Mercurial > repos > iuc > shovill
changeset 3:865119fcb694 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 7c14ae1fd4494808cc7be290dab100b828ee6a33
| author | iuc |
|---|---|
| date | Tue, 13 Nov 2018 10:41:12 -0500 |
| parents | f698c7604b3b |
| children | d9f6a00b6db7 |
| files | shovill.xml |
| diffstat | 1 files changed, 82 insertions(+), 28 deletions(-) [+] |
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--- a/shovill.xml Wed Oct 17 11:43:35 2018 -0400 +++ b/shovill.xml Tue Nov 13 10:41:12 2018 -0500 @@ -1,7 +1,7 @@ -<tool id="shovill" name="Shovill" version="0.9.0"> +<tool id="shovill" name="Shovill" version="1.0.4"> <description>Faster SPAdes assembly of Illumina reads</description> <requirements> - <requirement type="package" version="0.9.0">shovill</requirement> + <requirement type="package" version="1.0.4">shovill</requirement> </requirements> <version_command>shovill --version</version_command> <command detect_errors="exit_code"><![CDATA[ @@ -31,7 +31,7 @@ $adv.nocorr --minlen $adv.minlen --mincov $adv.mincov - --asm $adv.asm + --assembler $assembler ]]></command> <inputs> @@ -50,6 +50,12 @@ </conditional> <param name="trim" argument="--trim" type="boolean" truevalue="--trim" falsevalue="" label="Trim reads" help="Use Trimmomatic to remove common adaptors first (default: OFF)" /> <param name="log" type="boolean" label="Output log file?" checked="true" help="Return the Shovill log file as part of the output. Default is on" /> + <param name="assembler" argument="--assembler" type="select" label="Assembler to use" help="Which assembler would you like shovill to use, default is Spades"> + <option value="skesa">skesa</option> + <option value="megahit">megahit</option> + <option value="velvet">velvet</option> + <option value="spades" selected="true">Spades</option> + </param> <section name="adv" title="Advanced options" expanded="False"> <param name="namefmt" argument="--namefmt" type="text" value="contig%05d" label="Contig name format" help="Format of contig FASTA IDs in 'printf' style (default: 'contig%05d')" > <sanitizer> @@ -68,16 +74,11 @@ <param name="nocorr" argument="--nocorr" type="boolean" truevalue="--nocorr" falsevalue="" checked="True" label="Disable post-assembly correction" help="Disable post assembly correction with pilon (default: ON)" /> <param name="minlen" argument="--minlen" type="integer" value="0" label="Minimum contig length" help="Minimum length of contig to be output. 0 is AUTO (default: 0)" /> <param name="mincov" argument="--mincov" type="integer" value="2" label="Minimum contig coverage" help="Minimum coverage to call part of a contig. 0 is AUTO (default: 2)" /> - <param name="asm" argument="--asm" type="select" label="Spades result to correct" help="Which SPAdes output to correct for: before_rr, contigs or scaffolds. (default: 'contigs')"> - <option value="before_rr">before_rr</option> - <option value="contigs" selected="true">contigs</option> - <option value="scaffolds">scaffolds</option> - </param> </section> </inputs> <outputs> - <data name="shovill_std_log" format="txt" label="${tool.name} on ${on_string} Log file" from_work_dir="out/00-shovill.log" > + <data name="shovill_std_log" format="txt" label="${tool.name} on ${on_string} Log file" from_work_dir="out/shovill.log" > <filter>log</filter> </data> <data format="fasta" name="contigs" label="${tool.name} on ${on_string}: Contigs" from_work_dir="out/contigs.fa"/> @@ -85,7 +86,7 @@ </outputs> <tests> - <test> <!-- Test 0: Basic test --> + <test> <!-- Test 1: Basic test --> <param name="lib_type" value="paired" /> <param name="R1" value="mutant_R1.fastq" ftype="fastqsanger" /> <param name="R2" value="mutant_R2.fastq" ftype="fastqsanger" /> @@ -96,17 +97,14 @@ </output> <output name="shovill_std_log" ftype="txt" > <assert_contents> - <has_text text="Running: seqtk"/> - <has_text text="Running: kmc"/> - <has_text text="Running: lighter"/> - <has_text text="User supplied --nocorr"/> - <has_text text="Running: flash"/> - <has_text text="Running: spades"/> - <has_text text="Done."