Mercurial > repos > kkonganti > cfsan_centriflaken

comparison cfsan_centriflaken.xml @ 123:b9c76c256e2c

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planemo upload
author kkonganti
date Wed, 03 Jul 2024 12:54:16 -0400
parents b6fcae1983cb
children 45ccd0403784
comparison
equal deleted inserted replaced
122:98b5dd800883 123:b9c76c256e2c
3 <requirements> 3 <requirements>
4 <container type="docker">quay.io/biocontainers/nextflow:24.04.2--hdfd78af_0</container> 4 <container type="docker">quay.io/biocontainers/nextflow:24.04.2--hdfd78af_0</container>
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 mkdir -p cpipes-input || exit 1;
9 pwd_path=\$(pwd);
10 time_stamp=\$(date +%Y-%m-%d-%s); 8 time_stamp=\$(date +%Y-%m-%d-%s);
11 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="\${work_dir}/cpipes-input"
12 mkdir -p \$work_dir || exit 1; 11 mkdir -p \$work_dir || exit 1;
12 mkdir -p "\${input_path}" || exit 1;
13 #import re 13 #import re
14 #if (str($input_read_type_cond.input_read_type) == "single_long"): 14 #if (str($input_read_type_cond.input_read_type) == "single_long"):
15 #for _, $unpaired in enumerate($input_read_type_cond.input): 15 #for _, $unpaired in enumerate($input_read_type_cond.input):
16 #set read1 = str($unpaired.name) 16 #set read1 = str($unpaired.name)
17 #if not str($unpaired.name).endswith(('.fastq', '.fastq.gz')): 17 #if not str($unpaired.name).endswith(('.fastq', '.fastq.gz')):
18 #set read1_ext = re.sub('fastqsanger', 'fastq', str($unpaired.ext)) 18 #set read1_ext = re.sub('fastqsanger', 'fastq', str($unpaired.ext))
19 #set read1 = str($unpaired.name) + str('.') + $read1_ext 19 #set read1 = str($unpaired.name) + str('.') + $read1_ext
20 #end if 20 #end if
21 ln -sf '$unpaired' './cpipes-input/$read1'; 21 ln -sf '$unpaired' "\${input_path}/$read1";
22 #end for 22 #end for
23 #elif (str($input_read_type_cond.input_read_type) == "paired"): 23 #elif (str($input_read_type_cond.input_read_type) == "paired"):
24 #for _, $pair in enumerate($input_read_type_cond.input_pair) 24 #for _, $pair in enumerate($input_read_type_cond.input_pair)
25 #set read_R1 = re.sub('\:forward', '_forward', str($pair.forward.name)) 25 #set read_R1 = re.sub('\:forward', '_forward', str($pair.forward.name))
26 #set read_R2 = re.sub('\:reverse', '_reverse', str($pair.reverse.name)) 26 #set read_R2 = re.sub('\:reverse', '_reverse', str($pair.reverse.name))
30 #set read_R1 = $read_R1 + str('.') + $read_R1_ext 30 #set read_R1 = $read_R1 + str('.') + $read_R1_ext
31 #end if 31 #end if
32 #if not str($pair.reverse.name).endswith(('.fastq', '.fastq.gz')): 32 #if not str($pair.reverse.name).endswith(('.fastq', '.fastq.gz')):
33 #set read_R2 = $read_R2 + str('.') + $read_R2_ext 33 #set read_R2 = $read_R2 + str('.') + $read_R2_ext
34 #end if 34 #end if
35 ln -sf '$pair.forward' './cpipes-input/$read_R1'; 35 ln -sf '$pair.forward' "\${input_path}/$read_R1";
36 ln -sf '$pair.reverse' './cpipes-input/$read_R2'; 36 ln -sf '$pair.reverse' "\${input_path}/$read_R2";
37 #end for 37 #end for
38 #end if 38 #end if
39 $__tool_directory__/0.4.2/cpipes 39 nextflow /galaxy/cfsan-centriflaken-db/0.4.2/cpipes
40 --pipeline $input_read_type_cond.pipeline_cond.pipeline 40 --pipeline $input_read_type_cond.pipeline_cond.pipeline
41 -work-dir \${work_dir} 41 -work-dir \${work_dir}
42 #if ($input_read_type_cond.pipeline_cond.pipeline == "centriflaken"): 42 #if ($input_read_type_cond.pipeline_cond.pipeline == "centriflaken"):
43 --fq_single_end true 43 --fq_single_end true
44 --flye_genome_size '${genome_size}' 44 --flye_genome_size '${genome_size}'
58 --fq_single_end true 58 --fq_single_end true
59 #elif (str($input_read_type_cond.input_read_type) == "paired"): 59 #elif (str($input_read_type_cond.input_read_type) == "paired"):
60 --fq_single_end false --fq2_suffix '${input_read_type_cond.fq2_suffix}' 60 --fq_single_end false --fq2_suffix '${input_read_type_cond.fq2_suffix}'
61 #end if 61 #end if
62 #end if 62 #end if
63 --input \${pwd_path}/cpipes-input 63 --input \${input_path}
64 --output \${pwd_path}/cpipes-output 64 --output \${work_dir}/cpipes-output
65 --fq_suffix '${input_read_type_cond.fq_suffix}' 65 --fq_suffix '${input_read_type_cond.fq_suffix}'
66 #if ($fq_filter_by_len != ""): 66 #if ($fq_filter_by_len != ""):
67 --fq_filter_by_len $fq_filter_by_len 67 --fq_filter_by_len $fq_filter_by_len
68 #end if 68 #end if
69 --fq_filename_delim '${fq_filename_delim}' 69 --fq_filename_delim '${fq_filename_delim}'
71 --centrifuge_extract_bug '${centrifuge_extract_bug}' 71 --centrifuge_extract_bug '${centrifuge_extract_bug}'
72 #if (str($input_read_type_cond.pipeline_cond.rm_dup_seqs) == "true"): 72 #if (str($input_read_type_cond.pipeline_cond.rm_dup_seqs) == "true"):
73 --seqkit_rmdup_run true 73 --seqkit_rmdup_run true
74 #end if 74 #end if
75 -profile gxkubernetes; 75 -profile gxkubernetes;
76 mv './cpipes-output/${input_read_type_cond.pipeline_cond.pipeline}-multiqc/multiqc_report.html' './multiqc_report.html' > /dev/null 2>&1 || exit 1; 76 mv "\${work_dir}/cpipes-output/${input_read_type_cond.pipeline_cond.pipeline}-multiqc/multiqc_report.html" './multiqc_report.html' > /dev/null 2>&1 || exit 1;
77 mv './cpipes-output/${input_read_type_cond.pipeline_cond.pipeline}-results/kraken2_extract_contigs' kraken2_extract_contigs > /dev/null 2>&1 || 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;
78 rm -rf ./cpipes-output > /dev/null 2>&1 || exit 1; 78 rm -rf "\${work_dir}/cpipes-output" > /dev/null 2>&1 || exit 1;
79 rm -rf ./work > /dev/null 2>&1 || exit 1
80 ]]></command> 79 ]]></command>
81 <inputs> 80 <inputs>
82 <conditional name="input_read_type_cond"> 81 <conditional name="input_read_type_cond">
83 <param name="input_read_type" type="select" label="Select the read collection type"> 82 <param name="input_read_type" type="select" label="Select the read collection type">
84 <option value="single_long" selected="true">Unpaired reads (i.e. Single-End short reads or Long reads)</option> 83 <option value="single_long" selected="true">Unpaired reads (i.e. Single-End short reads or Long reads)</option>