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annotate metaspades.xml @ 0:e93c1a0678cd draft

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author nml
date Tue, 09 Aug 2016 10:46:28 -0400
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1 <tool id="metaspades" name="metaspades" version="1.0">
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2 <description>genome assembler for metagenomics datasets</description>
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3 <requirements>
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4 <requirement type="package" version="3.9.0">spades</requirement>
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5 </requirements>
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6 <command interpreter="perl">spades.pl
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7 $out_contigs
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8 $out_contig_stats
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9 $out_scaffolds
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10 $out_scaffold_stats
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11 $out_log
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12
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13 ## if the first fileset is a paired-collection, use the key as the name
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14 #if $files[0].file_type.type == "paired-collection":
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15 $files[0].file_type.fastq_collection.name
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16 #else:
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17 NODE
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18 #end if
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19 ## 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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20 spades.py
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21 ## Forces unzipped output, faster
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22 --disable-gzip-output
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23 --meta
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24 $onlyassembler
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25
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26 -t \${GALAXY_SLOTS:-16}
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27
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28 #if not $kmer_choice.auto_kmer_choice:
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29 -k "$kmer_choice.kmers"
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30 #end if
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31
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32 ## Sequence files
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33 #set num=1
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34 #if str( $lib_type ) == "paired_end":
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35 #set prefix = 'pe'
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36 #end if
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37 --$prefix$num-$orientation
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38 #for $file in $files
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39 #if $file.file_type.type == "separate"
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40 --$prefix$num-1 fastq:$file.file_type.fwd_reads
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41 --$prefix$num-2 fastq:$file.file_type.rev_reads
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42 #elif $file.file_type.type == "interleaved"
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43 --$prefix$num-12 fastq:$file.file_type.interleaved_reads
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44 #elif $file.file_type.type == "paired-collection"
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45 --$prefix$num-1 fastq:$file.file_type.fastq_collection.forward
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46 --$prefix$num-2 fastq:$file.file_type.fastq_collection.reverse
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47 #end if
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48 #end for
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49
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50
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51 </command>
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52 <inputs>
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53 <param name="onlyassembler" type="boolean" truevalue="--only-assembler" falsevalue="" checked="False" label="Run only assembly? (without read error correction)" />
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54 <conditional name="kmer_choice">
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55 <param name="auto_kmer_choice" type="boolean" checked="False" truevalue="true" falsevalue="false" label="Automatically choose k-mer values" help="k-mer choices can be chosen by SPAdes instead of being entered manually" />
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56 <when value="false">
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57 <param name="kmers" type="text" label="K-mers to use, separated by commas" value="21,33,55" 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." />
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58 </when>
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59 <when value="true"> </when>
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60 </conditional>
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61
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62 <!-- Reads -->
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63
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64 <param name="lib_type" type="select" label="Library type">
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65 <option value="paired_end">Paired-end</option>
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66 </param>
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67 <param name="orientation" type="select" label="Orientation">
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68 <option value="fr" selected="true">-> &lt;- (fr)</option>
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69 <option value="rf">&lt;- -> (rf)</option>
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70 <option value="ff">-> -> (ff)</option>
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71 </param>
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72 <repeat name="files" title="Files" min="1">
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73 <conditional name="file_type">
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74 <param name="type" type="select" label="Select file format">
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75 <option value="separate">Separate input files</option>
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76 <option value="interleaved">Interleaved files</option>
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77 <option value="paired-collection">Paired List Collection</option>
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78 </param>
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79 <when value="separate">
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80 <param name="fwd_reads" type="data" format="fastq" label="Forward reads" help="FASTQ format" />
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81 <param name="rev_reads" type="data" format="fastq" label="Reverse reads" help="FASTQ format" />
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82 </when>
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83 <when value="interleaved">
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84 <param name="interleaved_reads" type="data" format="fastq" label="Interleaved paired reads" help="FASTQ format" />
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85 </when>
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86 <when value="paired-collection">
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87 <param name="fastq_collection" type="data_collection" label="Paired-end reads collection" optional="false" format="fastq" collection_type="paired" help="FASTQ format" />
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88 </when>
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89 </conditional>
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90 </repeat>
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91
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92
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93 </inputs>
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94 <outputs>
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95 <data name="out_contigs" format="fasta" label="SPAdes contigs (fasta)" />
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96 <data name="out_contig_stats" format="tabular" label="SPAdes contig stats" />
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97 <data name="out_scaffolds" format="fasta" label="SPAdes scaffolds (fasta)" />
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98 <data name="out_scaffold_stats" format="tabular" label="SPAdes scaffold stats" />
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99 <data name="out_log" format="txt" label="SPAdes log" />
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100 </outputs>
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101 <tests>
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102 <test>
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103 <param name="sc" value="false" />
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104 <param name="careful" value="false" />
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105 <param name="kmers" value="33,55" />
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106 <param name="lib_type" value="paired_end" />
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107 <param name="fwd_reads" value="ecoli_1K_1.fq" ftype="fastq" />
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108 <param name="rev_reads" value="ecoli_1K_2.fq" ftype="fastq" />
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109 <output name="out_contigs" file="reference_1K.fa" ftype="fasta" compare="re_match" lines_diff="1" />
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110 </test>
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111 </tests>
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112 <help>
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113 **What it does**
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114
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115 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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116
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117 This wrapper runs SPAdes 3.9, 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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118
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119 **License**
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120
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121 SPAdes is developed by and copyrighted to Saint-Petersburg Academic University, and is released under GPLv2.
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122
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123 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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124
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125 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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126
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127 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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128
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129 ** Acknowledgments **
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130
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131 Original wrapper developed by Lionel Guy.
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132
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133 Anton Korobeynikov greatlty helped understanding how SPAdes work, and integrated handy features into SPAdes.
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134
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135 Nicola Soranzo fixed various bugs.
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136 </help>
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137 <citations>
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138 <citation type="doi">10.1089/cmb.2012.0021</citation>
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139 </citations>
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140 </tool>