Mercurial > repos > kkonganti > cfsan_bettercallsal

comparison cfsan_bettercallsal.xml @ 19:4b304d77bbfb

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload
author kkonganti
date Mon, 15 Jul 2024 11:20:22 -0400
parents 0e7a0053e4a6
children 4ce0e079377d
comparison
equal deleted inserted replaced
18:75558ffe3e68 19:4b304d77bbfb
34 #end for 34 #end for
35 #end if 35 #end if
36 $__tool_directory__/0.7.0/cpipes 36 $__tool_directory__/0.7.0/cpipes
37 --pipeline bettercallsal 37 --pipeline bettercallsal
38 --input \${input_path} 38 --input \${input_path}
39 --output \${pwd_path}/cpipes-output 39 --output cpipes-output
40 --fq_suffix '${input_read_type_cond.fq_suffix}' 40 --fq_suffix '${input_read_type_cond.fq_suffix}'
41 #if (str($input_read_type_cond.input_read_type) == "single_long"): 41 #if (str($input_read_type_cond.input_read_type) == "single_long"):
42 --fq_single_end true 42 --fq_single_end true
43 #elif (str($input_read_type_cond.input_read_type) == "paired"): 43 #elif (str($input_read_type_cond.input_read_type) == "paired"):
44 --fq_single_end false --fq2_suffix '${input_read_type_cond.fq2_suffix}' 44 --fq_single_end false --fq2_suffix '${input_read_type_cond.fq2_suffix}'
57 --bcs_thresholds $bcs_thresholds 57 --bcs_thresholds $bcs_thresholds
58 --fq_filename_delim '${fq_filename_delim}' 58 --fq_filename_delim '${fq_filename_delim}'
59 --fq_filename_delim_idx $fq_filename_delim_idx 59 --fq_filename_delim_idx $fq_filename_delim_idx
60 -profile gxkubernetes; 60 -profile gxkubernetes;
61 mv './cpipes-output/bettercallsal-multiqc/multiqc_report.html' './multiqc_report.html' || exit 1; 61 mv './cpipes-output/bettercallsal-multiqc/multiqc_report.html' './multiqc_report.html' || exit 1;
62 rm -rf ./cpipes-output > || exit 1; 62 rm -rf ./cpipes-output || exit 1;
63 rm -rf ./work || exit 1 63 rm -rf ./work || exit 1;
64 ]]></command> 64 ]]></command>
65 <inputs> 65 <inputs>
66 <conditional name="input_read_type_cond"> 66 <conditional name="input_read_type_cond">
67 <param name="input_read_type" type="select" label="Select the read collection type"> 67 <param name="input_read_type" type="select" label="Select the read collection type">
68 <option value="single_long" selected="true">Single-End short reads</option> 68 <option value="single_long" selected="true">Single-End short reads</option>