Mercurial > repos > ieguinoa > smap_design
changeset 0:fe9f46c3bd28 draft default tip
Uploaded
author | ieguinoa |
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date | Mon, 25 Apr 2022 12:08:35 +0000 (2022-04-25) |
parents | |
children | |
files | smap_design.xml |
diffstat | 1 files changed, 155 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/smap_design.xml Mon Apr 25 12:08:35 2022 +0000 @@ -0,0 +1,155 @@ +<tool id="smap_design" name="SMAP-design" version="0.1.0" python_template_version="3.5"> + <requirements> + <!--<requirement type="package">smap-design</requirement>--> + <requirement type="package">primer3-py</requirement> + <requirement type="package">pandas</requirement> + <requirement type="package">biopython</requirement> + <requirement type="package">matplotlib</requirement> + <requirement type="package">gffutils</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + #if $input_source_conditional.input_source == "pregenerated_inputs": + design_input_fasta=$input_source_conditional.input_fasta; + design_input_gff3=$input_source_conditional.input_gff3; + #else: + ln -s $input_source_conditional.fasta_file species_fasta.fasta; + ln -s $input_source_conditional.gff_file species.gff3; + ln -s $input_source_conditional.gene_families_file families_file.txt; + #if $input_source_conditional.interest_input_selector.interest_input == "genes": + ln -s $input_source_conditional.interest_input_selector.genes_file genes_file.txt; + #else + ln -s $input_source_conditional.interest_input_selector.homology_groups_file hom_groups_file.txt; + #end if + python3 $__tool_directory__/Get_fasta_and_gff_for_selected_hom_groups_extended_flanking_region.py ./species.gff3 ./species_fasta.fasta ./families_file.txt $input_source_conditional.species --region $input_source_conditional.region + #if $input_source_conditional.interest_input_selector.interest_input == "genes": + --genes genes_file.txt + #else + --hom_groups hom_groups_file.txt + #end if + && + ###### need to set the design_input_fasta and design_input_gff3 vars + design_input_fasta=`ls *_bp.fasta` && + design_input_gff3=`ls *_bp.gff`; + #end if + python3 $__tool_directory__/smap_design/SMAPdesign.py + --output 'OUTPUT' + --minimumAmpliconLength $min_amplicon_length + --maximumAmpliconLength $max_amplicon_length + --numbergRNAs $number_grnas + --numberAmplicons $number_amplicons + #if $print_summary: + --summary + #end if + $bordersOnly + --distance $distance + $print_summary + $allAmplicons + --gRNAfile $gRNAfile + --gRNAsource $gRNAsource.value + #if $selectGenes: + --selectGenes $selectGenes + #end if + --gRNAoverlap $gRNAoverlap + --generateAmplicons $generateAmplicons + --threshold $threshold + --borderLength $borderLength + $ampliconLabel + --targetRegion5 $targetRegion5 + --targetRegion3 $targetRegion3 + #if $targetSpecificRegion: + --targetSpecificRegion $targetSpecificRegion + #end if + $misPrimingAllowed + $restrictPrimerDesign + --promoter '$promoter' + --scaffold '$scaffold' + \$design_input_fasta \$design_input_gff3; + mv OUTPUT.gff3 $gff_output; + mv OUTPUT_primers.tsv $primers_output; + mv OUTPUT_gRNAs.tsv $gRNA_per_gene; + #if $print_summary: + mv OUTPUT_SMAPdesign_summary.tsv $summary; + #end if + #if $bordersOnly: + mv OUTPUT_SMAPdesign_borders.gff3 $borders_output; + #end if + ; + ]]></command> + <inputs> + <conditional name="input_source_conditional"> + <param name="input_source" type="select"> + <option value="smap_selector">Generate the target gene using SMAP selector</option> + <option value="pregenerated_inputs">Use pregenerated inputs</option> + </param> + <when value="smap_selector"> + <param name="species" type="text" label="Species, corresponding with species indicated in the gene family info file"/> + <param name="gene_families_file" type="data" format="tsv,tabular" label="gene family information file (tab-delimited) for the (coding) genes, separated per gene family type"/> + <param name="fasta_file" type="data" format="fasta" label="FASTA file containing the genomic sequence of the species"/> + <param name="gff_file" type="data" format="gff,gff3" label="gff3 file (tab-delimited) of the species containing gene, CDS, and exon features with positions relative to the fasta file"/> + <conditional name="interest_input_selector"> + <param name="interest_input" type="select"> + <option value="genes">list with genes of interest</option> + <option value="homology_groups">list with homology groups of interest</option> + </param> + <when value="genes"> + <param name="genes_file" type="data" format="txt" label="Genes file"/> + </when> + <when value="homology_groups"> + <param name="homology_groups_file" type="data" format="txt" label="Homology groups file"/> + </when> + </conditional> + <param argument="--region" type="integer" value="0" label="Region to extend the FASTA sequence of the genes of interest on both sides with the given number of basepairs or with the maximum possible" help="default: 0"/> + + </when> + <when value="pregenerated_inputs"> + <param name="input_fasta" type="data" optional="false" label="FASTA file containing all genes to screen" format="fasta"/> + <param name="input_gff3" type="data" optional="false" label="GFF3 File" help="GFF3 file