Mercurial > repos > kkonganti > cfsan_centriflaken

comparison cfsan_centriflaken.xml @ 24:05b6b4edfd58

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"planemo upload"
author kkonganti
date Wed, 29 Jun 2022 09:47:38 -0400
parents 4774fc77e872
children b9cd7722d51b
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23:4774fc77e872 24:05b6b4edfd58
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 multiqc_report.html; 35 mv './cpipes-output/${pipeline}-multiqc/multiqc_report.html' './multiqc_report.html';
36 mv './cpipes-output/${pipeline}-results/kraken2_extract_contigs' kraken2_extract_contigs;
36 ]]></command> 37 ]]></command>
37 <inputs> 38 <inputs>
38 <param name="input" type="data_collection" collection_type="list" format="fastq,fastq.gz,fastqsanger.gz,fastqsanger" label="Input read collection" /> 39 <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" 40 <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"> 41 help="centriflaken: for long reads (Nanopore or PacBio). centriflaken_hy: for short reads (paired or unpaired). Default: centriflaken">
61 </param> 62 </param>
62 </inputs> 63 </inputs>
63 <outputs> 64 <outputs>
64 <data name="multiqc_report" format="html" label="MultiQC Report on ${on_string}" from_work_dir="multiqc_report.html"/> 65 <data name="multiqc_report" format="html" label="MultiQC Report on ${on_string}" from_work_dir="multiqc_report.html"/>
65 <collection name="assembled_mags" type="list" label="CENTRIFLAKEN: Assembled MAGs on ${on_string}"> 66 <collection name="assembled_mags" type="list" label="CENTRIFLAKEN: Assembled MAGs on ${on_string}">
66 <discover_datasets pattern="(?P&lt;name&gt;.*)\.assembly_filtered_contigs\.fasta" directory="./cpipes-output/${pipeline}-results/kraken2_extract_contigs"/> 67 <discover_datasets pattern="(?P&lt;name&gt;.*)\.assembly_filtered_contigs\.fasta" ext="fasta" directory="kraken2_extract_contigs"/>
67 </collection> 68 </collection>
68 </outputs> 69 </outputs>
69 <tests> 70 <tests>
70 <!--Test 01: long reads--> 71 <!--Test 01: long reads-->
71 <test expect_num_outputs="2"> 72 <test expect_num_outputs="2">