Mercurial > repos > kkonganti > cfsan_centriflaken

comparison cfsan_centriflaken.xml @ 4:34d3ef477de3

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"planemo upload"
author kkonganti
date Mon, 27 Jun 2022 20:04:11 -0400
parents 3154e7efa1c4
children 8ab30c459b53
comparison
equal deleted inserted replaced
3:3154e7efa1c4 4:34d3ef477de3
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 && 9 mkdir -p cpipes-input &&
10 #for $input_dataset in $input 10 #for $key in $input.keys()
11 ln -sf '$input_dataset' './cpipes-input/${input.element_identifier}'; 11 ln -sf '$input[$key]' './cpipes-input/$key';
12 #end for 12 #end for
13 pwd_path=\$(pwd) && 13 pwd_path=\$(pwd) &&
14 $__tool_directory__/0.2.1/cpipes 14 $__tool_directory__/0.2.1/cpipes
15 #if (reads.type == "long"): 15 #if ($pipeline == "centriflaken"):
16 --pipeline centriflaken 16 --pipeline $pipeline
17 #else: 17 --fq_single_end true
18 --pipeline centriflaken_hy 18 #elif ($pipeline.name == "centriflaken_hy"):
19 --pipeline $pipeline
20 #if ($reads_lib_layout == "single"):
21 --fq_single_end true
22 #else:
23 --fq_single_end false
24 #end if
19 #end if 25 #end if
20 --input \${pwd_path}/cpipes-input 26 --input \${pwd_path}/cpipes-input
21 --output \${pwd_path}/cpipes-output 27 --output \${pwd_path}/cpipes-output
22 #if ($reads.reads_lib.paired_end == "true"): 28 --fq_suffix '${fq_suffix}'
23 --fq_single_end false
24 --fq_suffix '${reads.reads_lib.fq_suffix}'
25 --fq2_suffix '${reads.reads_lib.fq2_suffix}'
26 #else:
27 --fq_single_end true
28 --fq_suffix '${reads.fq_suffix}'
29 #end if
30 --fq_filename_delim '${fq_filename_delim}' 29 --fq_filename_delim '${fq_filename_delim}'
31 --fq_filename_delim_idx $fq_filename_delim_idx 30 --fq_filename_delim_idx $fq_filename_delim_idx
32 --centrifuge_extract_bug '${centrifuge_extract_bug}' 31 --centrifuge_extract_bug '${centrifuge_extract_bug}'
33 --flye_genome_size '${genome_size}' 32 --flye_genome_size '${genome_size}'
34 -profile $profile 33 -profile $runtime_profile
35 ]]></command> 34 ]]></command>
36 <inputs> 35 <inputs>
37 <param name="input" type="data_collection" collection_type="list" format="fastq,fastq.gz,fastqsanger.gz,fastqsanger" label="Input read collection" /> 36 <param name="input" type="data_collection" collection_type="list" format="fastq,fastq.gz,fastqsanger.gz,fastqsanger" label="Input read collection" />
38 <conditional name="reads"> 37 <param name="pipeline" type="select" label="CPIPES Workflow name" value="centriflaken"
39 <param name="type" type="select" label="Sequencing Read Library Type" value="long"> 38 help="centriflaken: for short reads (paired or unpaired). centriflaken_hy: for long reads (Nanopore or PacBio). Default: centriflaken">
40 <option value="long">Long reads</option> 39 <option value="centriflaken">centriflaken</option>
41 <option value="short">Short reads</option> 40 <option value="centriflaken_hy">centriflaken_hy</option>
42 </param> 41 </param>
43 <when value="short"> 42 <param name="read_lib_layout" type="select" label="Short Read Library Layout" value="single"
44 <conditional name="reads_lib"> 43 help="If the pipeline is centriflaken_hy (i.e for short reads), what is the library layout? Default: Single-End">
45 <param name="paired_end" type="select" label="Sequencing Read Library Layout" value="false"> 44 <option value="single">Single-End</option>
46 <option value="false">Short read Single-End or Long reads</option> 45 <option value="paired">Paired-End</option>
47 <option value="true">Short read Paired-End</option> 46 </param>
