Mercurial > repos > kkonganti > cfsan_centriflaken

comparison cfsan_centriflaken.xml @ 58:2256bc31d3bf

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"planemo upload"
author kkonganti
date Wed, 13 Jul 2022 12:47:22 -0400
parents cea27772bcb8
children a8d6f5950fbf
comparison
equal deleted inserted replaced
57:cea27772bcb8 58:2256bc31d3bf
5 <requirement type="package">graphviz</requirement> 5 <requirement type="package">graphviz</requirement>
6 </requirements> 6 </requirements>
7 <version_command>nextflow -version</version_command> 7 <version_command>nextflow -version</version_command>
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 mkdir -p cpipes-input || exit 1; 9 mkdir -p cpipes-input || exit 1;
10 #for $key in $input.keys() 10 pwd_path=\$(pwd);
11 ln -sf '$input[$key]' './cpipes-input/$key'; 11 #import os
12 #end for 12 #if (str($input_read_type_cond.input_read_type) == "single_long"):
13 pwd_path=\$(pwd); 13 #for $key in $input_read_type_cond.input.keys()
14 ln -sf '$input_read_type_cond.input[$key]' './cpipes-input/$key';
15 #end for
16 #elif (str($input_read_cond.input_read_type) == "paired"):
17 #for $key in $input_read_type_cond.input_pair.keys()
18 #set $read_R1 = os.path.basename($input_read_type_cond.input_pair[$key]['forward'])
19 #set $read_R2 = os.path.basename($input_read_type_cond.input_pair[$key]['reverse'])
20 ln -sf '$input_read_type_cond.input_pair[$key]['forward']' './cpipes-input/$read_R1';
21 ln -sf '$input_read_type_cond.input_pair[$key]['reverse']' './cpipes-input/$read_R2';
22 #end for
23 #endif
14 $__tool_directory__/0.2.1/cpipes 24 $__tool_directory__/0.2.1/cpipes
15 --pipeline $pipeline 25 --pipeline $input_read_type_cond.pipeline
16 #if ($pipeline == "centriflaken"): 26 #if ($input_read_type_cond.pipeline_cond.pipeline == "centriflaken"):
17 --fq_single_end true 27 --fq_single_end true
18 --flye_genome_size '${genome_size}' 28 --flye_genome_size '${genome_size}'
19 #if ($long_read_platform == "nanopore_corr"): 29 #if ($input_read_type_cond.pipeline_cond.long_read_platform == "nanopore_corr"):
20 --flye_nano_corr true --flye_nano_raw false 30 --flye_nano_corr true --flye_nano_raw false
21 #elif ($long_read_platform == "nanopore_hq"): 31 #elif ($input_read_type_cond.pipeline_cond.long_read_platform == "nanopore_hq"):
22 --flye_nano_hq true --flye_nano_raw false 32 --flye_nano_hq true --flye_nano_raw false
23 #elif ($long_read_platform == "pacbio_raw"): 33 #elif ($input_read_type_cond.pipeline_cond.long_read_platform == "pacbio_raw"):
24 --flye_pacbio_raw true --flye_nano_raw false 34 --flye_pacbio_raw true --flye_nano_raw false
25 #elif ($long_read_platform == "pacbio_corr"): 35 #elif ($input_read_type_cond.pipeline_cond.long_read_platform == "pacbio_corr"):
26 --flye_pacbio_corr true --flye_nano_raw false 36 --flye_pacbio_corr true --flye_nano_raw false
27 #elif ($long_read_platform == "pacbio_hifi"): 37 #elif ($input_read_type_cond.pipeline_cond.long_read_platform == "pacbio_hifi"):
28 --flye_pacbio_hifi true --flye_nano_raw false 38 --flye_pacbio_hifi true --flye_nano_raw false
29 #end if 39 #end if
30 #elif ($pipeline == "centriflaken_hy"): 40 #elif ($input_read_type_cond.pipeline_cond.pipeline == "centriflaken_hy"):
31 #if ($reads_lib_layout == "single"): 41 #if (str($input_read_cond.input_read_type) == "single_long"):
32 --fq_single_end true 42 --fq_single_end true
33 #elif ($reads_lib_layout == "paired"): 43 #elif (str($input_read_cond.input_read_type) == "paired"):
34 --fq_single_end false --fq2_suffix '${fq2_suffix}' 44 --fq_single_end false --fq2_suffix '${input_read_cond.fq2_suffix}'
35 #end if 45 #end if
36 #end if 46 #end if
37 --input \${pwd_path}/cpipes-input 47 --input \${pwd_path}/cpipes-input
38 --output \${pwd_path}/cpipes-output 48 --output \${pwd_path}/cpipes-output
39 --fq_suffix '${fq_suffix}' 49 --fq_suffix '${input_read_cond.fq_suffix}'