/> + <has_text text="[mash]"/> + <has_text text="[lighter] Processed 24960 reads"/> + <has_text text="[FLASH] FLASH v1.2.11 complete!"/> + <has_text text="[spades] ======= SPAdes pipeline finished."/> </assert_contents> </output> </test> - <test> <!-- Test 1: Auto everything + trim + different name format test --> + <test> <!-- Test 2: Auto everything + trim + different name format test --> <param name="lib_type" value="paired" /> <param name="R1" value="mutant_R1.fastq" ftype="fastqsanger" /> <param name="R2" value="mutant_R2.fastq" ftype="fastqsanger" /> @@ -125,16 +123,71 @@ </output> <output name="shovill_std_log" ftype="txt" > <assert_contents> - <has_text text="Running: seqtk"/> - <has_text text="Running: kmc"/> - <has_text_matching expression="Running:\s+\S+\s+trimmomatic"/> - <has_text text="Running: lighter"/> - <has_text text="Running: flash"/> - <has_text text="Running: spades"/> - <has_text text="Running: bwa index"/> - <has_text text="Running: (bwa mem"/> - <has_text text="Running: _JAVA"/> - <has_text text="Done."/> + <has_text text="[mash] Writing to"/> + <has_text text="[trimmomatic] TrimmomaticPE: Completed successfully"/> + <has_text text="[lighter] Processed 24960 reads:"/> + <has_text text="[FLASH] FLASH v1.2.11 complete!"/> + <has_text text="[spades] ======= SPAdes pipeline finished."/> + <has_text text="[bwa+samtools-sort] [samclip] Done."/> + <has_text text="[pilon] Mean total coverage:"/> + <has_text text="[shovill] Done."/> + </assert_contents> + </output> + </test> + <test> <!-- Test 3: Alternate assembler #1: Megahit --> + <param name="lib_type" value="paired" /> + <param name="R1" value="mutant_R1.fastq" ftype="fastqsanger" /> + <param name="R2" value="mutant_R2.fastq" ftype="fastqsanger" /> + <param name="assembler" value="megahit" /> + <output name="contigs" ftype="fasta"> + <assert_contents> + <has_text text=">contig00001"/> + </assert_contents> + </output> + <output name="shovill_std_log" ftype="txt" > + <assert_contents> + <has_text text="[mash]"/> + <has_text text="[lighter] Processed 24960 reads"/> + <has_text text="[FLASH] FLASH v1.2.11 complete!"/> + <has_text text="[megahit] --- [STAT]"/> + </assert_contents> + </output> + </test> + <test> <!-- Test 4: Alternate assembler #2: Skesa --> + <param name="lib_type" value="paired" /> + <param name="R1" value="mutant_R1.fastq" ftype="fastqsanger" /> + <param name="R2" value="mutant_R2.fastq" ftype="fastqsanger" /> + <param name="assembler" value="skesa" /> + <output name="contigs" ftype="fasta"> + <assert_contents> + <has_text text=">contig00001"/> + </assert_contents> + </output> + <output name="shovill_std_log" ftype="txt" > + <assert_contents> + <has_text text="[mash]"/> + <has_text text="[lighter] Processed 24960 reads"/> + <has_text text="[FLASH] FLASH v1.2.11 complete!"/> + <has_text text="[skesa] DONE"/> + </assert_contents> + </output> + </test> + <test> <!-- Test 5: Alternate assembler #3: Velvet --> + <param name="lib_type" value="paired" /> + <param name="R1" value="mutant_R1.fastq" ftype="fastqsanger" /> + <param name="R2" value="mutant_R2.fastq" ftype="fastqsanger" /> + <param name="assembler" value="velvet" /> + <output name="contigs" ftype="fasta"> + <assert_contents> + <has_text text=">contig00001"/> + </assert_contents> + </output> + <output name="shovill_std_log" ftype="txt" > + <assert_contents> + <has_text text="[mash]"/> + <has_text text="[lighter] Processed 24960 reads"/> + <has_text text="[FLASH] FLASH v1.2.11 complete!"/> + <has_text text="[velvetg] Final graph has"/> </assert_contents> </output> </test> @@ -147,6 +200,7 @@ - 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 + - Assembler: Which assembler should shovill use from: Skesa, Megahit, Velvet or Spades. Spades is the default. Advanced options: - Name format: Format of output contig FASTA IDs in 'printf' style (default: 'contig%05d')