annotate metaspades.xml @ 4:ce02f513e598 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
author iuc
date Fri, 19 Mar 2021 21:38:05 +0000
parents 2ecf5a570907
children 3ca2d2a9068c
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
4
ce02f513e598 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
iuc
parents: 3
diff changeset
1 <tool id="metaspades" name="metaSPAdes" version="3.9.0.1">
1
01a241476407 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 9401451df4a985ef5686864eaadafa077ffc0877
iuc
parents: 0
diff changeset
2 <description>assembler for metagenomics datasets</description>
01a241476407 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 9401451df4a985ef5686864eaadafa077ffc0877
iuc
parents: 0
diff changeset
3 <requirements>
01a241476407 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 9401451df4a985ef5686864eaadafa077ffc0877
iuc
parents: 0
diff changeset
4 <requirement type="package" version="3.9.0">spades</requirement>
01a241476407 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 9401451df4a985ef5686864eaadafa077ffc0877
iuc
parents: 0
diff changeset
5 </requirements>
01a241476407 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 9401451df4a985ef5686864eaadafa077ffc0877
iuc
parents: 0
diff changeset
6 <stdio>
01a241476407 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 9401451df4a985ef5686864eaadafa077ffc0877
iuc
parents: 0
diff changeset
7 <exit_code range="1:" />
01a241476407 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 9401451df4a985ef5686864eaadafa077ffc0877
iuc
parents: 0
diff changeset
8 </stdio>
01a241476407 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 9401451df4a985ef5686864eaadafa077ffc0877
iuc
parents: 0
diff changeset
9 <command>
01a241476407 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 9401451df4a985ef5686864eaadafa077ffc0877
iuc
parents: 0
diff changeset
10 <![CDATA[
3
2ecf5a570907 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 92f173d5036d86d6fd689c65b5a0fc2586d37697"
iuc
parents: 2
diff changeset
11
2ecf5a570907 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 92f173d5036d86d6fd689c65b5a0fc2586d37697"
iuc
parents: 2
diff changeset
12 if [[ -n \$GALAXY_MEMORY_MB ]]; then
2ecf5a570907 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 92f173d5036d86d6fd689c65b5a0fc2586d37697"
iuc
parents: 2
diff changeset
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"
iuc
parents: 2
diff changeset
14 fi &&
2ecf5a570907 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 92f173d5036d86d6fd689c65b5a0fc2586d37697"
iuc
parents: 2
diff changeset
15
0
e93c1a0678cd planemo upload commit 18fef9393a17a3442ab7927d76b301bb43ec3de4
nml
parents:
diff changeset
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
3
2ecf5a570907 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 92f173d5036d86d6fd689c65b5a0fc2586d37697"
iuc
parents: 2
diff changeset
17 spades.py -o . --disable-gzip-output --meta $onlyassembler -t \${GALAXY_SLOTS:-16} -m \${GALAXY_MEMORY_GB:-250}
0
e93c1a0678cd planemo upload commit 18fef9393a17a3442ab7927d76b301bb43ec3de4
nml
parents:
diff changeset
18 #if not $kmer_choice.auto_kmer_choice:
1
01a241476407 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 9401451df4a985ef5686864eaadafa077ffc0877
iuc
parents: 0
diff changeset
19 -k "$kmer_choice.kmers"
0
e93c1a0678cd planemo upload commit 18fef9393a17a3442ab7927d76b301bb43ec3de4
nml
parents:
diff changeset
20 #end if
e93c1a0678cd planemo upload commit 18fef9393a17a3442ab7927d76b301bb43ec3de4
nml
parents:
diff changeset
21 ## Sequence files
1
01a241476407 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 9401451df4a985ef5686864eaadafa077ffc0877
iuc
parents: 0
diff changeset
22 #set num=1
01a241476407 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 9401451df4a985ef5686864eaadafa077ffc0877
iuc
parents: 0
diff changeset
23 #if str( $lib_type ) == "paired_end":
0
e93c1a0678cd planemo upload commit 18fef9393a17a3442ab7927d76b301bb43ec3de4
nml
parents:
diff changeset
24 #set prefix = 'pe'
1
01a241476407 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 9401451df4a985ef5686864eaadafa077ffc0877
iuc
parents: 0
diff changeset
25 #end if
01a241476407 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 9401451df4a985ef5686864eaadafa077ffc0877
iuc
parents: 0
diff changeset
26 --$prefix$num-$orientation
01a241476407 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 9401451df4a985ef5686864eaadafa077ffc0877
iuc
parents: 0
diff changeset
27 #for $file in $files
01a241476407 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 9401451df4a985ef5686864eaadafa077ffc0877
iuc
parents: 0
diff changeset
28 #if $file.file_type.type == "separate"
01a241476407 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 9401451df4a985ef5686864eaadafa077ffc0877
