Mercurial > repos > kkonganti > cfsan_centriflaken

comparison cfsan_centriflaken.xml @ 20:91480ddc3fcd

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"planemo upload"
author kkonganti
date Wed, 29 Jun 2022 09:33:18 -0400
parents 2671e2d54a25
children abe3bc84455b
comparison
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19:2671e2d54a25 20:91480ddc3fcd
29 --fq_filename_delim '${fq_filename_delim}' 29 --fq_filename_delim '${fq_filename_delim}'
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 ]]></command> 36 ]]></command>
36 <inputs> 37 <inputs>
37 <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" />
38 <param name="pipeline" type="select" label="CPIPES Workflow name" value="centriflaken" 39 <param name="pipeline" type="select" label="CPIPES Workflow name" value="centriflaken"
39 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">
58 <option value="kondagac">conda</option> 59 <option value="kondagac">conda</option>
59 <option value="cingularitygac">singularity</option> 60 <option value="cingularitygac">singularity</option>
60 </param> 61 </param>
61 </inputs> 62 </inputs>
62 <outputs> 63 <outputs>
63 <data name="multiqc_report" format="html" label="MultiQC Report on ${on_string}" from_work_dir="./cpipes-output/${pipeline}-multiqc/multiqc_report.html"/> 64 <data name="multiqc_report" format="html" label="MultiQC Report on ${on_string}" from_work_dir="multiqc_report.html"/>
64 <collection name="assembled_mags" type="list" label="CENTRIFLAKEN: Assembled MAGs on ${on_string}"> 65 <collection name="assembled_mags" type="list" label="CENTRIFLAKEN: Assembled MAGs on ${on_string}">
65 <discover_datasets pattern="(?P&lt;name&gt;.*)\.assembly_filtered_contigs\.fasta" directory="./cpipes-output/${pipeline}-results/kraken2_extract_contigs"/> 66 <discover_datasets pattern="(?P&lt;name&gt;.*)\.assembly_filtered_contigs\.fasta" directory="./cpipes-output/${pipeline}-results/kraken2_extract_contigs"/>
66 </collection> 67 </collection>
67 </outputs> 68 </outputs>
68 <tests> 69 <tests>