Mercurial > repos > kkonganti > cfsan_centriflaken

comparison cfsan_centriflaken.xml @ 87:34d411a7bd4f

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"planemo upload"
author kkonganti
date Wed, 13 Jul 2022 17:27:58 -0400
parents 7e421f421b5e
children 0c59342d0144
comparison
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86:7e421f421b5e 87:34d411a7bd4f
62 #end if 62 #end if
63 --fq_filename_delim '${fq_filename_delim}' 63 --fq_filename_delim '${fq_filename_delim}'
64 --fq_filename_delim_idx $fq_filename_delim_idx 64 --fq_filename_delim_idx $fq_filename_delim_idx
65 --centrifuge_extract_bug '${centrifuge_extract_bug}' 65 --centrifuge_extract_bug '${centrifuge_extract_bug}'
66 -profile kondagac; 66 -profile kondagac;
67 mv './cpipes-output/${input_read_type_cond.pipeline_cond.pipeline}-multiqc/multiqc_report.html' './multiqc_report.html' || exit 1; 67 mv './cpipes-output/${input_read_type_cond.pipeline_cond.pipeline}-multiqc/multiqc_report.html' './multiqc_report.html' > /dev/null 2>&1 || exit 1;
68 mv './cpipes-output/${input_read_type_cond.pipeline_cond.pipeline}-results/kraken2_extract_contigs' kraken2_extract_contigs || exit 1; 68 mv './cpipes-output/${input_read_type_cond.pipeline_cond.pipeline}-results/kraken2_extract_contigs' kraken2_extract_contigs > /dev/null 2>&1 || exit 1;
69 rm -rf ./cpipes-output || exit 1; 69 rm -rf ./cpipes-output > /dev/null 2>&1 || exit 1;
70 rm -rf ./work || exit 1 70 rm -rf ./work > /dev/null 2>&1 || exit 1
71 ]]></command> 71 ]]></command>
72 <inputs> 72 <inputs>
73 <conditional name="input_read_type_cond"> 73 <conditional name="input_read_type_cond">
74 <param name="input_read_type" type="select" label="Select the read collection type"> 74 <param name="input_read_type" type="select" label="Select the read collection type">
75 <option value="single_long" selected="true">Unpaired reads (i.e. Single-End short reads or Long reads)</option> 75 <option value="single_long" selected="true">Unpaired reads (i.e. Single-End short reads or Long reads)</option>