Mercurial > repos > frogs > frogs_core
diff processing_short_reads_macros.xml @ 0:cd7675c5b15a draft
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 78ca62b54aee22893d278d9c3d495527be405f8a
| author | frogs |
|---|---|
| date | Wed, 04 Feb 2026 13:15:55 +0000 |
| parents | |
| children | 76ff9af5c0a3 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/processing_short_reads_macros.xml Wed Feb 04 13:15:55 2026 +0000 @@ -0,0 +1,286 @@ +<?xml version="1.0"?> +<macros> + <token name="@PROCESSING_SHORT_READS_CMD_LINE@"> + #set $sep = ' ' + + reads_processing.py illumina + @CPUS@ + + ## PAIRED END READS + #if $fastq_input.input_type == "paired" + ## INPUTS + #if $fastq_input.input_files.file_type == "archive" + --input-archive '${fastq_input.input_files.input_archive}' + #else + --samples-names + #for $current in $fastq_input.input_files.samples + $sep'${current.samples_names.strip()}' + #end for + --input-R1 + #for $current in $fastq_input.input_files.samples + $sep'${current.input_R1}' + #end for + --input-R2 + #for $current in $fastq_input.input_files.samples + $sep'${current.input_R2}' + #end for + #end if + + ## MERGING PARAMETERS + --R1-size $fastq_input.R1_size + --R2-size $fastq_input.R2_size + --mismatch-rate $fastq_input.mismatch_rate + --merge-software $fastq_input.merge_software_type.merge_software + #if $fastq_input.merge_software_type.merge_software == "flash" + --expected-amplicon-size $fastq_input.merge_software_type.expected_amplicon_size + #end if + #if $fastq_input.keep_unmerged + --keep-unmerged + #end if + + ## SINGLE END READS + #elif $fastq_input.input_type == "single" + --already-contiged + ## INPUTS + #if $fastq_input.input_files.file_type == "archive" + --input-archive '${fastq_input.input_files.input_archive}' + #else + --samples-names + #for $current in $fastq_input.input_files.samples + $sep'${current.samples_names.strip()}' + #end for + --input-R1 + #for $current in $fastq_input.input_files.samples + $sep'${current.input_R1}' + #end for + #end if + #end if + + ## AMPLICON PARAMETERS + --min-amplicon-size $min_amplicon_size + --max-amplicon-size $max_amplicon_size + + ## PRIMERS + #if $is_primer_in_seq.primer_choice == "true" + --five-prim-primer '$is_primer_in_seq.five_prim_primer' + --three-prim-primer '$is_primer_in_seq.three_prim_primer' + #else + --without-primers + #end if + + ## PROCESS TYPE + #if $process_type.process == "Preprocess only" + --process preprocess-only + #elif $process_type.process == "Clustering Swarm" + --process swarm + --distance $process_type.distance + #if $process_type.cluster_improvements.clustering_options != "no-refinement" + $process_type.cluster_improvements.clustering_options + #end if + #elif $process_type.process == "Denoising DADA2" + --process dada2 + --sample-inference $process_type.sample_inference + #end if + + ## OUTPUTS + --output-biom $output_biom + --output-fasta $output_fasta + --html $html + #if $process_type.process == "Clustering Swarm" + --output-compo $output_cluster_compo + #end if + </token> + + <xml name="processing_short_reads_inputs"> + <!-- Files --> + <conditional name="fastq_input"> + <param name="input_type" type="select" display="radio" label="Paired-end or Single-end reads" help=""> + <option value="paired" selected="true">Paired-end reads</option> + <option value="single">Single-end reads or Paired reads that have already been merged.</option> + </param> + <when value="paired"> + <conditional name="input_files"> + <param name="file_type" type="select" label="Input" help="Sample files can be provided either as a single TAR archive or as separate files per sample (one or two files each)."> + <option value="archive" selected="true">TAR Archive</option> + <option value="files_per_sample" >Files per sample</option> + </param> + <when value="archive"> + <param argument="--input-archive" type="data" format="tar,tgz" label="Archive file (.tar.gz)" help="The TAR file containing the short R1 R2 read pairs (.fastq.gz) for each sample. Each sample should ideally have its R1 and R2 reads named consistently (e.g., sampleX_R1.fastq.gz and sampleX_R2.fastq.gz). Supported sequencers: Illumina, Aviti and IonTorrent." /> + </when> + <when value="files_per_sample"> + <repeat name="samples" title="Samples" default="1" min="1"> + <param argument="--samples-names" type="text" label="Sample name" help="The sample name."> + <expand macro="restricted_sanitizer_validator"/> + </param> + <param argument="--input-R1" type="data" format="fastq" label="R1 reads (.fastq.gz)" help="R1 reads fastq file. Supported sequencers: Illumina and Aviti." /> + <param argument="--input-R2" type="data" format="fastq" label="R2 reads (.fastq.gz)" help="R2 reads fastq file. Supported sequencers: Illumina and Aviti." /> + </repeat> + </when> + </conditional> + <!