Mercurial > repos > iuc > shovill
diff shovill.xml @ 8:ad80238462c1 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 1e28eb4ffcf3d9168877c291d27e533b96021445
| author | iuc |
|---|---|
| date | Fri, 16 Sep 2022 14:39:43 +0000 |
| parents | 2a9baa0c4316 |
| children | ee17a294d3a3 |
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--- a/shovill.xml Thu Feb 03 20:41:04 2022 +0000 +++ b/shovill.xml Fri Sep 16 14:39:43 2022 +0000 @@ -1,11 +1,12 @@ -<tool id="shovill" name="Shovill" version="@TOOL_VERSION@+galaxy1"> +<tool id="shovill" name="Shovill" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> <description>Faster SPAdes assembly of Illumina reads</description> + <macros> + <token name="@TOOL_VERSION@">1.1.0</token> + <token name="@VERSION_SUFFIX@">1</token> + </macros> <xrefs> <xref type="bio.tools">shovill</xref> </xrefs> - <macros> - <token name="@TOOL_VERSION@">1.1.0</token> - </macros> <requirements> <requirement type="package" version="@TOOL_VERSION@">shovill</requirement> </requirements> @@ -19,10 +20,10 @@ #set r2_ext = $library.R2.extension #if $r1_ext == 'fastqsanger.gz' or $r1_ext == 'fastqsanger.bz2' cp '$library.R1' fastq_r1.'$r1_ext' && - cp '$library.R2' fastq_r2.'$r2_ext' && + cp '$library.R2' fastq_r2.'$r2_ext' && #else ln -s '$library.R1' fastq_r1.'$r1_ext' && - ln -s '$library.R2' fastq_r2.'$r2_ext' && + ln -s '$library.R2' fastq_r2.'$r2_ext' && #end if #else if str($library.lib_type) == "collection" #set r1_ext = $library.input1.forward.extension @@ -42,13 +43,13 @@ ## (3) Or default to 4 GB if GALAXY_MEMORY_MB is unset GALAXY_MEMORY_GB=\$((\${GALAXY_MEMORY_MB:-4096}/1024)) && SHOVILL_RAM=\${SHOVILL_RAM:-\${GALAXY_MEMORY_GB}} && - + shovill --outdir 'out' --cpus \${GALAXY_SLOTS:-1} --ram \${SHOVILL_RAM:-4} - --R1 fastq_r1.'$r1_ext' - --R2 fastq_r2.'$r2_ext' + --R1 'fastq_r1.$(r1_ext)' + --R2 'fastq_r2.$(r2_ext)' $trim --namefmt '$adv.namefmt' --depth '$adv.depth' @@ -61,11 +62,14 @@ #if $adv.opts --opts '$adv.opts' #end if - $adv.nocorr --minlen $adv.minlen --mincov $adv.mincov --assembler $assembler - + #if $adv.keep_files.nocorr == 'no_correction' + --nocorr + #else + $adv.keep_files.keepfiles + #end if ]]></command> <inputs> <conditional name="library"> @@ -82,7 +86,6 @@ </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)" /> - <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> @@ -104,22 +107,34 @@ <param name="gsize" argument="--gsize" type="text" value="" label="Estimated genome size" help="An estimate of the final genome size, it will autodetect if this is blank. (default: '')" /> <param name="kmers" argument="--kmers" type="text" value="" label="List of kmer sizes to use" help="List of K-mer sizes to use in SPAdes. Blank is AUTO. default: ''" /> <param name="opts" argument="--opts" type="text" value="" label="Extra SPAdes options" help="eg. --plasmid --sc ... (default: '')" /> - <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)" /> + <conditional name="keep_files"> + <param name="nocorr" argument="--nocorr" type="select" label="Disable post-assembly correction" help="Disable post assembly correction with pilon (default: ON)"> + <option value="no_correction" selected="true">No corrections</option> + <option value="yes_correction">Post assembly corrections</option> + </param> + <when value="no_correction"/> + <when value="yes_correction"> + <param name="keepfiles" argument="--keepfiles" type="boolean" truevalue="--keepfiles" checked="False" falsevalue="" label="Keep bam files" help="Keep bam files only if post-assembly correction is enable"/> + </when> + </conditional> <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)" /> </section> + <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" /> + </inputs> - <outputs> <data name="shovill_std_log" format="txt" label="${tool.name} on ${on_string} Log file" from_work_dir="out/shovill.log" > - <filter>log</filter> + <filter>log == True</filter> </data> - <data format="fasta" name="contigs" label="${tool.name} on ${on_string}: Contigs" from_work_dir="out/contigs.fa"/> - <data format="txt" name="contigs_graph" label="${tool.name} on ${on_string}: Contig Graph" from_work_dir="out/contigs.gfa"/> + <data name="contigs" format="fasta" label="${tool.name} on ${on_string}: Contigs" from_work_dir="out/contigs.fa"/> + <data name="contigs_graph" format="txt" label="${tool.name} on ${on_string}: Contig Graph" from_work_dir="out/contigs.gfa"/> + <data name="bamfiles" format="unsorted.bam" from_work_dir="out/shovill.bam" label="Bam file for ${tool.name} on ${on_string}"> + <filter> adv['keep_files']['nocorr'] == 'yes_correction' and adv['keep_files']['keepfiles'] == True </filter> + </data> </outputs> - <tests> - <test> <!-- Test 1: Basic test --> + <test expect_num_outputs="3"> <!