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annotate spades.xml @ 9:24fffa4fee40 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
author iuc
date Tue, 30 Oct 2018 20:27:11 -0400
parents 884dc0264950
children b8d633fbf5f5
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1 <tool id="spades" name="SPAdes" version="@TOOL_VERSION@">
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2 <description>genome assembler for regular and single-cell projects</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <requirements>
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7 <requirement type="package" version="@TOOL_VERSION@">spades</requirement>
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8 </requirements>
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9 <stdio>
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10 <exit_code range="1:" />
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11 <regex match="Cannot allocate memory"
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12 source="stdout"
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13 level="fatal_oom"
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14 description="Out of memory error occurred" />
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15 <regex match="The reads contain too many k-mers to fit into available memory"
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16 source="stdout"
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17 level="fatal_oom"
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18 description="Out of memory error occurred" />
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19 </stdio>
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20 <command>
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21 <![CDATA[
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22 ## A real command looks like: spades.py -k 21,33,55,77,99,127 --careful -1 Y.fastq.gz -2 X.fastq.gz -t 24 -o output
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23
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24 if [[ -n \$GALAXY_MEMORY_MB ]]; then
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25 GALAXY_MEMORY_GB=\$(( GALAXY_MEMORY_MB / 1024 ));
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26 fi &&
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28 spades.py -o . --disable-gzip-output $sc $onlyassembler $careful -t \${GALAXY_SLOTS:-16} -m \${GALAXY_MEMORY_GB:-250}
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29 #if not $kmer_choice.auto_kmer_choice:
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30 -k "$kmer_choice.kmers"
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31 #end if
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32 #if $cov.state == "auto":
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33 --cov-cutoff 'auto'
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34 #elif $cov.state == "value":
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35 --cov-cutoff '$cov.cutoff'
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36 #end if
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37 $iontorrent
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38 ## Sequence files, libraries
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39 #for $i, $library in enumerate( $libraries, start=1 )
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40 #if str( $library.lib_type ) == "paired_end":
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41 #set prefix = 'pe'
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42 #elif str( $library.lib_type ) == "mate_paired":
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43 #set prefix = 'mp'
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44 #elif str( $library.lib_type ) == "nxmate_paired":
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45 #set prefix = 'nxmate'
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46 #else:
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47 #set prefix = 'hqmp'
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48 #end if
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49 --$prefix$i-$library.orientation
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50 #for $file in $library.files
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51 #if $file.file_type.type == "separate"
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52 --$prefix$i-1 $file.file_type.fwd_reads.extension:$file.file_type.fwd_reads
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53 --$prefix$i-2 $file.file_type.fwd_reads.extension:$file.file_type.rev_reads
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54 #elif $file.file_type.type == "interleaved"
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55 --$prefix$i-12 $file.file_type.interleaved_reads.extension:$file.file_type.interleaved_reads
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56 #elif $file.file_type.type == "merged"
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57 --$prefix$i-m $file.file_type.merged_reads.extension:$file.file_type.merged_reads
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58 #elif $file.file_type.type == "unpaired"
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59 --$prefix$i-s $file.file_type.unpaired_reads.extension:$file.file_type.unpaired_reads
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60 #elif $file.file_type.type == "paired-collection"
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61 --$prefix$i-1 $file.file_type.fastq_collection.forward.extension:$file.file_type.fastq_collection.forward
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62 --$prefix$i-2 $file.file_type.fastq_collection.reverse.extension:$file.file_type.fastq_collection.reverse
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63 #end if
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64 #end for
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65 #end for
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66 #for $read in $pacbio_reads:
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67 #if $read:
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68 --pacbio fastq:$read
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69 #end if
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70 #end for
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71 #for $read in $nanopore_reads:
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72 #if $read:
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73 --nanopore fastq:$read
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74 #end if
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75 #end for
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76 #for $read in $sanger_reads:
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77 #if $read:
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78 --sanger $read.extension:$read
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79 #end if
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80 #end for
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81 #for $contig in $trusted_contigs:
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82 #if $contig:
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83 --trusted-contigs $contig.extension:$contig
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84 #end if
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85 #end for
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86 #for $contig in $untrusted_contigs:
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87 #if $contig:
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88 --untrusted-contigs $contig.extension:$contig
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89 #end if
0
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90 #end for
9
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91 && python '$write_tsv_script' < contigs.fasta > '$out_contig_stats'
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92 && python '$write_tsv_script' < scaffolds.fasta > '$out_scaffold_stats'
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93 ]]>
