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comparison metaspades.xml @ 1:01a241476407 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 9401451df4a985ef5686864eaadafa077ffc0877
author iuc
date Thu, 02 Mar 2017 16:04:56 -0500
parents e93c1a0678cd
children 05c394313b1c
comparison
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0:e93c1a0678cd 1:01a241476407
1 <tool id="metaspades" name="metaspades" version="1.0"> 1 <tool id="metaspades" name="metaSPAdes" version="3.9.0">
2 <description>genome assembler for metagenomics datasets</description> 2 <description>assembler for metagenomics datasets</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="3.9.0">spades</requirement> 4 <requirement type="package" version="3.9.0">spades</requirement>
5 </requirements> 5 </requirements>
6 <command interpreter="perl">spades.pl 6 <stdio>
7 $out_contigs 7 <exit_code range="1:" />
8 $out_contig_stats 8 </stdio>
9 $out_scaffolds 9 <command>
10 $out_scaffold_stats 10 <![CDATA[
11 $out_log 11 ## 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
12 12 spades.py -o . --disable-gzip-output --meta $onlyassembler -t \${GALAXY_SLOTS:-16}
13 ## if the first fileset is a paired-collection, use the key as the name 13 #if not $kmer_choice.auto_kmer_choice:
14 #if $files[0].file_type.type == "paired-collection": 14 -k "$kmer_choice.kmers"
15 $files[0].file_type.fastq_collection.name
16 #else:
17 NODE
18 #end if 15 #end if
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 16 ## Sequence files
20 spades.py 17 #set num=1
21 ## Forces unzipped output, faster 18 #if str( $lib_type ) == "paired_end":
22 --disable-gzip-output 19 #set prefix = 'pe'
23 --meta
24 $onlyassembler
25
26 -t \${GALAXY_SLOTS:-16}
27
28 #if not $kmer_choice.auto_kmer_choice:
29 -k "$kmer_choice.kmers"
30 #end if 20 #end if
31 21 --$prefix$num-$orientation
32 ## Sequence files 22 #for $file in $files
33 #set num=1 23 #if $file.file_type.type == "separate"
34 #if str( $lib_type ) == "paired_end": 24 --$prefix$num-1 fastq:$file.file_type.fwd_reads
35 #set prefix = 'pe' 25 --$prefix$num-2 fastq:$file.file_type.rev_reads
36 #end if
37 --$prefix$num-$orientation
38 #for $file in $files
39 #if $file.file_type.type == "separate"
40 --$prefix$num-1 fastq:$file.file_type.fwd_reads
41 --$prefix$num-2 fastq:$file.file_type.rev_reads
42 #elif $file.file_type.type == "interleaved" 26 #elif $file.file_type.type == "interleaved"
43 --$prefix$num-12 fastq:$file.file_type.interleaved_reads 27 --$prefix$num-12 fastq:$file.file_type.interleaved_reads
44 #elif $file.file_type.type == "paired-collection" 28 #elif $file.file_type.type == "paired-collection"
45 --$prefix$num-1 fastq:$file.file_type.fastq_collection.forward 29 --$prefix$num-1 fastq:$file.file_type.fastq_collection.forward
46 --$prefix$num-2 fastq:$file.file_type.fastq_collection.reverse 30 --$prefix$num-2 fastq:$file.file_type.fastq_collection.reverse
47 #end if 31 #end if
48 #end for 32 #end for
49 33 ]]>
50 34 </command>
51 </command> 35 <inputs>
52 <inputs> 36 <param name="onlyassembler" type="boolean" truevalue="--only-assembler" falsevalue="" checked="False" label="Run only assembly? (without read error correction)" />
53 <param name="onlyassembler" type="boolean" truevalue="--only-assembler" falsevalue="" checked="False" label="Run only assembly? (without read error correction)" /> 37 <conditional name="kmer_choice">
54 <conditional name="kmer_choice"> 38 <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" />
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" /> 39 <when value="false">
56 <when value="false"> 40 <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." />
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." /> 41 </when>
58 </when> 42 <when value="true" />
59 <when value="true"> </when> 43 </conditional>
60 </conditional> 44 <param name="lib_type" type="select" label="Library type">
61 45 <option value="paired_end">Paired-end</option>
62 <!-- Reads --> 46 </param>
63 47 <param label="Orientation" name="orientation" type="select">
64 <param name="lib_type" type="select" label="Library type"> 48 <option selected="true" value="fr"><![CDATA[-> <- (fr)]]></option>
65 <option value="paired_end">Paired-end</option> 49 <option value="rf"><![CDATA[<- -> (rf)]]></option>
66 </param> 50 <option value="ff"><![CDATA[-> -> (ff)]]></option>
67 <param name="orientation" type="select" label="Orientation"> 51 </param>
68 <option value="fr" selected="true">-> &lt;- (fr)</option> 52 <repeat name="files" title="Files" min="1">
69 <option value="rf">&lt;- -> (rf)</option> 53 <conditional name="file_type">
