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Update shovill tool to accept fastq and fastq.gz #5476

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merged 2 commits into from
Oct 12, 2023
Merged

Update shovill tool to accept fastq and fastq.gz #5476

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4dcecc3
fix problem with fastq.gz input
pimarin Sep 11, 2023
e111b05
update lint
pimarin Sep 11, 2023
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30 changes: 15 additions & 15 deletions tools/shovill/shovill.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@
<description>Faster SPAdes assembly of Illumina reads</description>
<macros>
<token name="@TOOL_VERSION@">1.1.0</token>
<token name="@VERSION_SUFFIX@">1</token>
<token name="@VERSION_SUFFIX@">2</token>
</macros>
<xrefs>
<xref type="bio.tools">shovill</xref>
Expand Down Expand Up @@ -78,22 +78,22 @@
<option value="collection">Paired Collection</option>
</param>
<when value="paired">
<param name="R1" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="Forward reads (R1)" help="The file of forward reads in FASTQ format"/>
<param name="R2" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="Reverse reads (R2)" help="The file of reverse reads in FASTQ format"/>
<param name="R1" type="data" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="Forward reads (R1)" help="The file of forward reads in FASTQ format"/>
<param name="R2" type="data" format="fastq,fastq.gz,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="fastq,fastq.gz,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)" />
<param name="assembler" argument="--assembler" type="select" label="Assembler to use" help="Which assembler would you like shovill to use, default is Spades">
<param argument="--trim" type="boolean" truevalue="--trim" falsevalue="" label="Trim reads" help="Use Trimmomatic to remove common adaptors first (default: OFF)" />
<param 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')" >
<param argument="--namefmt" type="text" value="contig%05d" label="Contig name format" help="Format of contig FASTA IDs in 'printf' style (default: 'contig%05d')" >
<sanitizer>
<valid initial="string.printable">
<remove value="&apos;" />
Expand All @@ -103,22 +103,22 @@
</mapping>
</sanitizer>
</param>
<param name="depth" argument="--depth" type="integer" value="100" label="Depth" help="Sub-sample --R1/--R2 to this depth. Disable with --depth 0 (default: 100)" />
<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 argument="--depth" type="integer" value="100" label="Depth" help="Sub-sample --R1/--R2 to this depth. Disable with --depth 0 (default: 100)" />
<param 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 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 argument="--opts" type="text" value="" label="Extra SPAdes options" help="eg. --plasmid --sc ... (default: '')" />
<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)">
<param 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"/>
<param 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)" />
<param argument="--minlen" type="integer" value="0" label="Minimum contig length" help="Minimum length of contig to be output. 0 is AUTO (default: 0)" />
<param 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" />

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