Mercurial > repos > kkonganti > cfsan_centriflaken

comparison cfsan_centriflaken.xml @ 64:ef8d8b8f41cc

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"planemo upload"
author kkonganti
date Wed, 13 Jul 2022 13:06:51 -0400
parents d1efe888e1ed
children ec3fca35a622
comparison
equal deleted inserted replaced
63:d1efe888e1ed 64:ef8d8b8f41cc
36 --flye_pacbio_corr true --flye_nano_raw false 36 --flye_pacbio_corr true --flye_nano_raw false
37 #elif ($input_read_type_cond.pipeline_cond.long_read_platform == "pacbio_hifi"): 37 #elif ($input_read_type_cond.pipeline_cond.long_read_platform == "pacbio_hifi"):
38 --flye_pacbio_hifi true --flye_nano_raw false 38 --flye_pacbio_hifi true --flye_nano_raw false
39 #end if 39 #end if
40 #elif ($input_read_type_cond.pipeline_cond.pipeline == "centriflaken_hy"): 40 #elif ($input_read_type_cond.pipeline_cond.pipeline == "centriflaken_hy"):
41 #if (str($input_read_cond.input_read_type) == "single_long"): 41 #if (str($input_read_type_cond.input_read_type) == "single_long"):
42 --fq_single_end true 42 --fq_single_end true
43 #elif (str($input_read_cond.input_read_type) == "paired"): 43 #elif (str($input_read_type_cond.input_read_type) == "paired"):
44 --fq_single_end false --fq2_suffix '${input_read_cond.fq2_suffix}' 44 --fq_single_end false --fq2_suffix '${input_read_type_cond.fq2_suffix}'
45 #end if 45 #end if
46 #end if 46 #end if
47 --input \${pwd_path}/cpipes-input 47 --input \${pwd_path}/cpipes-input
48 --output \${pwd_path}/cpipes-output 48 --output \${pwd_path}/cpipes-output
49 --fq_suffix '${input_read_cond.fq_suffix}' 49 --fq_suffix '${input_read_type_cond.fq_suffix}'
50 #if ($fq_filter_by_len != ""): 50 #if ($fq_filter_by_len != ""):
51 --fq_filter_by_len $fq_filter_by_len 51 --fq_filter_by_len $fq_filter_by_len
52 #end if 52 #end if
53 --fq_filename_delim '${fq_filename_delim}' 53 --fq_filename_delim '${fq_filename_delim}'
54 --fq_filename_delim_idx $fq_filename_delim_idx 54 --fq_filename_delim_idx $fq_filename_delim_idx