iuc
parents: 0
diff changeset
29 --$prefix$num-1 fastq:$file.file_type.fwd_reads
01a241476407 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 9401451df4a985ef5686864eaadafa077ffc0877
iuc
parents: 0
diff changeset
30 --$prefix$num-2 fastq:$file.file_type.rev_reads
0
e93c1a0678cd planemo upload commit 18fef9393a17a3442ab7927d76b301bb43ec3de4
nml
parents:
diff changeset
31 #elif $file.file_type.type == "interleaved"
1
01a241476407 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 9401451df4a985ef5686864eaadafa077ffc0877
iuc
parents: 0
diff changeset
32 --$prefix$num-12 fastq:$file.file_type.interleaved_reads
0
e93c1a0678cd planemo upload commit 18fef9393a17a3442ab7927d76b301bb43ec3de4
nml
parents:
diff changeset
33 #elif $file.file_type.type == "paired-collection"
1
01a241476407 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 9401451df4a985ef5686864eaadafa077ffc0877
iuc
parents: 0
diff changeset
34 --$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
iuc
parents: 0
diff changeset
35 --$prefix$num-2 fastq:$file.file_type.fastq_collection.reverse
0
e93c1a0678cd planemo upload commit 18fef9393a17a3442ab7927d76b301bb43ec3de4
nml
parents:
diff changeset
36 #end if
1
01a241476407 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 9401451df4a985ef5686864eaadafa077ffc0877
iuc
parents: 0
diff changeset
37 #end for
01a241476407 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 9401451df4a985ef5686864eaadafa077ffc0877
iuc
parents: 0
diff changeset
38 ]]>
01a241476407 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 9401451df4a985ef5686864eaadafa077ffc0877
iuc
parents: 0
diff changeset
39 </command>
01a241476407 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 9401451df4a985ef5686864eaadafa077ffc0877
iuc
parents: 0
diff changeset
40 <inputs>
01a241476407 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 9401451df4a985ef5686864eaadafa077ffc0877
iuc
parents: 0
diff changeset
41 <param name="onlyassembler" type="boolean" truevalue="--only-assembler" falsevalue="" checked="False" label="Run only assembly? (without read error correction)" />
01a241476407 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 9401451df4a985ef5686864eaadafa077ffc0877
iuc
parents: 0
diff changeset
42 <conditional name="kmer_choice">
01a241476407 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 9401451df4a985ef5686864eaadafa077ffc0877
iuc
parents: 0
diff changeset
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" />
01a241476407 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 9401451df4a985ef5686864eaadafa077ffc0877
iuc
parents: 0
diff changeset
44 <when value="false">
01a241476407 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 9401451df4a985ef5686864eaadafa077ffc0877
iuc
parents: 0
diff changeset
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
iuc
parents: 0
diff changeset
46 </when>
01a241476407 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 9401451df4a985ef5686864eaadafa077ffc0877
iuc
parents: 0
diff changeset
47 <when value="true" />
01a241476407 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 9401451df4a985ef5686864eaadafa077ffc0877
iuc
parents: 0
diff changeset
48 </conditional>
01a241476407 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 9401451df4a985ef5686864eaadafa077ffc0877
iuc
parents: 0
diff changeset
49 <param name="lib_type" type="select" label="Library type">
01a241476407 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 9401451df4a985ef5686864eaadafa077ffc0877
iuc
parents: 0
diff changeset
50 <option value="paired_end">Paired-end</option>
01a241476407 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 9401451df4a985ef5686864eaadafa077ffc0877
iuc
parents: 0
diff changeset
51 </param>
01a241476407 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 9401451df4a985ef5686864eaadafa077ffc0877
iuc
parents: 0
diff changeset
52 <param label="Orientation" name="orientation" type="select">
01a241476407 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 9401451df4a985ef5686864eaadafa077ffc0877
iuc
parents: 0
diff changeset
53 <option selected="true" value="fr"><![CDATA[-> <- (fr)]]></option>
01a241476407 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 9401451df4a985ef5686864eaadafa077ffc0877
iuc
parents: 0
diff changeset
54 <option value="rf"><![CDATA[<- -> (rf)]]></option>
01a241476407 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 9401451df4a985ef5686864eaadafa077ffc0877
iuc
parents: 0
diff changeset
55 <option value="ff"><![CDATA[-> -> (ff)]]></option>
01a241476407 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 9401451df4a985ef5686864eaadafa077ffc0877
iuc
parents: 0
diff changeset
56 </param>
01a241476407 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 9401451df4a985ef5686864eaadafa077ffc0877
