Mercurial > repos > kkonganti > cfsan_centriflaken

comparison cfsan_centriflaken.xml @ 130:04f6ac8ca13c

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planemo upload
author kkonganti
date Wed, 03 Jul 2024 15:16:39 -0400
parents 1bb0dacefa6d
children 45900148ca9e
comparison
equal deleted inserted replaced
129:1bb0dacefa6d 130:04f6ac8ca13c
5 </requirements> 5 </requirements>
6 <version_command>nextflow -version</version_command> 6 <version_command>nextflow -version</version_command>
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 time_stamp=\$(date +%Y-%m-%d-%s); 8 time_stamp=\$(date +%Y-%m-%d-%s);
9 work_dir="/galaxy/nf-work-dirs/centriflaken_work_dir-"\${time_stamp}; 9 work_dir="/galaxy/nf-work-dirs/centriflaken_work_dir-"\${time_stamp};
10 input_path=\$(pwd)/cpipes-input; 10 input_path=\$(pwd)"/cpipes-input";
11 mkdir -p "\${work_dir}" || exit 1;
12 mkdir -p "\${input_path}" || exit 1; 11 mkdir -p "\${input_path}" || exit 1;
13 #import re 12 #import re
14 #if (str($input_read_type_cond.input_read_type) == "single_long"): 13 #if (str($input_read_type_cond.input_read_type) == "single_long"):
15 #for _, $unpaired in enumerate($input_read_type_cond.input): 14 #for _, $unpaired in enumerate($input_read_type_cond.input):
16 #set read1 = str($unpaired.name) 15 #set read1 = str($unpaired.name)
34 #end if 33 #end if
35 ln -sf '$pair.forward' "\${input_path}/$read_R1"; 34 ln -sf '$pair.forward' "\${input_path}/$read_R1";
36 ln -sf '$pair.reverse' "\${input_path}/$read_R2"; 35 ln -sf '$pair.reverse' "\${input_path}/$read_R2";
37 #end for 36 #end for
38 #end if 37 #end if
39 nextflow /galaxy/cfsan-centriflaken-db/0.4.2/cpipes 38 $__tool_directory__/0.4.2/cpipes
40 --pipeline $input_read_type_cond.pipeline_cond.pipeline 39 --pipeline $input_read_type_cond.pipeline_cond.pipeline
41 #if ($input_read_type_cond.pipeline_cond.pipeline == "centriflaken"): 40 #if ($input_read_type_cond.pipeline_cond.pipeline == "centriflaken"):
42 --fq_single_end true 41 --fq_single_end true
43 --flye_genome_size '${genome_size}' 42 --flye_genome_size '${genome_size}'
44 #if ($input_read_type_cond.pipeline_cond.long_read_platform == "nanopore_corr"): 43 #if ($input_read_type_cond.pipeline_cond.long_read_platform == "nanopore_corr"):
58 #elif (str($input_read_type_cond.input_read_type) == "paired"): 57 #elif (str($input_read_type_cond.input_read_type) == "paired"):
59 --fq_single_end false --fq2_suffix '${input_read_type_cond.fq2_suffix}' 58 --fq_single_end false --fq2_suffix '${input_read_type_cond.fq2_suffix}'
60 #end if 59 #end if
61 #end if 60 #end if
62 --input \${input_path} 61 --input \${input_path}
63 --output \${work_dir}/cpipes-output 62 --output cpipes-output
64 --fq_suffix '${input_read_type_cond.fq_suffix}' 63 --fq_suffix '${input_read_type_cond.fq_suffix}'
65 #if ($fq_filter_by_len != ""): 64 #if ($fq_filter_by_len != ""):
66 --fq_filter_by_len $fq_filter_by_len 65 --fq_filter_by_len $fq_filter_by_len
67 #end if 66 #end if
68 --fq_filename_delim '${fq_filename_delim}' 67 --fq_filename_delim '${fq_filename_delim}'
69 --fq_filename_delim_idx $fq_filename_delim_idx 68 --fq_filename_delim_idx $fq_filename_delim_idx
70 --centrifuge_extract_bug '${centrifuge_extract_bug}' 69 --centrifuge_extract_bug '${centrifuge_extract_bug}'
71 #if (str($input_read_type_cond.pipeline_cond.rm_dup_seqs) == "true"): 70 #if (str($input_read_type_cond.pipeline_cond.rm_dup_seqs) == "true"):
72 --seqkit_rmdup_run true 71 --seqkit_rmdup_run true
73 #end if 72 #end if
74 -work-dir \${work_dir}
75 -profile gxkubernetes; 73 -profile gxkubernetes;
76 mv "\${work_dir}/cpipes-output/${input_read_type_cond.pipeline_cond.pipeline}-multiqc/multiqc_report.html" './multiqc_report.html' || exit 1; 74 mv "./cpipes-output/${input_read_type_cond.pipeline_cond.pipeline}-multiqc/multiqc_report.html" './multiqc_report.html' || exit 1;
77 mv "\${work_dir}/cpipes-output/${input_read_type_cond.pipeline_cond.pipeline}-results/kraken2_extract_contigs" kraken2_extract_contigs > /dev/null 2>&1 || exit 1; 75 mv "./cpipes-output/${input_read_type_cond.pipeline_cond.pipeline}-results/kraken2_extract_contigs" kraken2_extract_contigs || exit 1;
78 rm -rf "\${work_dir}/cpipes-output" || exit 1;
79 ]]></command> 76 ]]></command>
80 <inputs> 77 <inputs>
81 <conditional name="input_read_type_cond"> 78 <conditional name="input_read_type_cond">
82 <param name="input_read_type" type="select" label="Select the read collection type"> 79 <param name="input_read_type" type="select" label="Select the read collection type">
83 <option value="single_long" selected="true">Unpaired reads (i.e. Single-End short reads or Long reads)</option> 80 <option value="single_long" selected="true">Unpaired reads (i.e. Single-End short reads or Long reads)</option>