Mercurial > repos > peterjc > get_orfs_or_cdss
diff tools/get_orfs_or_cdss/get_orfs_or_cdss.xml @ 7:705a2e2df7fb draft
v0.1.1 fix typo; v0.1.0 BED output (Eric Rasche), NCBI genetic code 24; v0.0.7 embeds citation
author | peterjc |
---|---|
date | Thu, 30 Jul 2015 12:35:31 -0400 |
parents | 5208c15805ec |
children | 09a8be9247ca |
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--- a/tools/get_orfs_or_cdss/get_orfs_or_cdss.xml Thu Nov 21 10:47:53 2013 -0500 +++ b/tools/get_orfs_or_cdss/get_orfs_or_cdss.xml Thu Jul 30 12:35:31 2015 -0400 @@ -1,18 +1,18 @@ -<tool id="get_orfs_or_cdss" name="Get open reading frames (ORFs) or coding sequences (CDSs)" version="0.0.5"> +<tool id="get_orfs_or_cdss" name="Get open reading frames (ORFs) or coding sequences (CDSs)" version="0.1.1"> <description>e.g. to get peptides from ESTs</description> <requirements> - <requirement type="package" version="1.62">biopython</requirement> + <requirement type="package" version="1.65">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> + <version_command interpreter="python">get_orfs_or_cdss.py --version</version_command> + <command interpreter="python"> +get_orfs_or_cdss.py -i $input_file -f $input_file.ext --table $table -t $ftype -e $ends -m $mode --min_len $min_len -s $strand --on $out_nuc_file --op $out_prot_file --ob $out_bed_file + </command> <inputs> <param name="input_file" type="data" format="fasta,fastq,sff" label="Sequence file (nucleotides)" help="FASTA, FASTQ, or SFF format." /> <param name="table" type="select" label="Genetic code" help="Tables from the NCBI, these determine the start and stop codons"> @@ -33,6 +33,7 @@ <option value="21">21. Trematode Mitochondrial</option> <option value="22">22. Scenedesmus obliquus</option> <option value="23">23. Thraustochytrium Mitochondrial</option> + <option value="24">24. Pterobranchia Mitochondrial</option> </param> <param name="ftype" type="select" value="True" label="Look for ORFs or CDSs"> <option value="ORF">Look for ORFs (check for stop codons only, ignore start codons)</option> @@ -49,7 +50,7 @@ <option value="one">First ORF/CDS from each sequence with the maximum length</option> </param> <param name="min_len" type="integer" size="5" value="30" label="Minimum length ORF/CDS (in amino acids, e.g. 30 aa = 90 bp plus any stop codon)" /> - <param name="strand" type="select" label="Strand to search" help="Use the forward only option if your sequence directionality is known (e.g. from poly-A tails, or strand specific RNA sequencing."> + <param name="strand" type="select" label="Strand to search" help="Use the forward only option if your sequence directionality is known (e.g. from poly-A tails, or strand specific RNA sequencing)."> <option value="both">Search both the forward and reverse strand</option> <option value="forward">Only search the forward strand</option> <option value="reverse">Only search the reverse strand</option> @@ -58,6 +59,7 @@ <outputs> <data name="out_nuc_file" format="fasta" label="${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)" /> </outputs> <tests> <test> @@ -70,6 +72,7 @@ <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" /> + <output name="out_bed_file" file="get_orf_input.t1_bed_out.bed" /> </test> <test> <param name="input_file" value="get_orf_input.fasta" /> @@ -80,7 +83,8 @@ <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" /> + <output name="out_prot_file" file="get_orf_input.t11_prot_out.fasta" /> + <output name="out_bed_file" file="get_orf_input.t11_bed_out.bed" /> </test> <test> <param name="input_file" value="get_orf_input.fasta" /> @@ -92,6 +96,7 @@ <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" /> + <output name="out_bed_file" file="get_orf_input.t11_open_bed_out.bed" /> </test> <test> <param name="input_file" value="Ssuis.fasta" /> @@ -103,6 +108,7 @@ <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" /> + <output name="out_bed_file" file="get_orf_input.Suis_ORF.bed" /> </test> </tests> <help> @@ -134,7 +140,7 @@ 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 +correct start codon, it may not be appropriate for signal peptide detection etc. **Example Usage** @@ -145,7 +151,7 @@ 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 +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** @@ -168,4 +174,8 @@ 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>