| Previous changeset 10:e504a2e18cba (2013-09-26) Next changeset 12:09b5b1af9b8f (2013-11-20) |
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Commit message:
Uploaded v0.0.5h, depend on Biopython 1.62 |
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modified:
tools/get_orfs_or_cdss/get_orfs_or_cdss.xml tools/get_orfs_or_cdss/repository_dependencies.xml |
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| diff -r e504a2e18cba -r 308ec20faefb tools/get_orfs_or_cdss/get_orfs_or_cdss.xml --- a/tools/get_orfs_or_cdss/get_orfs_or_cdss.xml Thu Sep 26 10:04:13 2013 -0400 +++ b/tools/get_orfs_or_cdss/get_orfs_or_cdss.xml Fri Sep 27 06:11:59 2013 -0400 |
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| b'@@ -1,113 +1,111 @@\n <tool id="get_orfs_or_cdss" name="Get open reading frames (ORFs) or coding sequences (CDSs)" version="0.0.5">\n-\t<description>e.g. to get peptides from ESTs</description>\n-\t<version_command interpreter="python">get_orfs_or_cdss.py --version</version_command>\n-\t<command interpreter="python">\n+ <description>e.g. to get peptides from ESTs</description>\n+ <requirements>\n+ <requirement type="package" version="1.62">biopython</requirement>\n+ <requirement type="python-module">Bio</requirement>\n+ </requirements>\n+ <version_command interpreter="python">get_orfs_or_cdss.py --version</version_command>\n+ <command interpreter="python">\n get_orfs_or_cdss.py $input_file $input_file.ext $table $ftype $ends $mode $min_len $strand $out_nuc_file $out_prot_file\n-\t</command>\n-\t<stdio>\n-\t\t<!-- Anything other than zero is an error -->\n-\t\t<exit_code range="1:" />\n-\t\t<exit_code range=":-1" />\n-\t</stdio>\n-\t<inputs>\n-\t\t<param name="input_file" type="data" format="fasta,fastq,sff" label="Sequence file (nucleotides)" help="FASTA, FASTQ, or SFF format." />\n-\t\t<param name="table" type="select" label="Genetic code" help="Tables from the NCBI, these determine the start and stop codons">\n-\t\t\t<option value="1">1. Standard</option>\n-\t\t\t<option value="2">2. Vertebrate Mitochondrial</option>\n-\t\t\t<option value="3">3. Yeast Mitochondrial</option>\n-\t\t\t<option value="4">4. Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma</option>\n-\t\t\t<option value="5">5. Invertebrate Mitochondrial</option>\n-\t\t\t<option value="6">6. Ciliate Macronuclear and Dasycladacean</option>\n-\t\t\t<option value="9">9. Echinoderm Mitochondrial</option>\n-\t\t\t<option value="10">10. Euplotid Nuclear</option>\n-\t\t\t<option value="11">11. Bacterial</option>\n-\t\t\t<option value="12">12. Alternative Yeast Nuclear</option>\n-\t\t\t<option value="13">13. Ascidian Mitochondrial</option>\n-\t\t\t<option value="14">14. Flatworm Mitochondrial</option>\n-\t\t\t<option value="15">15. Blepharisma Macronuclear</option>\n-\t\t\t<option value="16">16. Chlorophycean Mitochondrial</option>\n-\t\t\t<option value="21">21. Trematode Mitochondrial</option>\n-\t\t\t<option value="22">22. Scenedesmus obliquus</option>\n-\t\t\t<option value="23">23. Thraustochytrium Mitochondrial</option>\n-\t\t</param>\n-\t\t<param name="ftype" type="select" value="True" label="Look for ORFs or CDSs">\n- <option value="ORF">Look for ORFs (check for stop codons only, ignore start codons)</option>\n- <option value="CDS">Look for CDSs (with start and stop codons)</option>\n-\t\t</param>\n- <param name="ends" type="select" value="open" label="Sequence end treatment">\n-\t\t\t<option value="open">Open ended (will allow missing start/stop codons at the ends)</option>\n- <option value="closed">Complete (will check for start/stop codons at the ends)</option>\n- <!