40 #if ($fq_filter_by_len != ""): 50 #if ($fq_filter_by_len != ""):
41 --fq_filter_by_len $fq_filter_by_len 51 --fq_filter_by_len $fq_filter_by_len
42 #end if 52 #end if
43 --fq_filename_delim '${fq_filename_delim}' 53 --fq_filename_delim '${fq_filename_delim}'
44 --fq_filename_delim_idx $fq_filename_delim_idx 54 --fq_filename_delim_idx $fq_filename_delim_idx
45 --centrifuge_extract_bug '${centrifuge_extract_bug}' 55 --centrifuge_extract_bug '${centrifuge_extract_bug}'
46 -profile kondagac; 56 -profile kondagac;
47 mv './cpipes-output/${pipeline}-multiqc/multiqc_report.html' './multiqc_report.html'; 57 mv './cpipes-output/${pipeline}-multiqc/multiqc_report.html' './multiqc_report.html' || exit 1;
48 mv './cpipes-output/${pipeline}-results/kraken2_extract_contigs' kraken2_extract_contigs; 58 mv './cpipes-output/${pipeline}-results/kraken2_extract_contigs' kraken2_extract_contigs || exit 1;
49 rm -rf ./cpipes-output; 59 rm -rf ./cpipes-output || exit 1;
50 rm -rf ./work 60 rm -rf ./work || exit 1
51 ]]></command> 61 ]]></command>
52 <inputs> 62 <inputs>
53 <param name="input" type="data_collection" collection_type="list" format="fastq,fastq.gz,fastqsanger.gz,fastqsanger" label="Input read collection" /> 63 <conditional name="input_read_type_cond">
54 <param name="pipeline" type="select" label="CPIPES Workflow name" 64 <param name="input_read_type" type="select" label="Select the read collection type">
55 help="centriflaken: for long reads (Nanopore or PacBio). centriflaken_hy: for short reads (paired or unpaired). Default: centriflaken"> 65 <option value="single_long" selected="true">Unpaired reads (i.e. Single-End short reads/Long reads)</option>
56 <option value="centriflaken" selected="true">centriflaken</option> 66 <option value="paired">Paired-End reads</option>
57 <option value="centriflaken_hy">centriflaken_hy</option> 67 </param>
58 </param> 68 <when value="single_long">
59 <param name="reads_lib_layout" type="select" label="Short Read Library Layout" 69 <param name="input" type="data_collection" collection_type="list" format="fastq,fastq.gz,fastqsanger.gz,fastqsanger"
60 help="Leave this option as Single-End for centriflaken. If the pipeline is centriflaken_hy (i.e for short reads), what is the library layout? Default: Single-End"> 70 label="Dataset list of unpaired short reads / long reads" />
61 <option value="single" selected="true">Single-End</option> 71 <conditional name="pipeline_cond">
62 <option value="paired">Paired-End</option> 72 <param name="pipeline" type="select" label="CPIPES Workflow name"
63 </param> 73 help="centriflaken: for long reads (Nanopore or PacBio). centriflaken_hy: for short reads (paired or unpaired). Default: centriflaken">
64 <param name="long_read_platform" type="select" label="Mention long read sequencing platform and type" 74 <option value="centriflaken" selected="true">centriflaken</option>
65 help="THIS OPTION IS IGNORED IF THE INPUT READS ARE SHORT READS."> 75 <option value="centriflaken_hy">centriflaken_hy</option>
66 <option value="nanopore_raw" selected="true">Nanopore raw reads, pre-Guppy5 (&lt;20% error)</option> 76 </param>
67 <option value="nanopore_corr">Nanopore reads that were corrected with other methods (&lt;3% error)</option> 77 <when value="centriflaken">
68 <option value="nanopore_hq">Nanopore high-quality reads, Guppy5+ SUP or Q20 (5% error)</option> 78 <param name="long_read_platform" type="select" label="Mention long read sequencing platform and type">
69 <option value="pacbio_raw">PacBio regular CLR reads (&lt;20% error)</option> 79 <option value="nanopore_raw" selected="true">Nanopore raw reads, pre-Guppy5 (&lt;20% error)</option>
70 <option value="pacbio_corr">PacBio reads that were corrected with other methods (&lt;3% error)</option> 80 <option value="nanopore_corr">Nanopore reads that were corrected with other methods (&lt;3% error)</option>
