| Previous changeset 0:196a599ec43d (2017-10-25) Next changeset 2:f698c7604b3b (2018-10-17) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 |
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modified:
shovill.xml |
| b |
| diff -r 196a599ec43d -r 57d5928f456e shovill.xml --- a/shovill.xml Wed Oct 25 03:39:03 2017 -0400 +++ b/shovill.xml Wed Mar 07 02:10:01 2018 -0500 |
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| @@ -1,7 +1,7 @@ -<tool id="shovill" name="Shovill" version="0.8.0"> +<tool id="shovill" name="Shovill" version="0.9.0"> <description>Faster SPAdes assembly of Illumina reads</description> <requirements> - <requirement type="package" version="0.8.0">shovill</requirement> + <requirement type="package" version="0.9.0">shovill</requirement> </requirements> <version_command>shovill --version</version_command> <command detect_errors="exit_code"><![CDATA[ @@ -32,7 +32,7 @@ --minlen $adv.minlen --mincov $adv.mincov --asm $adv.asm - + ]]></command> <inputs> <conditional name="library"> @@ -45,7 +45,7 @@ <param name="R2" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="Reverse reads (R2)" help="The file of reverse reads in FASTQ format"/> </when> <when value="collection"> - <param name="input1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" type="data_collection" collection_type="paired" label="Paired collection" help="See help section for an explanation of dataset collections"/> + <param name="input1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" type="data_collection" collection_type="paired" label="Paired collection" help="See help section for an explanation of dataset collections"/> </when> </conditional> <param name="trim" argument="--trim" type="boolean" truevalue="--trim" falsevalue="" label="Trim reads" help="Use Trimmomatic to remove common adaptors first (default: OFF)" /> @@ -70,7 +70,7 @@ </param> </section> </inputs> - + <outputs> <data name="shovill_std_log" format="txt" label="${tool.name} on ${on_string} Log file" from_work_dir="out/00-shovill.log" > <filter>log</filter> @@ -78,7 +78,7 @@ <data format="fasta" name="contigs" label="${tool.name} on ${on_string}: Contigs" from_work_dir="out/contigs.fa"/> <data format="txt" name="contigs_graph" label="${tool.name} on ${on_string}: Contig Graph" from_work_dir="out/contigs.gfa"/> </outputs> - + <tests> <test> <!-- Test 0: Basic test --> <param name="lib_type" value="paired" /> @@ -122,7 +122,7 @@ <assert_contents> <has_text text="Running: seqtk"/> <has_text text="Running: kmc"/> - <has_text text="Running: trimmomatic"/> + <has_text_matching expression="Running:\s+\S+\s+trimmomatic"/> <has_text text="Running: lighter"/> <has_text text="Running: flash"/> <has_text text="Running: spades"/> @@ -142,8 +142,8 @@ - Takes paired end Illumina fastq reads - Trim reads: Use Trimmomatic to remove common adaptors first (default: OFF) - Output log file: If set to "Yes", tool will return Shovill's log file as part of the output - -Advanced options: + +Advanced options: - Name format: Format of output contig FASTA IDs in 'printf' style (default: 'contig%05d') - Depth: Sub-sample the reads to this depth. Disable with *Depth: 0* (default: 100) - Estimated genomesize: An estimate of the final genome size, it will autodetect if this is blank. (default: '') |