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annotate metaspades.xml @ 3:2ecf5a570907 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 92f173d5036d86d6fd689c65b5a0fc2586d37697"
author iuc
date Fri, 15 Jan 2021 12:28:26 +0000
parents 05c394313b1c
children ce02f513e598
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1 <tool id="metaspades" name="metaSPAdes" version="3.9.0">
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2 <description>assembler for metagenomics datasets</description>
01a241476407 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 9401451df4a985ef5686864eaadafa077ffc0877
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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 <stdio>
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7 <exit_code range="1:" />
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8 </stdio>
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9 <command>
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10 <![CDATA[
3
2ecf5a570907 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 92f173d5036d86d6fd689c65b5a0fc2586d37697"
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11
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12 if [[ -n \$GALAXY_MEMORY_MB ]]; then
2ecf5a570907 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 92f173d5036d86d6fd689c65b5a0fc2586d37697"
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13 GALAXY_MEMORY_GB=\$(( GALAXY_MEMORY_MB / 1024 ));
2ecf5a570907 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 92f173d5036d86d6fd689c65b5a0fc2586d37697"
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14 fi &&
2ecf5a570907 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 92f173d5036d86d6fd689c65b5a0fc2586d37697"
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15
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16 ## 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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17 spades.py -o . --disable-gzip-output --meta $onlyassembler -t \${GALAXY_SLOTS:-16} -m \${GALAXY_MEMORY_GB:-250}
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18 #if not $kmer_choice.auto_kmer_choice:
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19 -k "$kmer_choice.kmers"
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20 #end if
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21 ## Sequence files
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22 #set num=1
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23 #if str( $lib_type ) == "paired_end":
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24 #set prefix = 'pe'
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25 #end if
01a241476407 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 9401451df4a985ef5686864eaadafa077ffc0877
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26 --$prefix$num-$orientation
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27 #for $file in $files
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28 #if $file.file_type.type == "separate"
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29 --$prefix$num-1 fastq:$file.file_type.fwd_reads
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30 --$prefix$num-2 fastq:$file.file_type.rev_reads
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31 #elif $file.file_type.type == "interleaved"
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32 --$prefix$num-12 fastq:$file.file_type.interleaved_reads
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33 #elif $file.file_type.type == "paired-collection"
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34 --$prefix$num-1 fastq:$file.file_type.fastq_collection.forward
01a241476407 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 9401451df4a985ef5686864eaadafa077ffc0877
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35 --$prefix$num-2 fastq:$file.file_type.fastq_collection.reverse
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36 #end if
1
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37 #end for
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38 ]]>
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39 </command>
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40 <inputs>
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41 <param name="onlyassembler" type="boolean" truevalue="--only-assembler" falsevalue="" checked="False" label="Run only assembly? (without read error correction)" />
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42 <conditional name="kmer_choice">
01a241476407 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 9401451df4a985ef5686864eaadafa077ffc0877
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43 <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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44 <when value="false">
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45 <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." />
01a241476407 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 9401451df4a985ef5686864eaadafa077ffc0877
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46 </when>
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47 <when value="true" />
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48 </conditional>
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49 <param name="lib_type" type="select" label="Library type">
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50 <option value="paired_end">Paired-end</option>
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51 </param>
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52 <param label="Orientation" name="orientation" type="select">
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53 <option selected="true" value="fr"><![CDATA[-> <- (fr)]]></option>
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54 <option value="rf"><![CDATA[<- -> (rf)]]></option>
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55 <option value="ff"><![CDATA[-> -> (ff)]]></option>
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56 </param>
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57 <repeat name="files" title="Files" min="1">
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58 <conditional name="file_type">
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59 <param name="type" type="select" label="Select file format">
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60 <option value="separate">Separate input files</option>
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61 <option value="interleaved">Interleaved files</option>
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62 <option value="paired-collection">Paired List Collection</option>
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63 </param>
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64 <when value="separate">
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65 <param name="fwd_reads" type="data" format="fastq" label="Forward reads" help="FASTQ format" />
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66 <param name="rev_reads" type="data" format="fastq" label="Reverse reads" help="FASTQ format" />
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67 </when>
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68 <when value="interleaved">
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69 <param name="interleaved_reads" type="data" format="fastq" label="Interleaved paired reads" help="FASTQ format" />
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70 </when>
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71 <when value="paired-collection">
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72 <param name="fastq_collection" type="data_collection" label="Paired-end reads collection" format="fastq" collection_type="paired" help="FASTQ format" />
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73 </when>
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74 </conditional>
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75 </repeat>
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76 </inputs>
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77 <outputs>
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78 <data name="out_contigs" format="fasta" from_work_dir="contigs.fasta" label="SPAdes contigs (fasta)" />
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79 <data name="out_scaffolds" format="fasta" from_work_dir="scaffolds.fasta" label="SPAdes scaffolds (fasta)" />
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80 <data name="out_fastg" format="txt" from_work_dir="assembly_graph.fastg" label="SPAdes assembly graph (fastg)" />
1
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81 <data name="out_log" format="txt" from_work_dir="spades.log" label="SPAdes log" />
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82 </outputs>
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83 <tests>
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84 <test>
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85 <param name="sc" value="false" />
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86 <param name="careful" value="false" />
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87 <param name="kmers" value="33,55" />
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88 <param name="lib_type" value="paired_end" />
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89 <param name="fwd_reads" value="ecoli_1K_1.fq" ftype="fastq" />
01a241476407 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 9401451df4a985ef5686864eaadafa077ffc0877
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90 <param name="rev_reads" value="ecoli_1K_2.fq" ftype="fastq" />
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91 <output name="out_contigs" file="reference_1K.fa" ftype="fasta" compare="re_match" lines_diff="1" />
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92 </test>
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93 </tests>
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94 <help>
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95 <![CDATA[
0
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96 **What it does**
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97
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98 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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99 ]]>
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100 </help>
0
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101 <citations>
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102 <citation type="doi">10.1089/cmb.2012.0021</citation>
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103 </citations>
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104 </tool>