iuc
parents: 0
diff changeset
57 <repeat name="files" title="Files" min="1">
01a241476407 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 9401451df4a985ef5686864eaadafa077ffc0877
iuc
parents: 0
diff changeset
58 <conditional name="file_type">
01a241476407 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 9401451df4a985ef5686864eaadafa077ffc0877
iuc
parents: 0
diff changeset
59 <param name="type" type="select" label="Select file format">
01a241476407 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 9401451df4a985ef5686864eaadafa077ffc0877
iuc
parents: 0
diff changeset
60 <option value="separate">Separate input files</option>
01a241476407 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 9401451df4a985ef5686864eaadafa077ffc0877
iuc
parents: 0
diff changeset
61 <option value="interleaved">Interleaved files</option>
01a241476407 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 9401451df4a985ef5686864eaadafa077ffc0877
iuc
parents: 0
diff changeset
62 <option value="paired-collection">Paired List Collection</option>
01a241476407 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 9401451df4a985ef5686864eaadafa077ffc0877
iuc
parents: 0
diff changeset
63 </param>
01a241476407 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 9401451df4a985ef5686864eaadafa077ffc0877
iuc
parents: 0
diff changeset
64 <when value="separate">
4
ce02f513e598 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
iuc
parents: 3
diff changeset
65 <param name="fwd_reads" type="data" format="fastq,fastq.gz" label="Forward reads" help="FASTQ format" />
ce02f513e598 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
iuc
parents: 3
diff changeset
66 <param name="rev_reads" type="data" format="fastq,fastq.gz" label="Reverse reads" help="FASTQ format" />
1
01a241476407 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 9401451df4a985ef5686864eaadafa077ffc0877
iuc
parents: 0
diff changeset
67 </when>
01a241476407 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 9401451df4a985ef5686864eaadafa077ffc0877
iuc
parents: 0
diff changeset
68 <when value="interleaved">
4
ce02f513e598 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
iuc
parents: 3
diff changeset
69 <param name="interleaved_reads" type="data" format="fastq,fastq.gz" label="Interleaved paired reads" help="FASTQ format" />
1
01a241476407 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 9401451df4a985ef5686864eaadafa077ffc0877
iuc
parents: 0
diff changeset
70 </when>
01a241476407 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 9401451df4a985ef5686864eaadafa077ffc0877
iuc
parents: 0
diff changeset
71 <when value="paired-collection">
4
ce02f513e598 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
iuc
parents: 3
diff changeset
72 <param name="fastq_collection" type="data_collection" label="Paired-end reads collection" format="fastq,fastq.gz" collection_type="paired" help="FASTQ format" />
1
01a241476407 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 9401451df4a985ef5686864eaadafa077ffc0877
iuc
parents: 0
diff changeset
73 </when>
01a241476407 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 9401451df4a985ef5686864eaadafa077ffc0877
iuc
parents: 0
diff changeset
74 </conditional>
01a241476407 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 9401451df4a985ef5686864eaadafa077ffc0877
iuc
parents: 0
diff changeset
75 </repeat>
01a241476407 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 9401451df4a985ef5686864eaadafa077ffc0877
iuc
parents: 0
diff changeset
76 </inputs>
01a241476407 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 9401451df4a985ef5686864eaadafa077ffc0877
iuc
parents: 0
diff changeset
77 <outputs>
01a241476407 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 9401451df4a985ef5686864eaadafa077ffc0877
iuc
parents: 0
diff changeset
78 <data name="out_contigs" format="fasta" from_work_dir="contigs.fasta" label="SPAdes contigs (fasta)" />
01a241476407 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 9401451df4a985ef5686864eaadafa077ffc0877
iuc
parents: 0
diff changeset
79 <data name="out_scaffolds" format="fasta" from_work_dir="scaffolds.fasta" label="SPAdes scaffolds (fasta)" />
2
05c394313b1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit e2f82dabda7848017302214b99404c8466351b08
iuc
parents: 1
diff changeset
80 <data name="out_fastg" format="txt" from_work_dir="assembly_graph.fastg" label="SPAdes assembly graph (fastg)" />
1
01a241476407 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 9401451df4a985ef5686864eaadafa077ffc0877
iuc
parents: 0
diff changeset
81 <data name="out_log" format="txt" from_work_dir="spades.log" label="SPAdes log" />
01a241476407 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 9401451df4a985ef5686864eaadafa077ffc0877