71 <option value="pacbio_hifi">PacBio HiFi reads (&lt;1% error)</option> 81 <option value="nanopore_hq">Nanopore high-quality reads, Guppy5+ SUP or Q20 (5% error)</option>
72 </param> 82 <option value="pacbio_raw">PacBio regular CLR reads (&lt;20% error)</option>
73 <param name="fq_suffix" value=".fastq.gz" type="text" label="Suffix of the R1 FASTQ or Unpaired FASTQ"/> 83 <option value="pacbio_corr">PacBio reads that were corrected with other methods (&lt;3% error)</option>
74 <param name="fq2_suffix" value="_R2_001.fastq.gz" type="text" label="Suffix of the R2 FASTQ" 84 <option value="pacbio_hifi">PacBio HiFi reads (&lt;1% error)</option>
75 help="THIS OPTION IS IGNORED IF THE INPUT READS ARE UNPAIRED/LONG READS."/> 85 </param>
86 </when>
87 <when value="centriflaken_hy">
88 <param name="long_read_platform" value="N/A" type="text" optional="true" label="Mention long read sequencing platform and type"
89 help="THIS OPTION IS IGNORED IF THE INPUT READS ARE SHORT READS."/>
90 </when>
91 </conditional>
92 <param name="fq_suffix" value=".fastq.gz" type="text" label="Suffix of the R1 FASTQ or Unpaired FASTQ"/>
93 </when>
94 <when value="paired">
95 <param name="input_pair" type="data_collection" collection_type="list:paired" format="fastq,fastq.gz,fastqsanger.gz,fastqsanger"
96 label="List of Dataset pairs" />
97 <param name="fq_suffix" value=".fastq.gz" type="text" label="Suffix of the R1 FASTQ or Unpaired FASTQ"/>
98 <param name="fq2_suffix" value="_R2_001.fastq.gz" type="text" label="Suffix of the R2 FASTQ"/>
99 </when>
100 </conditional>
76 <param name="fq_filter_by_len" optional="true" value="" type="integer" label="Enter minimum read length to retain before starting the analysis" 101 <param name="fq_filter_by_len" optional="true" value="" type="integer" label="Enter minimum read length to retain before starting the analysis"
77 help="Keep this option empty to use default values. Default for centriflaken (long reads) is 4000 bp and for centriflaken_hy (short reads) is 75 bp."/> 102 help="Keep this option empty to use default values. Default for centriflaken (long reads) is 4000 bp and for centriflaken_hy (short reads) is 75 bp."/>
78 <param name="fq_filename_delim" type="text" value="_" label="File name delimitor by which samples are grouped together (--fq_filename_delim)" 103 <param name="fq_filename_delim" type="text" value="_" label="File name delimitor by which samples are grouped together (--fq_filename_delim)"
79 help="This is the delimitor by which samples are grouped together to display in the final MultiQC report. For example, if your input data sets are mango_replicate1.fastq.gz, mango_replicate2.fastq.gz, orange_replicate1_maryland.fastq.gz, orange_replicate2_maryland.fastq.gz, then to create 2 samples mango and orange, the value for --fq_filename_delim would be _ (underscore) and the value for --fq_filename_delim_idx would be 1, since you want to group by the first word (i.e. mango or orange) after splitting the filename based on _ (underscore)."/> 104 help="This is the delimitor by which samples are grouped together to display in the final MultiQC report. For example, if your input data sets are mango_replicate1.fastq.gz, mango_replicate2.fastq.gz, orange_replicate1_maryland.fastq.gz, orange_replicate2_maryland.fastq.gz, then to create 2 samples mango and orange, the value for --fq_filename_delim would be _ (underscore) and the value for --fq_filename_delim_idx would be 1, since you want to group by the first word (i.e. mango or orange) after splitting the filename based on _ (underscore)."/>
80 <param name="fq_filename_delim_idx" type="integer" value="1" label="File name delimitor index (--fq_filename_delim_idx)" /> 105 <param name="fq_filename_delim_idx" type="integer" value="1" label="File name delimitor index (--fq_filename_delim_idx)" />