-- 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" /> @@ -134,10 +149,10 @@ <has_text text="[lighter] Processed 820 reads"/> <has_text text="[FLASH] FLASH v1.2.11 complete!"/> <has_text text="[spades] ======= SPAdes pipeline finished."/> - </assert_contents> - </output> + </assert_contents> + </output> </test> - <test> <!-- Test 2: Auto everything + trim + different name format test --> + <test expect_num_outputs="3"> <!-- 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" /> @@ -146,7 +161,9 @@ <param name="depth" value="0"/> <param name="minlen" value="0"/> <param name="mincov" value="0"/> - <param name="nocorr" value="false"/> + <conditional name="keep_files"> + <param name="nocorr" value="yes_correction"/> + </conditional> <param name="namefmt" value="contig%03d"/> </section> <output name="contigs" ftype="fasta"> @@ -166,7 +183,7 @@ </assert_contents> </output> </test> - <test> <!-- Test 3: Alternate assembler #1: Megahit --> + <test expect_num_outputs="3"> <!-- 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" /> @@ -174,7 +191,7 @@ <output name="contigs" ftype="fasta"> <assert_contents> <has_text text=">contig00001"/> - </assert_contents> + </assert_contents> </output> <output name="shovill_std_log" ftype="txt" > <assert_contents> @@ -185,7 +202,7 @@ </assert_contents> </output> </test> - <test> <!-- Test 4: Alternate assembler #2: Skesa --> + <test expect_num_outputs="3"> <!-- 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" /> @@ -204,7 +221,7 @@ </assert_contents> </output> </test> - <test> <!-- Test 5: Alternate assembler #3: Velvet --> + <test expect_num_outputs="3"> <!-- 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" /> @@ -223,7 +240,7 @@ </assert_contents> </output> </test> - <test> <!-- Test 6: Gzipped input with trimming --> + <test expect_num_outputs="3"> <!-- Test 6: Gzipped input with trimming --> <param name="lib_type" value="paired" /> <param name="R1" value="mutant_R1.fastq.gz" ftype="fastqsanger.gz" /> <param name="R2" value="mutant_R2.fastq.gz" ftype="fastqsanger.gz" /> @@ -242,29 +259,53 @@ </assert_contents> </output> </test> + <test expect_num_outputs="4"> <!-- Test 7: Add keepfiles option --> + <param name="lib_type" value="paired" /> + <param name="R1" value="mutant_R1.fastq.gz" ftype="fastqsanger.gz" /> + <param name="R2" value="mutant_R2.fastq.gz" ftype="fastqsanger.gz" /> + <param name="trim" value="true" /> + <section name="adv"> + <conditional name="keep_files"> + <param name="nocorr" value="yes_correction" /> + <param name="keepfiles" value="True" /> + </conditional> + <param name="log" value="true"/> + </section> + <output name="contigs" ftype="fasta"> + <assert_contents> + <has_text text=">contig00001"/> + </assert_contents> + </output> + <output name="bamfiles" ftype="unsorted.bam"> + <assert_contents> + <has_size value="36359" delta="1000" /> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[ -Synopsis: - Faster de novo assembly pipeline for Illumina paired end reads based around Spades + Synopsis: + Faster de novo assembly pipeline for Illumina paired end reads based around Spades -Details and options: - - 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. + Details and options: + - 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') - - 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: '') - - List of kmers to use: List of K-mer sizes to use in SPAdes. Blank is AUTO. (default: '') - - Extra SPAdes options: Extra SPAdes options eg. --plasmid --sc ... (default: '') - - Disable post-assembly correction: Disable post assembly correction with pilon (default: ON) - - Minimum contig length: Minimum length of contig to be output. 0 is AUTO (default: 0) - - Minimum contig coverage: Minimum coverage to call part of a contig. 0 is AUTO (default: 2) - - Spades result to correct: Spades result to correct: before_rr, contigs or scaffolds (default: 'contigs') + 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: '') + - List of kmers to use: List of K-mer sizes to use in SPAdes. Blank is AUTO. (default: '') + - Extra SPAdes options: Extra SPAdes options eg. --plasmid --sc ... (default: '') + - Disable post-assembly correction: Disable post assembly correction with pilon (default: ON) + - Keep the bam files : Enable to keep mapped files from bwa in the post assembly correction (default: OFF) + - Minimum contig length: Minimum length of contig to be output. 0 is AUTO (default: 0) + - Minimum contig coverage: Minimum coverage to call part of a contig. 0 is AUTO (default: 2) + - Spades result to correct: Spades result to correct: before_rr, contigs or scaffolds (default: 'contigs') -Documentation can be found at Torsten Seemann `site <https://github.com/tseemann/shovill>`_. + Documentation can be found at Torsten Seemann `site <https://github.com/tseemann/shovill>`_. ]]></help> <citations> <citation type="bibtex">