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comparison metaspades.xml @ 4:ce02f513e598 draft

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"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
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3:2ecf5a570907 4:ce02f513e598
1 <tool id="metaspades" name="metaSPAdes" version="3.9.0"> 1 <tool id="metaspades" name="metaSPAdes" version="3.9.0.1">
2 <description>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 <stdio> 6 <stdio>
60 <option value="separate">Separate input files</option> 60 <option value="separate">Separate input files</option>
61 <option value="interleaved">Interleaved files</option> 61 <option value="interleaved">Interleaved files</option>
62 <option value="paired-collection">Paired List Collection</option> 62 <option value="paired-collection">Paired List Collection</option>
63 </param> 63 </param>
64 <when value="separate"> 64 <when value="separate">
65 <param name="fwd_reads" type="data" format="fastq" label="Forward reads" help="FASTQ format" /> 65 <param name="fwd_reads" type="data" format="fastq,fastq.gz" label="Forward reads" help="FASTQ format" />
66 <param name="rev_reads" type="data" format="fastq" label="Reverse reads" help="FASTQ format" /> 66 <param name="rev_reads" type="data" format="fastq,fastq.gz" label="Reverse reads" help="FASTQ format" />
67 </when> 67 </when>
68 <when value="interleaved"> 68 <when value="interleaved">
69 <param name="interleaved_reads" type="data" format="fastq" label="Interleaved paired reads" help="FASTQ format" /> 69 <param name="interleaved_reads" type="data" format="fastq,fastq.gz" label="Interleaved paired reads" help="FASTQ format" />
70 </when> 70 </when>
71 <when value="paired-collection"> 71 <when value="paired-collection">
72 <param name="fastq_collection" type="data_collection" label="Paired-end reads collection" format="fastq" collection_type="paired" help="FASTQ format" /> 72 <param name="fastq_collection" type="data_collection" label="Paired-end reads collection" format="fastq,fastq.gz" collection_type="paired" help="FASTQ format" />
73 </when> 73 </when>
74 </conditional> 74 </conditional>
75 </repeat> 75 </repeat>
76 </inputs> 76 </inputs>
77 <outputs> 77 <outputs>
88 <param name="lib_type" value="paired_end" /> 88 <param name="lib_type" value="paired_end" />
89 <param name="fwd_reads" value="ecoli_1K_1.fq" ftype="fastq" /> 89 <param name="fwd_reads" value="ecoli_1K_1.fq" ftype="fastq" />
90 <param name="rev_reads" value="ecoli_1K_2.fq" ftype="fastq" /> 90 <param name="rev_reads" value="ecoli_1K_2.fq" ftype="fastq" />
91 <output name="out_contigs" file="reference_1K.fa" ftype="fasta" compare="re_match" lines_diff="1" /> 91 <output name="out_contigs" file="reference_1K.fa" ftype="fasta" compare="re_match" lines_diff="1" />
92 </test> 92 </test>
93 <test>
94 <param name="sc" value="false" />
95 <param name="careful" value="false" />
96 <param name="kmers" value="33,55" />
97 <param name="lib_type" value="paired_end" />
98 <param name="fwd_reads" value="ecoli_1K_1.fq.gz" ftype="fastq.gz" />
99 <param name="rev_reads" value="ecoli_1K_2.fq.gz" ftype="fastq.gz" />
100 <output name="out_contigs" file="reference_1K.fa" ftype="fasta" compare="re_match" lines_diff="1" />
101 </test>
93 </tests> 102 </tests>
94 <help> 103 <help>
95 <![CDATA[ 104 <![CDATA[
96 **What it does** 105 **What it does**
97 106