--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/get_orfs_or_cdss.xml	Mon Jun 05 02:43:41 2023 +0000
@@ -0,0 +1,154 @@
+<tool id="get_orfs_or_cdss" name="Get open reading frames (ORFs) or coding sequences (CDSs)" version="19.1.0.0">
+    <description>e.g. to get peptides from ESTs</description>
+    <macros>
+        <import>macros.xml</import>
+        <import>cpt-macros.xml</import>
+    </macros>
+    <expand macro="requirements">
+        <requirement type="package" version="2022.1.18">regex</requirement>
+    </expand>
+    <command interpreter="python" detect_errors="aggressive"><![CDATA[
+get_orfs_or_cdss.py '$input_file' -f '$input_file.ext' --table '$table' -t '$ftype' -e "closed" -m "all" --min_len '$min_len' --strand '$strand' --on '$out_nuc_file' --op '$out_prot_file' --ob '$out_bed_file' --og '$out_gff3_file' ]]>
+	</command>
+    <inputs>
+        <param name="input_file" type="data" format="fasta,fastq,sff" label="Sequence file (nucleotides)" help="FASTA, FASTQ, or SFF format."/>
+        <param name="table" type="select" label="Genetic code" help="Tables from the NCBI, these determine the start and stop codons">
+            <option value="1">1. Standard</option>
+            <option value="2">2. Vertebrate Mitochondrial</option>
+            <option value="3">3. Yeast Mitochondrial</option>
+            <option value="4">4. Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma</option>
+            <option value="5">5. Invertebrate Mitochondrial</option>
+            <option value="6">6. Ciliate Macronuclear and Dasycladacean</option>
+            <option value="9">9. Echinoderm Mitochondrial</option>
+            <option value="10">10. Euplotid Nuclear</option>
+            <option value="11">11. Bacterial</option>
+            <option value="12">12. Alternative Yeast Nuclear</option>
+            <option value="13">13. Ascidian Mitochondrial</option>
+            <option value="14">14. Flatworm Mitochondrial</option>
+            <option value="15">15. Blepharisma Macronuclear</option>
+            <option value="16">16. Chlorophycean Mitochondrial</option>
+            <option value="21">21. Trematode Mitochondrial</option>
+            <option value="22">22. Scenedesmus obliquus</option>
+            <option value="23">23. Thraustochytrium Mitochondrial</option>
+            <option value="24">24. Pterobranchia Mitochondrial</option>
+        </param>
+        <param name="ftype" type="select" value="True" label="Look for ORFs or CDSs">
+            <option value="ORF">Look for ORFs (check for stop codons only, ignore start codons)</option>
+            <option value="CDS">Look for CDSs (with start and stop codons)</option>
+        </param>
+        <param name="min_len" type="integer" size="5" value="30" label="Minimum length ORF/CDS (in amino acids, e.g. 30 aa = 90 bp plus any stop codon)"/>
+        <param name="strand" type="select" label="Strand to search" help="Use the forward only option if your sequence directionality is known (e.g. from poly-A tails, or strand specific RNA sequencing).">
+            <option value="both">Search both the forward and reverse strand</option>
+            <option value="forward">Only search the forward strand</option>
+            <option value="reverse">Only search the reverse strand</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="out_nuc_file" format="fasta" label="${ftype.value}s (nucleotides)"/>
+        <data name="out_prot_file" format="fasta" label="${ftype.value}s (amino acids)"/>
+        <data name="out_bed_file" format="bed6" label="${ftype.value}s (bed)"/>
+        <data name="out_gff3_file" format="gff3" label="${ftype.value}s (gff3)"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_file" value="Orf_T7In.fasta"/>
+            <param name="table" value="11"/>
+            <param name="ftype" value="ORF"/>
+            <param name="min_len" value="30"/>
+            <param name="strand" value="both"/>
+            <output name="out_nuc_file" file="Orf_T7Out_Nuc.fasta"/>
+            <output name="out_prot_file" file="Orf_T7Out_AA.fasta"/>
+            <output name="out_bed_file" file="Orf_T7Out_Bed.bed"/>
+            <output name="out_gff3_file" file="Orf_T7Out_Gff.gff3"/>
+        </test>
+        <test>