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94 </command>
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95
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96 <configfiles>
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97 <configfile name="write_tsv_script"><![CDATA[#!/usr/bin/env python
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98 import sys,re
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99 search_str = r'^>(NODE|\S+)_(\d+)(?:_|\s)length_(\d+)_cov_(\d+\.*\d*).*\$'
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100 replace_str = r'\1_\2\t\3\t\4'
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101 cmd = re.compile(search_str)
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102 sys.stdout.write('#name\tlength\tcoverage\n')
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103 for i,line in enumerate(sys.stdin):
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104 if cmd.match(line):
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105 sys.stdout.write(cmd.sub(replace_str,line))
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106 ]]>
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107 </configfile>
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108 </configfiles>
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109
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110 <inputs>
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111 <param argument="--sc" falsevalue="" help="This option is required for MDA (single-cell) data." label="Single-cell?" name="sc" truevalue="--sc" type="boolean">
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112 <option value="false">No</option>
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113 <option value="true">Yes</option>
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114 </param>
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115 <param argument="--only-assembler" checked="False" falsevalue="" label="Run only assembly? (without read error correction)" name="onlyassembler" truevalue="--only-assembler" type="boolean" />
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116 <param argument="----careful" checked="True" falsevalue="" help="Tries to reduce number of mismatches and short indels. Also runs MismatchCorrector &#8211; a post processing tool, which uses BWA tool (comes with SPAdes)." label="Careful correction?" name="careful" truevalue="--careful" type="boolean" />
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117 <conditional name="kmer_choice">
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118 <param checked="False" falsevalue="false" help="k-mer choices can be chosen by SPAdes instead of being entered manually" label="Automatically choose k-mer values" name="auto_kmer_choice" truevalue="true" type="boolean" />
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119 <when value="false">
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120 <param help="Comma-separated list of k-mer sizes to be used (all values must be odd, less than 128, listed in ascending order, and smaller than the read length). The default value is 21,33,55." label="K-mers to use, separated by commas" name="kmers" type="text" value="21,33,55" />
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121 </when>
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122 <when value="true" />
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123 </conditional>
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124 <conditional name="cov">
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125 <param label="Coverage Cutoff" name="state" type="select">
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126 <option value="off">Off</option>
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127 <option value="value">User Specific</option>
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128 <option value="auto">Auto</option>
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129 </param>
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130 <when value="off" />
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131 <when value="value">
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132 <param help="coverage cutoff value (a positive float number, or 'auto', or 'off') [default: 'off']" label="Coverage cutoff value" name="cutoff" type="float" value="" />
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133 </when>
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134 <when value="auto" />
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135 </conditional>
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136 <param checked="False" falsevalue="" label="Libraries are IonTorrent reads?" name="iontorrent" truevalue="--iontorrent" type="boolean" />
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137 <repeat help="It is not possible to specify only mate-pair libraries. Scaffolds are not produced if neither a paired-end nor a mate-pair library is provided." min="1" max="9" name="libraries" title="Libraries">
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138 <param label="Library type" name="lib_type" type="select">
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139 <option value="paired_end">Paired-end / Single reads</option>
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140 <option value="mate_paired">Mate pairs</option>
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141 <option value="high_mate_paired">High Quality Mate pairs</option>
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142 <option value="nxmate_paired">Lucigen NxMate pairs</option>
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143 </param>
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144 <param label="Orientation" name="orientation" type="select">
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145 <option selected="true" value="fr"><![CDATA[-> <- (fr)]]></option>
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146 <option value="rf"><![CDATA[<- -> (rf)]]></option>
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147 <option value="ff"><![CDATA[-> -> (ff)]]></option>
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148 </param>
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149 <repeat min="1" name="files" title="Files">
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150 <conditional name="file_type">
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151 <param label="Select file format" name="type" type="select">
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152 <option value="separate">Separate input files</option>
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153 <option value="interleaved">Interleaved files</option>
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154 <option value="merged">Merged files</option>
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155 <option value="unpaired">Unpaired/Single reads</option>
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156 <option value="paired-collection">Paired List Collection</option>
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157 </param>
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158 <when value="separate">
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159 <param format="@INTYPES@" help="FASTQ format" label="Forward reads" name="fwd_reads" type="data" />
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160 <param format="@INTYPES@" help="FASTQ format" label="Reverse reads" name="rev_reads" type="data" />
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161 </when>
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162 <when value="interleaved">
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163 <param format="@INTYPES@" help="FASTQ format" label="Interleaved paired reads" name="interleaved_reads" type="data" />
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164 </when>
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165 <when value="merged">
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166 <param format="@INTYPES@" help="FASTQ format" label="Merged paired reads" name="merged_reads" type="data" />