-- Paired parameters --> + <param argument="--R1-size" type="integer" label="R1 read length" help="Please provide the maximum length of the R1 reads." /> + <param argument="--R2-size" type="integer" label="R2 read length" help="Please provide the maximum length of the R2 reads." /> + <param argument="--mismatch-rate" type="float" value="0.1" label="Mismatch rate (used for R1-R2 merging)" help="Maximum allowed mismatch rate in the overlap region between R1 and R2 reads."/> + <conditional name="merge_software_type"> + <param argument="--merge-software" type="select" display="radio" label="Paired-end merging tool" help="Select the tool used to merge paired-end reads"> + <!-- <option value="pear" >Pear (only for non commercial, non military use. See Pear licence)</option> --> + <option value="vsearch" >Vsearch</option> + <option value="flash">Flash</option> + </param> + <when value="vsearch"/> + <when value="flash"> + <param argument="--expected-amplicon-size" type="integer" min="0" label="Expected amplicon length" help="Specify the maximum expected amplicon length (covers ~90% of amplicons)" /> + </when> + </conditional> + <param argument="keep_unmerged" type="boolean" truevalue="--keep-unmerged" falsevalue="" checked="false" label="Would you like to keep unmerged reads?" help="No = unmerged reads will be removed; Yes = unmerged reads will be artificially combined with 100 N to allow further processing." /> + </when> + <when value="single"> + <conditional name="input_files"> + <param name="file_type" type="select" label="Input" help="Sample files can be provided either as a single TAR archive or as separate files per sample (one or two files each)."> + <option value="archive" selected="true">TAR Archive</option> + <option value="files_per_sample" >Files per sample</option> + </param> + <when value="archive"> + <param argument="--input-archive" type="data" format="tar,tgz" label="Archive file (tar format)" help="The TAR file containing the short single-end reads or merged paired-end reads (.fastq.gz) for each sample. Supported sequencers: Illumina and Aviti." /> + </when> + <when value="files_per_sample"> + <repeat name="samples" title="Samples" default="1" min="1"> + <param argument="--samples-names" type="text" label="Name" help="The sample name."> + <expand macro="restricted_sanitizer_validator"/> + </param> + <param argument="--input-R1" type="data" format="fastq" label="The short single-end reads or merged paired-end reads (.fastq.gz)" help="Single-end short reads or merge paired-end reads (.fastq.gz). Supported sequencers: Illumina and Aviti." /> + </repeat> + </when> + </conditional> + </when> + </conditional> + + <!-- Amplicons Parameters--> + <param argument="--min-amplicon-size" type="integer" value="" label="Minimum amplicon length" help="The minimum length of the amplicons (including primers). For paired-end reads, substract 10 bases to account for the minimum overlap between R1 and R2 reads."/> + <param argument="--max-amplicon-size" type="integer" value="" label="Maximum amplicon length" help="The maximum length of the amplicons (including primers). For paired-end reads, substract 10 bases to account for the minimum overlap between R1 and R2 reads."/> + + <!-- Primers --> + <conditional name="is_primer_in_seq"> + <param name="primer_choice" type="select" display="radio" label="Do the sequences include PCR primers?" help="Indicate whether the sequences still include PCR primers. Select “Yes” if primers are present, “No” if they have already been removed." > + <option value="true" selected="true">Yes</option> + <option value="false">No</option> + </param> + <when value="true"> + <param argument="--five-prim-primer" type="text" label="5' primer" help="Enter the 5' primer sequence. Wildcards are allowed. The sequence must be provided in 5' → 3' orientation."> + <expand macro="only_letter_sanitizer_validator"/> + </param> + <param argument="--three-prim-primer" type="text" label="3' primer" help="Enter the 3' primer sequence. Wildcards are allowed. The sequence must be provided in 5' → 3' orientation."> + <expand macro="only_letter_sanitizer_validator"/> + </param> + </when> + <when value="false"/> + </conditional> + + <!-- Preprocessing only, clustering or denoising --> + <conditional name="process_type"> + <param argument="--process" type="select" display="radio" label="Process type" help="Select the type of process to run"> + <option value="Preprocess only">Preprocessing only</option> + <option value="Clustering Swarm" selected="true">Preprocessing and clustering with Swarm</option> + <option value="Denoising DADA2">Preprocessing and denoising with DADA2</option> + </param> + <when value="Preprocess only"/> + <when value="Clustering Swarm"> + <param argument="--distance" type="integer" min="1" value="1" optional="false" label="Swarm distance threshold" help="Distance threshold used by Swarm for clustering."