Mercurial > repos > kkonganti > cfsan_centriflaken

comparison cfsan_centriflaken.xml @ 31:b928b20149a9

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"planemo upload"
author kkonganti
date Wed, 29 Jun 2022 14:45:10 -0400
parents 2c910ebd043e
children 9c06429a2ffb
comparison
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30:2c910ebd043e 31:b928b20149a9
45 mv './cpipes-output/${pipeline}-multiqc/multiqc_report.html' './multiqc_report.html'; 45 mv './cpipes-output/${pipeline}-multiqc/multiqc_report.html' './multiqc_report.html';
46 mv './cpipes-output/${pipeline}-results/kraken2_extract_contigs' kraken2_extract_contigs; 46 mv './cpipes-output/${pipeline}-results/kraken2_extract_contigs' kraken2_extract_contigs;
47 ]]></command> 47 ]]></command>
48 <inputs> 48 <inputs>
49 <param name="input" type="data_collection" collection_type="list" format="fastq,fastq.gz,fastqsanger.gz,fastqsanger" label="Input read collection" /> 49 <param name="input" type="data_collection" collection_type="list" format="fastq,fastq.gz,fastqsanger.gz,fastqsanger" label="Input read collection" />
50 <param name="pipeline" type="select" label="CPIPES Workflow name" value="centriflaken" 50 <param name="pipeline" type="select" label="CPIPES Workflow name"
51 help="centriflaken: for long reads (Nanopore or PacBio). centriflaken_hy: for short reads (paired or unpaired). Default: centriflaken"> 51 help="centriflaken: for long reads (Nanopore or PacBio). centriflaken_hy: for short reads (paired or unpaired). Default: centriflaken">
52 <option value="centriflaken">centriflaken</option> 52 <option value="centriflaken" selected="true">centriflaken</option>
53 <option value="centriflaken_hy">centriflaken_hy</option> 53 <option value="centriflaken_hy">centriflaken_hy</option>
54 </param> 54 </param>
55 <param name="reads_lib_layout" type="select" label="Short Read Library Layout" value="single" 55 <param name="reads_lib_layout" type="select" label="Short Read Library Layout"
56 help="Leave this option as Single-End for centriflaken. If the pipeline is centriflaken_hy (i.e for short reads), what is the library layout? Default: Single-End"> 56 help="Leave this option as Single-End for centriflaken. If the pipeline is centriflaken_hy (i.e for short reads), what is the library layout? Default: Single-End">
57 <option value="single">Single-End</option> 57 <option value="single" selected="true">Single-End</option>
58 <option value="paired">Paired-End</option> 58 <option value="paired">Paired-End</option>
59 </param> 59 </param>
60 <param name="long_read_platform" type="select" label="Mention long read sequencing platform and type" value="nanopore_raw" 60 <param name="long_read_platform" type="select" label="Mention long read sequencing platform and type"
61 help="THIS OPTION IS IGNORED IF THE INPUT READS ARE SHORT READS."> 61 help="THIS OPTION IS IGNORED IF THE INPUT READS ARE SHORT READS.">
62 <option value="nanopore_raw">Nanopore raw reads, pre-Guppy5 (&lt;20% error)</option> 62 <option value="nanopore_raw" selected="true">Nanopore raw reads, pre-Guppy5 (&lt;20% error)</option>
63 <option value="nanopore_corr">Nanopore reads that were corrected with other methods (&lt;3% error)</option> 63 <option value="nanopore_corr">Nanopore reads that were corrected with other methods (&lt;3% error)</option>
64 <option value="nanopore_hq">Nanopore high-quality reads, Guppy5+ SUP or Q20 (5% error)</option> 64 <option value="nanopore_hq">Nanopore high-quality reads, Guppy5+ SUP or Q20 (5% error)</option>
65 <option value="pacbio_raw">PacBio regular CLR reads (&lt;20% error)</option> 65 <option value="pacbio_raw">PacBio regular CLR reads (&lt;20% error)</option>
66 <option value="pacbio_corr">PacBio reads that were corrected with other methods (&lt;3% error)</option> 66 <option value="pacbio_corr">PacBio reads that were corrected with other methods (&lt;3% error)</option>
67 <option value="pacbio_hifi">PacBio HiFi reads (&lt;1% error)</option> 67 <option value="pacbio_hifi">PacBio HiFi reads (&lt;1% error)</option>
73 <param name="fq_filename_delim_idx" type="integer" value="1" label="File name delimitor index (--fq_filename_delim_idx)" /> 73 <param name="fq_filename_delim_idx" type="integer" value="1" label="File name delimitor index (--fq_filename_delim_idx)" />
74 <param name="centrifuge_extract_bug" type="text" value="Escherichia coli" label="Reads belonging to this taxa are extracted and a MAG is generated to allow for serotyping"/> 74 <param name="centrifuge_extract_bug" type="text" value="Escherichia coli" label="Reads belonging to this taxa are extracted and a MAG is generated to allow for serotyping"/>
75 <param name="genome_size" type="text" optional="true" value="5.5m" label="Estimated genome size" help="For example, 5m or 2.6g."> 75 <param name="genome_size" type="text" optional="true" value="5.5m" label="Estimated genome size" help="For example, 5m or 2.6g.">
76 <validator type="regex" message="Genome size must be a float or integer, optionally followed by the a unit prefix (kmg)">^([0-9]*[.])?[0-9]+[kmg]?$</validator> 76 <validator type="regex" message="Genome size must be a float or integer, optionally followed by the a unit prefix (kmg)">^([0-9]*[.])?[0-9]+[kmg]?$</validator>
77 </param> 77 </param>
78 <param name="runtime_profile" type="select" label="Run time profile" value="kondagac"> 78 <param name="runtime_profile" type="select" label="Run time profile">
79 <option value="kondagac">conda</option> 79 <option value="kondagac" selected="true">conda</option>
80 <option value="cingularitygac">singularity</option> 80 <option value="cingularitygac">singularity</option>
81 </param> 81 </param>
82 </inputs> 82 </inputs>
83 <outputs> 83 <outputs>
84 <data name="multiqc_report" format="html" label="MultiQC Report on ${on_string}" from_work_dir="multiqc_report.html"/> 84 <data name="multiqc_report" format="html" label="MultiQC Report on ${on_string}" from_work_dir="multiqc_report.html"/>