Mercurial > repos > iuc > rnaspades
changeset 3:a8a278849c18 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rnaspades commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
| author | iuc |
|---|---|
| date | Fri, 19 Mar 2021 21:38:27 +0000 |
| parents | 03fd468e158f |
| children | 16e0eb91072f |
| files | rnaspades.xml test-data/rnaspades-in1-1.fq.gz test-data/rnaspades-in1-2.fq.gz |
| diffstat | 3 files changed, 15 insertions(+), 8 deletions(-) [+] |
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--- a/rnaspades.xml Thu Jan 07 17:50:06 2021 +0000 +++ b/rnaspades.xml Fri Mar 19 21:38:27 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="rnaspades" name="rnaSPAdes" version="3.9.0.1"> +<tool id="rnaspades" name="rnaSPAdes" version="3.9.0.2"> <description>assembler for RNA-Seq data</description> <requirements> <requirement type="package" version="3.9.0">spades</requirement> @@ -81,23 +81,23 @@ <option value="paired-collection">Paired List Collection</option> </param> <when value="separate"> - <param format="fastq" help="FASTQ format" label="Forward reads" name="fwd_reads" type="data" /> - <param format="fastq" help="FASTQ format" label="Reverse reads" name="rev_reads" type="data" /> + <param format="fastq,fastq.gz" help="FASTQ format" label="Forward reads" name="fwd_reads" type="data" /> + <param format="fastq,fastq.gz" help="FASTQ format" label="Reverse reads" name="rev_reads" type="data" /> </when> <when value="interleaved"> - <param format="fastq" help="FASTQ format" label="Interleaved paired reads" name="interleaved_reads" type="data" /> + <param format="fastq,fastq.gz" help="FASTQ format" label="Interleaved paired reads" name="interleaved_reads" type="data" /> </when> <when value="unpaired"> - <param format="fastq" help="FASTQ format" label="Unpaired reads" name="unpaired_reads" type="data" /> + <param format="fastq,fastq.gz" help="FASTQ format" label="Unpaired reads" name="unpaired_reads" type="data" /> </when> <when value="paired-collection"> - <param collection_type="paired" format="fastq" help="FASTQ format" label="Paired-end reads collection" name="fastq_collection" optional="false" type="data_collection" /> + <param collection_type="paired" format="fastq,fastq.gz" help="FASTQ format" label="Paired-end reads collection" name="fastq,fastq.gz_collection" optional="false" type="data_collection" /> </when> </conditional> </repeat> </repeat> - <param optional="true" format="fasta,fastq" label="Trusted contigs" multiple="true" name="trusted_contigs" type="data" /> - <param optional="true" format="fasta,fastq" label="Untrusted contigs" multiple="true" name="untrusted_contigs" type="data" /> + <param optional="true" format="fasta,fastq,fastq.gz" label="Trusted contigs" multiple="true" name="trusted_contigs" type="data" /> + <param optional="true" format="fasta,fastq,fastq.gz" label="Untrusted contigs" multiple="true" name="untrusted_contigs" type="data" /> </inputs> <outputs> <data format="fasta" label="rnaSPAdes transcripts" name="output_transcripts" from_work_dir="transcripts.fasta" /> @@ -110,6 +110,13 @@ <param name="rev_reads" value="rnaspades-in1-2.fq" ftype="fastq" /> <output name="output_transcripts" file="rnaspades-out1.fa" ftype="fasta" compare="re_match" lines_diff="1" /> </test> + <test> + <param name="lib_type" value="paired_end" /> + <param name="type" value="separate" /> + <param name="fwd_reads" value="rnaspades-in1-1.fq.gz" ftype="fastq.gz" /> + <param name="rev_reads" value="rnaspades-in1-2.fq.gz" ftype="fastq.gz" /> + <output name="output_transcripts" file="rnaspades-out1.fa" ftype="fasta" compare="re_match" lines_diff="1" /> + </test> </tests> <help> **What it does**