/> + <conditional name="cluster_improvements"> + <param name="clustering_options" type="select" display="radio" label="Clustering refinement" help="(i) With --distance = 1, use the Swarm --fastidious option to refine clustering (recommended since FROGS 3.2). (ii) With --distance > 1, enable pre-clustering to reduce redundancy before final clustering step. (iii) Select this option to apply neither refinement nor pre-clustering."> + <option value="--fastidious" selected="true">With --distance = 1, refine clusters with Swarm --fastidious option (recommended since FROGS 3.2)</option> + <option value="--pre-clustering">With --distance > 1, perform a pre-clustering step with FROGS --pre-clustering option</option> + <option value="no-refinement">No clustering refinement</option> + </param> + <when value="--fastidious"/> + <when value="--pre-clustering"/> + <when value="no-refinement"/> + </conditional> + </when> + <when value="Denoising DADA2"> + <param argument="--sample-inference" type="select" display="radio" label="DADA2 pooling method" help="Choose how to consider sample prior to sample inference"> + <option value="pseudo-pooling" selected="true">Pseudo pooling, samples will be pseudo-pooled prior to sample inference.</option> + <option value="independent">Independent, sample inference will be performed on each sample individually.</option> + <option value="pooling">Full pooling, all samples will be pooled together prior to sample inference.</option> + </param> + </when> + </conditional> + </xml> + + <!-- Test swarm --> + <xml name="swarm_processing_short_reads_test_input"> + <!-- Files --> + <conditional name="fastq_input"> + <param name="input_type" value="paired" /> + <conditional name="input_files"> + <param name="file_type" value="archive" /> + <param name="input_archive" ftype="tgz" value="input/test_dataset.tar.gz" /> + </conditional> + <!-- Paired parameters --> + <param name="R1_size" value="266" /> + <param name="R2_size" value="267"/> + <param name="mismatch_rate" value="0.15"/> + </conditional> + + <!-- Amplicons Parameters--> + <param name="min_amplicon_size" value="44"/> + <param name="max_amplicon_size" value="490"/> + + <!-- Primers --> + <conditional name="is_primer_in_seq"> + <param name="primer_choice" value="true" /> + <param name="five_prim_primer" value="GGCGVACGGGTGAGTAA" /> + <param name="three_prim_primer" value="GTGCCAGCNGCNGCGG"/> + </conditional> + + <!-- Preprocessing only, clustering or denoising --> + <conditional name="process_type"> + <param name="process" value="Clustering Swarm" /> + </conditional> + </xml> + + <xml name="swarm_processing_short_reads_test_output"> + <output name="output_biom" file="references/01-reads_processing-swarm-vsearch.biom" compare="sim_size" delta="0" /> + <output name="output_fasta" file="references/01-reads_processing-swarm-vsearch.fasta" compare="diff" lines_diff="0" /> + <output name="output_cluster_compo" file="references/01-reads_processing-swarm-vsearch_compo.tsv" compare="diff" lines_diff="0" /> + <output name="html" file="references/01-reads_processing-swarm-vsearch.html" compare="diff" lines_diff="0" /> + </xml> + + <!-- Test dada2 --> + <xml name="dada2_processing_short_reads_test_input"> + <!-- Files --> + <conditional name="fastq_input"> + <param name="input_type" value="paired" /> + <conditional name="input_files"> + <param name="file_type" value="archive" /> + <param name="input_archive" ftype="tgz" value="input/verysmallITS.tar.gz" /> + </conditional> + <!-- Paired parameters --> + <param name="R1_size" value="300" /> + <param name="R2_size" value="300"/> + <param name="keep_unmerged" value="true" /> + </conditional> + + <!-- Amplicons Parameters--> + <param name="min_amplicon_size" value="50"/> + <param name="max_amplicon_size" value="1000"/> + + <!-- Primers --> + <conditional name="is_primer_in_seq"> + <param name="primer_choice" value="true" /> + <param name="five_prim_primer" value="TAGACTCGTCAHCGATGAAGAACGYRG" /> + <param name="three_prim_primer" value="GCATATCAATAAGCGSAGGAA"/> + </conditional> + + <!-- Preprocessing only, clustering or denoising --> + <conditional name="process_type"> + <param name="process" value="Denoising DADA2" /> + </conditional> + </xml> + + <xml name="dada2_processing_short_reads_test_output"> + <output name="output_biom" file="references/01-reads_processing-dada2-clusters.biom" compare="sim_size" delta="0" /> + <output name="output_fasta" file="references/01-reads_processing-dada2-clusters.fasta" compare="diff" lines_diff="0" /> + <output name="html" file="references/01-reads_processing-dada2.html" compare="diff" lines_diff="0" /> + </xml> +</macros>