Mercurial > repos > ieguinoa > smap_selector
comparison smap_selector.xml @ 0:10a610301cf7 draft default tip
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| author | ieguinoa |
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| date | Mon, 25 Apr 2022 12:21:35 +0000 |
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| -1:000000000000 | 0:10a610301cf7 |
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| 1 <tool id="smap_selector" name="SMAP-selector" version="0.1.0" python_template_version="3.5"> | |
| 2 <requirements> | |
| 3 <!--<requirement type="package">smap-design</requirement>--> | |
| 4 <requirement type="package">biopython</requirement> | |
| 5 <requirement type="package">gffutils</requirement> | |
| 6 </requirements> | |
| 7 <command detect_errors="exit_code"><![CDATA[ | |
| 8 ln -s $fasta_file species_fasta.fa; | |
| 9 ln -s $gff_file species.gff3; | |
| 10 ln -s $gene_families_file families_file.txt; | |
| 11 #if $interest_input_selector.interest_input == "genes": | |
| 12 ln -s $interest_input_selector.genes_file genes_file.txt; | |
| 13 #else | |
| 14 ln -s $interest_input_selector.homology_groups_file hom_groups_file.txt; | |
| 15 #end if | |
| 16 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 | |
| 17 #if $interest_input_selector.interest_input == "genes": | |
| 18 --genes genes_file.txt | |
| 19 #else | |
| 20 --hom_groups hom_groups_file.txt | |
| 21 #end if | |
| 22 ; | |
| 23 rm species.gff3; | |
| 24 ]]></command> | |
| 25 <inputs> | |
| 26 <param name="species" type="text" label="Species, corresponding with species indicated in the gene family info file"/> | |
| 27 <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"/> | |
| 28 <param name="fasta_file" type="data" format="fasta" label="FASTA file containing the genomic sequence of the species"/> | |
| 29 <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"/> | |
| 30 <conditional name="interest_input_selector"> | |
| 31 <param name="interest_input" type="select"> | |
| 32 <option value="genes">list with genes of interest</option> | |
| 33 <option value="homology_groups">list with homology groups of interest</option> | |
| 34 </param> | |
| 35 <when value="genes"> | |
| 36 <param name="genes_file" type="data" format="txt" label="Genes file"/> | |
| 37 </when> | |
| 38 <when value="homology_groups"> | |
| 39 <param name="homology_groups_file" type="data" format="txt" label="Homology groups file"/> | |
| 40 </when> | |
| 41 </conditional> | |
| 42 <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"/> | |
| 43 </inputs> | |
| 44 <outputs> | |
| 45 <data format="fasta" name="fasta_outputs" label="SMAP-Selector FASTA outputs"> | |
| 46 <discover_datasets pattern="(?P<designation>.+)\.fasta" ext="fasta" format="fasta" visible="true" assign_primary_output="true"/> | |
| 47 </data> | |
| 48 <data format="gff" name="gff_outputs" label="SMAP-Selector GFF outputs"> | |
| 49 <discover_datasets pattern="(?P<designation>.+)\.gff" ext="gff" visible="true" format="gff" assign_primary_output="true"/> | |
| 50 </data> | |
| 51 </outputs> | |
| 52 <help><![CDATA[ | |
| 53 TODO: Fill in help. | |
| 54 ]]></help> | |
| 55 </tool> |