|
Commit message:
Uploaded |
|
added:
smap_selector.xml |
| b |
| diff -r 000000000000 -r 10a610301cf7 smap_selector.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/smap_selector.xml Mon Apr 25 12:21:35 2022 +0000 |
| [ |
| @@ -0,0 +1,55 @@ +<tool id="smap_selector" name="SMAP-selector" version="0.1.0" python_template_version="3.5"> + <requirements> + <!--<requirement type="package">smap-design</requirement>--> + <requirement type="package">biopython</requirement> + <requirement type="package">gffutils</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + ln -s $fasta_file species_fasta.fa; + ln -s $gff_file species.gff3; + ln -s $gene_families_file families_file.txt; + #if $interest_input_selector.interest_input == "genes": + ln -s $interest_input_selector.genes_file genes_file.txt; + #else + ln -s $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.fa ./families_file.txt $species --region $region + #if $interest_input_selector.interest_input == "genes": + --genes genes_file.txt + #else + --hom_groups hom_groups_file.txt + #end if + ; + rm species.gff3; + ]]></command> + <inputs> + <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"/> + </inputs> + <outputs> + <data format="fasta" name="fasta_outputs" label="SMAP-Selector FASTA outputs"> + <discover_datasets pattern="(?P<designation>.+)\.fasta" ext="fasta" format="fasta" visible="true" assign_primary_output="true"/> + </data> + <data format="gff" name="gff_outputs" label="SMAP-Selector GFF outputs"> + <discover_datasets pattern="(?P<designation>.+)\.gff" ext="gff" visible="true" format="gff" assign_primary_output="true"/> + </data> + </outputs> + <help><![CDATA[ + TODO: Fill in help. + ]]></help> +</tool> |