Mercurial > repos > kkonganti > cfsan_centriflaken

comparison cfsan_centriflaken.xml @ 46:0dd0ebe5cddf

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"planemo upload"
author kkonganti
date Thu, 07 Jul 2022 10:37:59 -0400
parents d532ac969904
children 30191f39a957
comparison
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45:62d848f2a128 46:0dd0ebe5cddf
45 --centrifuge_extract_bug '${centrifuge_extract_bug}' 45 --centrifuge_extract_bug '${centrifuge_extract_bug}'
46 -profile $runtime_profile 46 -profile $runtime_profile
47 -resume; 47 -resume;
48 mv './cpipes-output/${pipeline}-multiqc/multiqc_report.html' './multiqc_report.html'; 48 mv './cpipes-output/${pipeline}-multiqc/multiqc_report.html' './multiqc_report.html';
49 mv './cpipes-output/${pipeline}-results/kraken2_extract_contigs' kraken2_extract_contigs; 49 mv './cpipes-output/${pipeline}-results/kraken2_extract_contigs' kraken2_extract_contigs;
50 rm -rf ./cpipes-output;
51 rm -rf ./work
50 ]]></command> 52 ]]></command>
51 <inputs> 53 <inputs>
52 <param name="input" type="data_collection" collection_type="list" format="fastq,fastq.gz,fastqsanger.gz,fastqsanger" label="Input read collection" /> 54 <param name="input" type="data_collection" collection_type="list" format="fastq,fastq.gz,fastqsanger.gz,fastqsanger" label="Input read collection" />
53 <param name="pipeline" type="select" label="CPIPES Workflow name" 55 <param name="pipeline" type="select" label="CPIPES Workflow name"
54 help="centriflaken: for long reads (Nanopore or PacBio). centriflaken_hy: for short reads (paired or unpaired). Default: centriflaken"> 56 help="centriflaken: for long reads (Nanopore or PacBio). centriflaken_hy: for short reads (paired or unpaired). Default: centriflaken">