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