diff tools/get_orfs_or_cdss/get_orfs_or_cdss.xml @ 5:5208c15805ec draft

Uploaded v0.0.5 dependant on Biopython 1.62

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/get_orfs_or_cdss/get_orfs_or_cdss.xml	Mon Oct 28 05:19:38 2013 -0400
@@ -0,0 +1,171 @@
+<tool id="get_orfs_or_cdss" name="Get open reading frames (ORFs) or coding sequences (CDSs)" version="0.0.5">
+    <description>e.g. to get peptides from ESTs</description>
+    <requirements>
+        <requirement type="package" version="1.62">biopython</requirement>
+        <requirement type="python-module">Bio</requirement>
+    </requirements>
+    <version_command interpreter="python">get_orfs_or_cdss.py --version</version_command>
+    <command interpreter="python">
+get_orfs_or_cdss.py $input_file $input_file.ext $table $ftype $ends $mode $min_len $strand $out_nuc_file $out_prot_file
+    </command>
+    <stdio>
+        <!-- Anything other than zero is an error -->
+        <exit_code range="1:" />
+        <exit_code range=":-1" />
+    </stdio>
+    <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>
+        </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="ends" type="select" value="open" label="Sequence end treatment">
+            <option value="open">Open ended (will allow missing start/stop codons at the ends)</option>
+            <option value="closed">Complete (will check for start/stop codons at the ends)</option>
+            <!-- TODO? Circular, for using this on finished bacteria etc -->
+        </param>
+        <param name="mode" type="select" label="Selection criteria" help="Suppose a sequence has ORFs/CDSs of lengths 100, 102 and 102 -- which should be taken? These options would return 3, 2 or 1 ORF.">
+            <option value="all">All ORFs/CDSs from each sequence</option>
+            <option value="top">All ORFs/CDSs from each sequence with the maximum length</option>
+            <option value="one">First ORF/CDS from each sequence with the maximum length</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)" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_file" value="get_orf_input.fasta" />
+            <param name="table" value="1" />
+            <param name="ftype" value="CDS" />
+            <param name="ends" value="open" />
+            <param name="mode" value="all" />
+            <param name="min_len" value="10" />
+            <param name="strand" value="forward" />
+            <output name="out_nuc_file" file="get_orf_input.t1_nuc_out.fasta" />
+            <output name="out_prot_file" file="get_orf_input.t1_prot_out.fasta" />
+        </test>
+        <test>
+            <param name="input_file" value="get_orf_input.fasta" />
+            <param name="table" value="11" />
+            <param name="ftype" value="CDS" />
+            <param name="ends" value="closed" />
+            <param name="mode" value="all" />
+            <param name="min_len" value="10" />
+            <param name="strand" value="forward" />
+            <output name="out_nuc_file" file="get_orf_input.t11_nuc_out.fasta" />
+            <output    name="out_prot_file" file="get_orf_input.t11_prot_out.fasta" />
+        </test>
+        <test>
+            <param name="input_file" value="get_orf_input.fasta" />
+            <param name="table" value="11" />
+            <param name="ftype" value="CDS" />
+            <param name="ends" value="open" />
+            <param name="mode" value="all" />
+            <param name="min_len" value="10" />
+            <param name="strand" value="forward" />
+            <output name="out_nuc_file" file="get_orf_input.t11_open_nuc_out.fasta" />
+            <output name="out_prot_file" file="get_orf_input.t11_open_prot_out.fasta" />
+        </test>
+        <test>
+            <param name="input_file" value="Ssuis.fasta" />
+            <param name="table" value="11" />
+            <param name="ftype" value="ORF" />
+            <param name="ends" value="open" />
+            <param name="mode" value="all" />
+            <param name="min_len" value="100" />
+            <param name="strand" value="both" />
+            <output name="out_nuc_file" file="get_orf_input.Suis_ORF.nuc.fasta" />
+            <output name="out_prot_file" file="get_orf_input.Suis_ORF.prot.fasta" />
+        </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 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 RNS-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>
+</tool>