+            <param name="input_file" value="Orf_In2.fasta"/>
+            <param name="table" value="1"/>
+            <param name="ftype" value="CDS"/>
+            <param name="min_len" value="10"/>
+            <param name="strand" value="forward"/>
+            <output name="out_nuc_file" file="Orf_Out2T1_Nuc.fasta"/>
+            <output name="out_prot_file" file="Orf_Out2T1_AA.fasta"/>
+            <output name="out_bed_file" file="Orf_Out2T1_Bed.bed"/>
+            <output name="out_gff3_file" file="Orf_Out2T1_Gff.gff3"/>
+        </test>
+        <test>
+            <param name="input_file" value="Orf_In2.fasta"/>
+            <param name="table" value="11"/>
+            <param name="ftype" value="CDS"/>
+            <param name="min_len" value="10"/>
+            <param name="strand" value="forward"/>
+            <output name="out_nuc_file" file="Orf_Out2T11_Nuc.fasta"/>
+            <output name="out_prot_file" file="Orf_Out2T11_AA.fasta"/>
+            <output name="out_bed_file" file="Orf_Out2T11_Bed.bed"/>
+            <output name="out_gff3_file" file="Orf_Out2T11_Gff.gff3"/>
+        </test>
+    </tests>
+    <help>
+**What it does**
+
+Takes an input file of nucleotide sequences (typically FASTA, but also FASTQ
+and Standard Flowgram Format (SFF) are supported), and searches each sequence
+for open reading frames (ORFs) or potential coding sequences (CDSs) of the
+given minimum length. These are returned as FASTA files of nucleotides and
+protein sequences.
+
+You can choose to have all the ORFs/CDSs above the minimum length for each
+sequence (similar to the EMBOSS getorf tool), those with the longest length
+equal, or the first ORF/CDS with the longest length (in the special case
+where a sequence encodes two or more long ORFs/CDSs of the same length). The
+last option is a reasonable choice when the input sequences represent EST or
+mRNA sequences, where only one ORF/CDS is expected.
+
+Note that if no ORFs/CDSs in a sequence match the criteria, there will be no
+output for that sequence.
+
+Also note that the ORFs/CDSs are assigned modified identifiers to distinguish
+them from the original full length sequences, by appending a suffix.
+
+The start and stop codons are taken from the `NCBI Genetic Codes
+&lt;http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi&gt;`_.
+When searching for ORFs, the sequences will run from stop codon to stop
+codon, and any start codons are ignored. When searching for CDSs, the first
+potential start codon will be used, giving the longest possible CDS within
+each ORF, and thus the longest possible protein sequence. This is useful
+for things like BLAST or domain searching, but since this may not be the
+correct start codon, it may not be appropriate for signal peptide detection
+etc.
+
+**Example Usage**
+
+Given some EST sequences (Sanger capillary reads) assembled into unigenes,
+or a transcriptome assembly from some RNA-Seq, each of your nucleotide
+sequences should (barring sequencing, assembly errors, frame-shifts etc)
+encode one protein as a single ORF/CDS, which you wish to extract (and
+perhaps translate into amino acids).
+
+If your RNA-Seq data was strand specific, and assembled taking this into
+account, you should only search for ORFs/CDSs on the forward strand.
+
+**Citation**
+
+If you use this Galaxy tool in work leading to a scientific publication please
+cite the following paper:
+
+Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013).
+Galaxy tools and workflows for sequence analysis with applications
+in molecular plant pathology. PeerJ 1:e167
+http://dx.doi.org/10.7717/peerj.167
+
+This tool uses Biopython, so you may also wish to cite the Biopython
+application note (and Galaxy too of course):
+
+Cock et al (2009). Biopython: freely available Python tools for computational
+molecular biology and bioinformatics. Bioinformatics 25(11) 1422-3.
+http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878.
+
+This tool is available to install into other Galaxy Instances via the Galaxy
+Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss
+	</help>
+    <citations>
+        <citation type="doi">10.7717/peerj.167</citation>
+        <citation type="doi">10.1093/bioinformatics/btp163</citation>
+    </citations>
+</tool>