-- TODO? Circular, for using this on finished bacteria etc -->\n- </param>\n-\n-\t\t<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.">\n- <option value="all">All ORFs/CDSs from each sequence</option>\n- <option value="top">All ORFs/CDSs from each sequence with the maximum length</option>\n- <option value="one">First ORF/CDS from each sequence with the maximum length</option>\n-\t\t</param>\n- <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)">\n- </param>\n- <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.">\n- <option value="both">Search both the forward and reverse str'..b'sing this on finished bacteria etc -->\n+ </param>\n+ <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.">\n+ <option value="all">All ORFs/CDSs from each sequence</option>\n+ <option value="top">All ORFs/CDSs from each sequence with the maximum length</option>\n+ <option value="one">First ORF/CDS from each sequence with the maximum length</option>\n+ </param>\n+ <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)" />\n+ <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.">\n+ <option value="both">Search both the forward and reverse strand</option>\n+ <option value="forward">Only search the forward strand</option>\n+ <option value="reverse">Only search the reverse strand</option>\n+ </param>\n+ </inputs>\n+ <outputs>\n+ <data name="out_nuc_file" format="fasta" label="${ftype.value}s (nucleotides)" />\n+ <data name="out_prot_file" format="fasta" label="${ftype.value}s (amino acids)" />\n+ </outputs>\n+ <tests>\n+ <test>\n+ <param name="input_file" value="get_orf_input.fasta" />\n+ <param name="table" value="1" />\n+ <param name="ftype" value="CDS" />\n+ <param name="ends" value="open" />\n+ <param name="mode" value="all" />\n+ <param name="min_len" value="10" />\n+ <param name="strand" value="forward" />\n+ <output name="out_nuc_file" file="get_orf_input.t1_nuc_out.fasta" />\n+ <output name="out_prot_file" file="get_orf_input.t1_prot_out.fasta" />\n+ </test>\n+ <test>\n+ <param name="input_file" value="get_orf_input.fasta" />\n+ <param name="table" value="11" />\n+ <param name="ftype" value="CDS" />\n+ <param name="ends" value="closed" />\n+ <param name="mode" value="all" />\n+ <param name="min_len" value="10" />\n+ <param name="strand" value="forward" />\n+ <output name="out_nuc_file" file="get_orf_input.t11_nuc_out.fasta" />\n+ <output name="out_prot_file" file="get_orf_input.t11_prot_out.fasta" />\n+ </test>\n+ <test>\n+ <param name="input_file" value="get_orf_input.fasta" />\n+ <param name="table" value="11" />\n+ <param name="ftype" value="CDS" />\n+ <param name="ends" value="open" />\n+ <param name="mode" value="all" />\n+ <param name="min_len" value="10" />\n+ <param name="strand" value="forward" />\n+ <output name="out_nuc_file" file="get_orf_input.t11_open_nuc_out.fasta" />\n+ <output name="out_prot_file" file="get_orf_input.t11_open_prot_out.fasta" />\n+ </test>\n+ <test>\n+ <param name="input_file" value="Ssuis.fasta" />\n+ <param name="table" value="11" />\n+ <param name="ftype" value="ORF" />\n+ <param name="ends" value="open" />\n+ <param name="mode" value="all" />\n+ <param name="min_len" value="100" />\n+ <param name="strand" value="both" />\n+ <output name="out_nuc_file" file="get_orf_input.Suis_ORF.nuc.fasta" />\n+ <output name="out_prot_file" file="get_orf_input.Suis_ORF.prot.fasta" />\n+ </test>\n+ </tests>\n+ <help>\n **What it does**\n \n Takes an input file of nucleotide sequences (typically FASTA, but also FASTQ\n@@ -169,5 +167,5 @@\n \n This tool is available to install into other Galaxy Instances via the Galaxy\n Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss\n-\t</help>\n+ </help>\n </tool>\n' |
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| diff -r e504a2e18cba -r 308ec20faefb tools/get_orfs_or_cdss/repository_dependencies.xml --- a/tools/get_orfs_or_cdss/repository_dependencies.xml Thu Sep 26 10:04:13 2013 -0400 +++ b/tools/get_orfs_or_cdss/repository_dependencies.xml Fri Sep 27 06:11:59 2013 -0400 |
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| @@ -2,5 +2,5 @@ <repositories description="This requires Biopython as a dependency."> <!-- Leave out the tool shed and revision to get the current tool shed and latest revision at the time of upload --> -<repository changeset_revision="2f6c871cfa35" name="package_biopython_1_61" owner="biopython" toolshed="http://testtoolshed.g2.bx.psu.edu" /> +<repository changeset_revision="ac9cc2992b69" name="package_biopython_1_62" owner="biopython" toolshed="http://testtoolshed.g2.bx.psu.edu" /> </repositories> |