48 </param> 47 <param name="fq_suffix" value=".fastq.gz" type="text" label="Suffix of the R1 FASTQ or Unpaired FASTQ"/>
49 <when value="true"> 48 <param name="fq2_suffix" value="_R2_001.fastq.gz" type="text" label="Suffix of the R2 FASTQ R2"/>
50 <param name="fq_suffix" value="_R1_001.fastq.gz" type="text" label="Suffix of the FASTQ R1 file of Paired-End reads."/>
51 <param name="fq2_suffix" value="_R2_001.fastq.gz" type="text" label="Suffix of the FASTQ R2 file of Paired-End reads."/>
52 </when>
53 <when value="false">
54 <param name="fq_suffix" value="_R1_001.fastq.gz" type="text" label="Suffix of the FASTQ R1 file of Paired-End reads."/>
55 </when>
56 </conditional>
57 </when>
58 <when value="long">
59 <param name="fq_suffix" value=".fastq.gz" type="text" label="Suffix of the FASTQ file of Long reads."/>
60 </when>
61 </conditional>
62 <param name="fq_filename_delim" type="text" value="_" label="File name delimitor by which samples are grouped together (--fq_filename_delim)" 49 <param name="fq_filename_delim" type="text" value="_" label="File name delimitor by which samples are grouped together (--fq_filename_delim)"
63 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_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)"/> 50 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_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)"/>
64 <param name="fq_filename_delim_idx" type="integer" value="1" label="File name delimitor index (--fq_filename_delimitor_idx)" /> 51 <param name="fq_filename_delim_idx" type="integer" value="1" label="File name delimitor index (--fq_filename_delimitor_idx)" />
65 <param name="centrifuge_extract_bug" type="text" value="Escherichia coli" label="Reads belonging to this taxa are extracted and a MAG is generated to allow for serotyping"/> 52 <param name="centrifuge_extract_bug" type="text" value="Escherichia coli" label="Reads belonging to this taxa are extracted and a MAG is generated to allow for serotyping"/>
66 <param name="genome_size" type="text" optional="true" value="5.5m" label="Estimated genome size" help="For example, 5m or 2.6g."> 53 <param name="genome_size" type="text" optional="true" value="5.5m" label="Estimated genome size" help="For example, 5m or 2.6g.">
80 </data> 67 </data>
81 </outputs> 68 </outputs>
82 <tests> 69 <tests>
83 <!--Test 01: long reads--> 70 <!--Test 01: long reads-->
84 <test expect_num_outputs="2"> 71 <test expect_num_outputs="2">
85 <param name="input" value="FAL11127.fastq.gz" > 72 <param name="input">
86 <collection type="list"> 73 <collection type="list">
87 <element name="file1" value="FAL11127.fastq.gz" /> 74 <element name="FAL11127.fastq.gz" value="FAL11127.fastq.gz" />
88 <element name="file2" value="FAL11341.fastq.gz" /> 75 <element name="FAL11341.fastq.gz" value="FAL11341.fastq.gz" />
89 <element name="file3" value="FAL11342.fastq.gz" /> 76 <element name="FAL11342.fastq.gz" value="FAL11342.fastq.gz" />
90 </collection> 77 </collection>
91 </param> 78 </param>
92 <param name="fq_suffix" value=".fastq.gz"/> 79 <param name="fq_suffix" value=".fastq.gz"/>
93 <output name="multiqc_report" file="multiqc_report.html" ftype="html" compare="sim_size"/> 80 <output name="multiqc_report" file="multiqc_report.html" ftype="html" compare="sim_size"/>
94 <output name="assembled_mags" file="FAL11127.assembly_filtered.contigs.fasta" ftype="fasta" compare="sim_size"/> 81 <output name="assembled_mags" file="FAL11127.assembly_filtered.contigs.fasta" ftype="fasta" compare="sim_size"/>