with at least the CDS feature with positions relative to the FASTA file " format="gff3,gff"/> + </when> + </conditional> + + <param name="number_amplicons" type="integer" value="2" label="The maximum number of non-overlapping amplicons in the output (default = 2)" help="sets the seed for the random number generator"/> + <param name="number_grnas" type="integer" value="2" label="Maximum number of gRNAs to retain per amplicon (default = 2)" help=""/> + <param name="min_amplicon_length" type="integer" value="120" label="The minimum length of the amplicons in base pairs (default = 120)" help=""/> + <param name="max_amplicon_length" type="integer" value="150" label="The maximum length of the amplicons in base pairs (default = 120)" help=""/> + <param name="distance" type="integer" optional="true" value="15" label="Minimum number of bases between primer and gRNA (default = 15)" help=""/> + <param name="print_summary" type="boolean" truevalue="--summary" falsevalue="" label="Write summary file and plot of the output"/> + <param argument='--allAmplicons' type="boolean" truevalue="--allAmplicons" falsevalue="" label='Return all amplicons with their respective gRNAs per gene (extra file)'/> + <param name='bordersOnly' type="boolean" truevalue="-bo" falsevalue="" checked="false" label='Write additional GFF file with only borders (for SMAP)'/> + <param argument='--gRNAfile' type="data" format="tsv,tabular" label='CRISPOR, FlashFry or other gRNA design program output file' help="The CRISPOR and Flashfry file must contain a header and 12 columns. Check the manual for specifics"/> + <param name='gRNAsource' type="select" label="What is the source of the gRNA file?"> + <option value="crispor">CRISPOR</option> + <option value="flashfry">FlashFry</option> + <option value="other">Other</option> + </param> + <param argument='--selectGenes' type="data" optional="true" format="txt" label="OPTIONAL List of genes (one per line) to which amplicons and guides must be designed" help='The other genes in the fasta file will be used to check for specificity only. default: if no list is used then, for all genes in the fasta the design is done'/> + <param argument='--gRNAoverlap' label='The minimum number of bases between the start of two gRNAs' type="integer" value="5"/> + <param argument='--generateAmplicons' label="Number of amplicons to generate per gene by Primer3." help="To generate 50 amplicons per 1000 bases per gene enter -1" value="150" type="integer"/> + <param argument='--threshold' label='Minimum gRNA MIT score allowed (default = 80)' value="80" type="integer"/> + <param argument='--borderLength' value="10" type="integer" label='The length of the borders (for SMAP)'/> + <param argument='--ampliconLabel' type="boolean" truevalue="--ampliconLabel" falsevalue="" checked="false" label='Number the amplicons from left to right instead of from best to worst'/> + <param argument='--gRNAlabel' type="boolean" truevalue="--gRNAlabel" falsevalue="" checked="false" label='Number the gRNAs from left to right instead of from best to worst (based on specificity scores)'/> + <param argument='--targetRegion5' label="The fraction of the coding sequencing that cannot be targeted at the 5' end as indicated by a float between 0 and 1 (default = 0.2)" value="0.2" type="float"/> + <param argument='--targetRegion3' label="The fraction of the coding sequencing that cannot be targeted at the 3' end as indicated by a float between 0 and 1 (default = 0.2)" value="0.2" type="float"/> + <param argument='--targetSpecificRegion' label='Only target a specific region in the gene indicated by the feature name in the GFF file' value="" type="text"/> + <param argument='--misPrimingAllowed' type="boolean" truevalue="--misPrimingAllowed" falsevalue="" label='Do not check for mispriming in the gene set when designing primers' help='By default Primer3 will not allow primers that can prime at other genes in the gene set' checked="false"/> + <param argument='--restrictPrimerDesign' type="boolean" truevalue="--restrictPrimerDesign" falsevalue="" label='Restrict primer design in large introns' help="Increases the speed of amplicon design. This should have no impact on the output" checked="false"/> + <param argument="--promoter" type="text" label='Give the last 6 bases of the promoter that will be used to express the gRNA. This will be taken into account when checking for BsaI or BbsI sites in the gRNA' help="default: U6 promoter = GTAGTG)" value="GTAGTG" /> + + <param argument="--scaffold" type="text" label="Give the first 6 bases of the scaffold that will be used. This will be taken into account when checking for BsaI or BbsI sites in the gRNA" value="GTTTTA"/> + + </inputs> + <outputs> + <data format="gff3" name="gff_output" label="GFF3 design" /> + <data format="tsv" name="primers_output" label="Primers sequences per gene" /> + <data format="tsv" name="gRNA_per_gene" label="gRNA sequences per gene" /> + <data format="tsv" name="summary" label="Summary"> + <filter>print_summary == "--summary"</filter> + </data> + <data format="gff3" name="borders_output" label="Borders"> + <filter>bordersOnly == "-bo"</filter> + </data> + </outputs> + <help><![CDATA[ + TODO: Fill in help. + ]]></help> +</tool>