Mercurial > repos > kkonganti > cfsan_centriflaken

comparison cfsan_centriflaken.xml @ 21:abe3bc84455b

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"planemo upload"
author kkonganti
date Wed, 29 Jun 2022 09:37:16 -0400
parents 91480ddc3fcd
children 0c42dc147b29
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20:91480ddc3fcd 21:abe3bc84455b
30 --fq_filename_delim_idx $fq_filename_delim_idx 30 --fq_filename_delim_idx $fq_filename_delim_idx
31 --centrifuge_extract_bug '${centrifuge_extract_bug}' 31 --centrifuge_extract_bug '${centrifuge_extract_bug}'
32 --flye_genome_size '${genome_size}' 32 --flye_genome_size '${genome_size}'
33 -profile $runtime_profile 33 -profile $runtime_profile
34 -resume; 34 -resume;
35 cp ./cpipes-output/${pipeline}-multiqc/multiqc_report.html .; 35 cp \${pwd_path}/cpipes-output/${pipeline}-multiqc/multiqc_report.html ${pwd_path}/;
36 ]]></command> 36 ]]></command>
37 <inputs> 37 <inputs>
38 <param name="input" type="data_collection" collection_type="list" format="fastq,fastq.gz,fastqsanger.gz,fastqsanger" label="Input read collection" /> 38 <param name="input" type="data_collection" collection_type="list" format="fastq,fastq.gz,fastqsanger.gz,fastqsanger" label="Input read collection" />
39 <param name="pipeline" type="select" label="CPIPES Workflow name" value="centriflaken" 39 <param name="pipeline" type="select" label="CPIPES Workflow name" value="centriflaken"
40 help="centriflaken: for long reads (Nanopore or PacBio). centriflaken_hy: for short reads (paired or unpaired). Default: centriflaken"> 40 help="centriflaken: for long reads (Nanopore or PacBio). centriflaken_hy: for short reads (paired or unpaired). Default: centriflaken">