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167 </when>
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168 <when value="unpaired">
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169 <param format="@INTYPES@" help="FASTQ format" label="Unpaired reads" name="unpaired_reads" type="data" />
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170 </when>
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171 <when value="paired-collection">
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172 <param collection_type="paired" format="@INTYPES@" help="FASTQ format" label="Paired-end reads collection" name="fastq_collection" optional="false" type="data_collection" />
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173 </when>
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174 </conditional>
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175 </repeat>
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176 </repeat>
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177 <param optional="true" format="@INTYPES@" label="PacBio CLR reads" multiple="true" name="pacbio_reads" type="data" />
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178 <param optional="true" format="@INTYPES@" label="Nanopore reads" multiple="true" name="nanopore_reads" type="data" />
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179 <param optional="true" format="@INTYPES@" label="Sanger reads" multiple="true" name="sanger_reads" type="data" />
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180 <param optional="true" format="@INTYPES@" label="Trusted contigs" multiple="true" name="trusted_contigs" type="data" />
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181 <param optional="true" format="@INTYPES@" label="Untrusted contigs" multiple="true" name="untrusted_contigs" type="data" />
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182 <param name="contig_graph_out" type="boolean" checked="False" label="Output final assembly graph (contigs)?" help="Will output the final assembly graph (contigs) in fastg format for visualisation" />
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183 <param name="scaffold_graph_out" type="boolean" checked="False" label="Output final assembly graph with scaffolds?" help="Will output the final assembly graph with scaffold information in gfa format for visualisation" />
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184 </inputs>
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185
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186 <outputs>
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187 <data format="tabular" label="${tool.name} on ${on_string}: contig stats" name="out_contig_stats" >
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188 <actions>
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189 <action name="column_names" type="metadata" default="name,length,coverage"/>
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190 </actions>
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191 </data>
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192 <data format="tabular" label="${tool.name} on ${on_string}: scaffold stats" name="out_scaffold_stats" >
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193 <actions>
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194 <action name="column_names" type="metadata" default="name,length,coverage"/>
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195 </actions>
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196 </data>
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197 <data format="fasta" from_work_dir="contigs.fasta" label="${tool.name} on ${on_string}: contigs (fasta)" name="out_contigs" />
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198 <data format="fasta" from_work_dir="scaffolds.fasta" label="${tool.name} on ${on_string}: scaffolds (fasta)" name="out_scaffolds" />
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199 <data format="txt" from_work_dir="spades.log" label="${tool.name} on ${on_string}: log" name="out_log" />
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200 <data format="txt" from_work_dir="assembly_graph.fastg" label="${tool.name} on ${on_string}: assembly graph" name="contig_graph">
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201 <filter>contig_graph_out</filter>
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202 </data>
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203 <data format="txt" from_work_dir="assembly_graph_with_scaffolds.gfa" label="${tool.name} on ${on_string}: assembly graph with scaffolds" name="scaffold_graph">
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204 <filter>scaffold_graph_out</filter>
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205 </data>
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206 </outputs>
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207 <tests>
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208 <test> <!-- Test 1 - basic test with k=33 -->
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209 <param name="sc" value="false" />
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210 <param name="careful" value="false" />
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211 <param name="kmers" value="33" />
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212 <param name="lib_type" value="paired_end" />
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213 <param ftype="fastq" name="fwd_reads" value="ecoli_1K_1.fq" />
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214 <param ftype="fastq" name="rev_reads" value="ecoli_1K_2.fq" />
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215 <output compare="re_match" file="kmer_33_output.fa" ftype="fasta" lines_diff="1" name="out_contigs" />
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216 <output name="out_contig_stats">
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217 <assert_contents>
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218 <has_text_matching expression="NODE_1\t1000"/>
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219 </assert_contents>
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220 </output>
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221 </test>
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222 <test> <!-- Test 1 - basic test with k=33 fasta input -->
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223 <param name="sc" value="false" />
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224 <param name="onlyassembler" value="true"/>
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225 <param name="careful" value="false" />
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226 <param name="kmers" value="33" />
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227 <param name="lib_type" value="paired_end" />
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228 <param ftype="fasta" name="fwd_reads" value="ecoli_1K_1.fasta" />
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229 <param ftype="fasta" name="rev_reads" value="ecoli_1K_2.fasta" />
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230 <output compare="re_match" file="kmer_33_output.fa" ftype="fasta" lines_diff="1" name="out_contigs" />
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231 <output name="out_contig_stats">
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232 <assert_contents>
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233 <has_text_matching expression="NODE_1\t1000"/>
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234 </assert_contents>
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235 </output>
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236 </test>
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237 <test> <!-- Test 1 - basic test with k=33 and gzipped input -->
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238 <param name="sc" value="false" />
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239 <param name="careful" value="false" />
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240 <param name="kmers" value="33" />