iuc
parents: 0
diff changeset
82 </outputs>
01a241476407 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 9401451df4a985ef5686864eaadafa077ffc0877
iuc
parents: 0
diff changeset
83 <tests>
01a241476407 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 9401451df4a985ef5686864eaadafa077ffc0877
iuc
parents: 0
diff changeset
84 <test>
01a241476407 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 9401451df4a985ef5686864eaadafa077ffc0877
iuc
parents: 0
diff changeset
85 <param name="sc" value="false" />
01a241476407 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 9401451df4a985ef5686864eaadafa077ffc0877
iuc
parents: 0
diff changeset
86 <param name="careful" value="false" />
01a241476407 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 9401451df4a985ef5686864eaadafa077ffc0877
iuc
parents: 0
diff changeset
87 <param name="kmers" value="33,55" />
01a241476407 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 9401451df4a985ef5686864eaadafa077ffc0877
iuc
parents: 0
diff changeset
88 <param name="lib_type" value="paired_end" />
01a241476407 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 9401451df4a985ef5686864eaadafa077ffc0877
iuc
parents: 0
diff changeset
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
iuc
parents: 0
diff changeset
90 <param name="rev_reads" value="ecoli_1K_2.fq" ftype="fastq" />
01a241476407 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 9401451df4a985ef5686864eaadafa077ffc0877
iuc
parents: 0
diff changeset
91 <output name="out_contigs" file="reference_1K.fa" ftype="fasta" compare="re_match" lines_diff="1" />
01a241476407 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 9401451df4a985ef5686864eaadafa077ffc0877
iuc
parents: 0
diff changeset
92 </test>
4
ce02f513e598 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
iuc
parents: 3
diff changeset
93 <test>
ce02f513e598 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
iuc
parents: 3
diff changeset
94 <param name="sc" value="false" />
ce02f513e598 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
iuc
parents: 3
diff changeset
95 <param name="careful" value="false" />
ce02f513e598 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
iuc
parents: 3
diff changeset
96 <param name="kmers" value="33,55" />
ce02f513e598 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
iuc
parents: 3
diff changeset
97 <param name="lib_type" value="paired_end" />
ce02f513e598 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
iuc
parents: 3
diff changeset
98 <param name="fwd_reads" value="ecoli_1K_1.fq.gz" ftype="fastq.gz" />
ce02f513e598 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
iuc
parents: 3
diff changeset
99 <param name="rev_reads" value="ecoli_1K_2.fq.gz" ftype="fastq.gz" />
ce02f513e598 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
iuc
parents: 3
diff changeset
100 <output name="out_contigs" file="reference_1K.fa" ftype="fasta" compare="re_match" lines_diff="1" />
ce02f513e598 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
iuc
parents: 3
diff changeset
101 </test>
1
01a241476407 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 9401451df4a985ef5686864eaadafa077ffc0877
iuc
parents: 0
diff changeset
102 </tests>
01a241476407 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 9401451df4a985ef5686864eaadafa077ffc0877
iuc
parents: 0
diff changeset
103 <help>
01a241476407 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 9401451df4a985ef5686864eaadafa077ffc0877
iuc
parents: 0
diff changeset
104 <![CDATA[
0
e93c1a0678cd planemo upload commit 18fef9393a17a3442ab7927d76b301bb43ec3de4
nml
parents:
diff changeset
105 **What it does**
e93c1a0678cd planemo upload commit 18fef9393a17a3442ab7927d76b301bb43ec3de4
nml
parents:
diff changeset
106
e93c1a0678cd planemo upload commit 18fef9393a17a3442ab7927d76b301bb43ec3de4
nml
parents:
diff changeset
107 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.
1
01a241476407 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 9401451df4a985ef5686864eaadafa077ffc0877
iuc
parents: 0
diff changeset
108 ]]>
01a241476407 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaspades commit 9401451df4a985ef5686864eaadafa077ffc0877
iuc
parents: 0
diff changeset
109 </help>
0
e93c1a0678cd planemo upload commit 18fef9393a17a3442ab7927d76b301bb43ec3de4
nml
parents:
diff changeset
110 <citations>
e93c1a0678cd planemo upload commit 18fef9393a17a3442ab7927d76b301bb43ec3de4
nml
parents:
diff changeset
111 <citation type="doi">10.1089/cmb.2012.0021</citation>
e93c1a0678cd planemo upload commit 18fef9393a17a3442ab7927d76b301bb43ec3de4
nml
parents:
diff changeset
112 </citations>
e93c1a0678cd planemo upload commit 18fef9393a17a3442ab7927d76b301bb43ec3de4
nml
parents:
diff changeset
113 </tool>