reads: Use Trimmomatic to remove common adaptors first (default: OFF)
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237 - Output log file: If set to "Yes", tool will return Shovill's log file as part of the output
3
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238 - Assembler: Which assembler should shovill use from: Skesa, Megahit, Velvet or Spades. Spades is the default.
1
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239
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240 Advanced options:
0
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241 - Name format: Format of output contig FASTA IDs in 'printf' style (default: 'contig%05d')
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242 - Depth: Sub-sample the reads to this depth. Disable with *Depth: 0* (default: 100)
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243 - Estimated genomesize: An estimate of the final genome size, it will autodetect if this is blank. (default: '')
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244 - List of kmers to use: List of K-mer sizes to use in SPAdes. Blank is AUTO. (default: '')
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245 - Extra SPAdes options: Extra SPAdes options eg. --plasmid --sc ... (default: '')
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246 - Disable post-assembly correction: Disable post assembly correction with pilon (default: ON)
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247 - Minimum contig length: Minimum length of contig to be output. 0 is AUTO (default: 0)
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248 - Minimum contig coverage: Minimum coverage to call part of a contig. 0 is AUTO (default: 2)
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249 - Spades result to correct: Spades result to correct: before_rr, contigs or scaffolds (default: 'contigs')
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250
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251 Documentation can be found at Torsten Seemann `site <https://github.com/tseemann/shovill>`_.
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252 ]]></help>
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253 <citations>
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254 <citation type="bibtex">
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255 @UNPUBLISHED{Seemann2017,
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256 author = {Seemann, Torsten},
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257 title = {Shovill: Faster SPAdes assembly of Illumina reads},
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258 year = {2017},
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259 url = {https://github.com/tseemann/shovill},
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260 }
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261 </citation>
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262 </citations>
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263 </tool>