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241 <param name="lib_type" value="paired_end" />
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242 <param ftype="fastq.gz" name="fwd_reads" value="ecoli_1K_1.fq.gz" />
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243 <param ftype="fastq.gz" name="rev_reads" value="ecoli_1K_2.fq.gz" />
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244 <output compare="re_match" file="kmer_33_output.fa" ftype="fasta" lines_diff="1" name="out_contigs" />
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245 <output name="out_contig_stats">
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246 <assert_contents>
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247 <has_text_matching expression="NODE_1\t1000"/>
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248 </assert_contents>
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249 </output>
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250 </test>
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251 <test> <!-- Test 2 - auto k -->
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252 <param name="sc" value="false" />
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253 <param name="careful" value="false" />
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254 <param name="auto_kmer_choice" value="true" />
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255 <param name="lib_type" value="paired_end" />
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256 <param ftype="fastq" name="fwd_reads" value="ecoli_1K_1.fq" />
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257 <param ftype="fastq" name="rev_reads" value="ecoli_1K_2.fq" />
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258 <output compare="re_match" file="auto_kmer_output.fa" ftype="fasta" lines_diff="1" name="out_contigs" />
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259 </test>
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260 <test> <!-- Test 3 - k=77 -->
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261 <param name="sc" value="false" />
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262 <param name="careful" value="false" />
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263 <param name="kmers" value="77" />
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264 <param name="lib_type" value="paired_end" />
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265 <param ftype="fastq" name="fwd_reads" value="ecoli_1K_1.fq" />
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266 <param ftype="fastq" name="rev_reads" value="ecoli_1K_2.fq" />
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267 <output compare="re_match" file="kmer_77_output.fa" ftype="fasta" lines_diff="1" name="out_contigs" />
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268 </test>
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269 <test> <!-- Test 4 - test for extra graph outputs -->
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270 <param name="sc" value="false" />
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271 <param name="careful" value="false" />
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272 <param name="kmers" value="33" />
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273 <param name="lib_type" value="paired_end" />
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274 <param ftype="fastq" name="fwd_reads" value="ecoli_1K_1.fq" />
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275 <param ftype="fastq" name="rev_reads" value="ecoli_1K_2.fq" />
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276 <param name="contig_graph_out" value="true" />
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277 <param name="scaffold_graph_out" value="true" />
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278 <output compare="re_match" file="kmer_33_output.fa" ftype="fasta" lines_diff="1" name="out_contigs" />
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279 <output name="out_contig_stats">
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280 <assert_contents>
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281 <has_text_matching expression="NODE_1\t1000"/>
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282 </assert_contents>
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283 </output>
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284 <output name="contig_graph">
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285 <assert_contents>
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286 <has_text text=">EDGE_"/>
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287 </assert_contents>
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288 </output>
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289 <output name="scaffold_graph">
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290 <assert_contents>
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291 <has_text text="NODE_"/>
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292 </assert_contents>
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293 </output>
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294 </test>
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295 </tests>
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296 <help>
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297 <![CDATA[
0
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298 **What it does**
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299
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300 SPAdes – St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. See http://bioinf.spbau.ru/en/spades for more details on SPAdes.
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301
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302 This wrapper runs SPAdes, collects the output, and throws away all the temporary files. It also produces a tab file with contig names, length and coverage.
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303
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304 **License**
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305
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306 SPAdes is developed by and copyrighted to Saint-Petersburg Academic University, and is released under GPLv2.
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307
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308 This wrapper is copyrighted by Philip Mabon and is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
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309
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310 This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
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311
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312 You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.
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313
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314 ** Acknowledgments **
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315
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316 Original wrapper developed by Lionel Guy.
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317
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318 Anton Korobeynikov greatlty helped understanding how SPAdes work, and integrated handy features into SPAdes.
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319
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320 Nicola Soranzo fixed various bugs.
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321
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322 Simon Gladman added fastg optional outputs.
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323 ]]>
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324 </help>
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325 <citations>
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326 <citation type="doi">10.1089/cmb.2012.0021</citation>
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327 </citations>
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328 </tool>