Mercurial > repos > nml > metaspades
changeset 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 |
| files | metaspades.xml test-data/ecoli_1K_1.fq.gz test-data/ecoli_1K_2.fq.gz |
| diffstat | 3 files changed, 14 insertions(+), 5 deletions(-) [+] |
line wrap: on
line diff
--- a/metaspades.xml Fri Jan 15 12:28:26 2021 +0000 +++ b/metaspades.xml Fri Mar 19 21:38:05 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="metaspades" name="metaSPAdes" version="3.9.0"> +<tool id="metaspades" name="metaSPAdes" version="3.9.0.1"> <description>assembler for metagenomics datasets</description> <requirements> <requirement type="package" version="3.9.0">spades</requirement> @@ -62,14 +62,14 @@ <option value="paired-collection">Paired List Collection</option> </param> <when value="separate"> - <param name="fwd_reads" type="data" format="fastq" label="Forward reads" help="FASTQ format" /> - <param name="rev_reads" type="data" format="fastq" label="Reverse reads" help="FASTQ format" /> + <param name="fwd_reads" type="data" format="fastq,fastq.gz" label="Forward reads" help="FASTQ format" /> + <param name="rev_reads" type="data" format="fastq,fastq.gz" label="Reverse reads" help="FASTQ format" /> </when> <when value="interleaved"> - <param name="interleaved_reads" type="data" format="fastq" label="Interleaved paired reads" help="FASTQ format" /> + <param name="interleaved_reads" type="data" format="fastq,fastq.gz" label="Interleaved paired reads" help="FASTQ format" /> </when> <when value="paired-collection"> - <param name="fastq_collection" type="data_collection" label="Paired-end reads collection" format="fastq" collection_type="paired" help="FASTQ format" /> + <param name="fastq_collection" type="data_collection" label="Paired-end reads collection" format="fastq,fastq.gz" collection_type="paired" help="FASTQ format" /> </when> </conditional> </repeat> @@ -90,6 +90,15 @@ <param name="rev_reads" value="ecoli_1K_2.fq" ftype="fastq" /> <output name="out_contigs" file="reference_1K.fa" ftype="fasta" compare="re_match" lines_diff="1" /> </test> + <test> + <param name="sc" value="false" /> + <param name="careful" value="false" /> + <param name="kmers" value="33,55" /> + <param name="lib_type" value="paired_end" /> + <param name="fwd_reads" value="ecoli_1K_1.fq.gz" ftype="fastq.gz" /> + <param name="rev_reads" value="ecoli_1K_2.fq.gz" ftype="fastq.gz" /> + <output name="out_contigs" file="reference_1K.fa" ftype="fasta" compare="re_match" lines_diff="1" /> + </test> </tests> <help> <![CDATA[