70 <option value="ff">-> -> (ff)</option> 54 <param name="type" type="select" label="Select file format">
71 </param> 55 <option value="separate">Separate input files</option>
72 <repeat name="files" title="Files" min="1"> 56 <option value="interleaved">Interleaved files</option>
73 <conditional name="file_type"> 57 <option value="paired-collection">Paired List Collection</option>
74 <param name="type" type="select" label="Select file format"> 58 </param>
75 <option value="separate">Separate input files</option> 59 <when value="separate">
76 <option value="interleaved">Interleaved files</option> 60 <param name="fwd_reads" type="data" format="fastq" label="Forward reads" help="FASTQ format" />
77 <option value="paired-collection">Paired List Collection</option> 61 <param name="rev_reads" type="data" format="fastq" label="Reverse reads" help="FASTQ format" />
78 </param> 62 </when>
79 <when value="separate"> 63 <when value="interleaved">
80 <param name="fwd_reads" type="data" format="fastq" label="Forward reads" help="FASTQ format" /> 64 <param name="interleaved_reads" type="data" format="fastq" label="Interleaved paired reads" help="FASTQ format" />
81 <param name="rev_reads" type="data" format="fastq" label="Reverse reads" help="FASTQ format" /> 65 </when>
82 </when> 66 <when value="paired-collection">
83 <when value="interleaved"> 67 <param name="fastq_collection" type="data_collection" label="Paired-end reads collection" format="fastq" collection_type="paired" help="FASTQ format" />
84 <param name="interleaved_reads" type="data" format="fastq" label="Interleaved paired reads" help="FASTQ format" /> 68 </when>
85 </when> 69 </conditional>
86 <when value="paired-collection"> 70 </repeat>
87 <param name="fastq_collection" type="data_collection" label="Paired-end reads collection" optional="false" format="fastq" collection_type="paired" help="FASTQ format" /> 71 </inputs>
88 </when> 72 <outputs>
89 </conditional> 73 <data name="out_contigs" format="fasta" from_work_dir="contigs.fasta" label="SPAdes contigs (fasta)" />
90 </repeat> 74 <data name="out_scaffolds" format="fasta" from_work_dir="scaffolds.fasta" label="SPAdes scaffolds (fasta)" />
91 75 <data name="out_log" format="txt" from_work_dir="spades.log" label="SPAdes log" />
92 76 </outputs>
93 </inputs> 77 <tests>
94 <outputs> 78 <test>
95 <data name="out_contigs" format="fasta" label="SPAdes contigs (fasta)" /> 79 <param name="sc" value="false" />
96 <data name="out_contig_stats" format="tabular" label="SPAdes contig stats" /> 80 <param name="careful" value="false" />
97 <data name="out_scaffolds" format="fasta" label="SPAdes scaffolds (fasta)" /> 81 <param name="kmers" value="33,55" />
98 <data name="out_scaffold_stats" format="tabular" label="SPAdes scaffold stats" /> 82 <param name="lib_type" value="paired_end" />
99 <data name="out_log" format="txt" label="SPAdes log" /> 83 <param name="fwd_reads" value="ecoli_1K_1.fq" ftype="fastq" />
100 </outputs> 84 <param name="rev_reads" value="ecoli_1K_2.fq" ftype="fastq" />
101 <tests> 85 <output name="out_contigs" file="reference_1K.fa" ftype="fasta" compare="re_match" lines_diff="1" />
102 <test> 86 </test>
103 <param name="sc" value="false" /> 87 </tests>
104 <param name="careful" value="false" /> 88 <help>
105 <param name="kmers" value="33,55" /> 89 <![CDATA[
106 <param name="lib_type" value="paired_end" />
107 <param name="fwd_reads" value="ecoli_1K_1.fq" ftype="fastq" />
108 <param name="rev_reads" value="ecoli_1K_2.fq" ftype="fastq" />
109 <output name="out_contigs" file="reference_1K.fa" ftype="fasta" compare="re_match" lines_diff="1" />
110 </test>
111 </tests>
112 <help>
113 **What it does** 90 **What it does**
114 91
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. 92 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.
116 93 ]]>
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. 94 </help>
118
119 **License**
120
121 SPAdes is developed by and copyrighted to Saint-Petersburg Academic University, and is released under GPLv2.
122
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.
124
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.
126
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/.
128
129 ** Acknowledgments **
130
131 Original wrapper developed by Lionel Guy.
132
133 Anton Korobeynikov greatlty helped understanding how SPAdes work, and integrated handy features into SPAdes.
134
135 Nicola Soranzo fixed various bugs.
136 </help>
137 <citations> 95 <citations>
138 <citation type="doi">10.1089/cmb.2012.0021</citation> 96 <citation type="doi">10.1089/cmb.2012.0021</citation>
139 </citations> 97 </citations>
140 </tool> 98 </tool>