Mercurial > repos > jamueller > codon_analysis
diff gcs.xml @ 0:caadae802e65 draft
Uploaded
| author | jamueller |
|---|---|
| date | Thu, 23 May 2019 05:15:08 -0400 |
| parents | |
| children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/gcs.xml Thu May 23 05:15:08 2019 -0400 @@ -0,0 +1,118 @@ +<tool id="GeCoS" name="GeCoS" version="1.0.0"> + <description>(GeneCodonSearch) calculates the codon composition in a DNA sequence.</description> + <command interpreter="python">GeneCodonSearch1_2.py -c $codon -m $minimum -i $input_sequences -r $resultfile</command> + <inputs> + <param type="data" format="fasta" name="input_sequences" label="Input Sequences"/> + <param name="codon" type="select" label="Codons" multiple="true"> + <option value="ATA" selected="false">ATG</option> + <option value="ATC" selected="false">ATC</option> + <option value="ATT" selected="false">ATT</option> + <option value="ATG" selected="false">ATG</option> + <option value="ACA" selected="false">ACA</option> + <option value="ACC" selected="false">ACC</option> + <option value="ACG" selected="false">ACG</option> + <option value="ACT" selected="false">ACT</option> + <option value="AAC" selected="false">AAC</option> + <option value="AAT" selected="false">AAT</option> + <option value="AAA" selected="false">AAA</option> + <option value="AAG" selected="false">AAG</option> + <option value="AGC" selected="false">AGC</option> + <option value="AGT" selected="false">AGT</option> + <option value="AGA" selected="false">AGA</option> + <option value="AGG" selected="false">AGG</option> + <option value="CTA" selected="false">CTA</option> + <option value="CTC" selected="false">CTC</option> + <option value="CTG" selected="false">CTG</option> + <option value="CTT" selected="false">CTT</option> + <option value="CCA" selected="false">CCA</option> + <option value="CCC" selected="false">CCC</option> + <option value="CCG" selected="false">CCG</option> + <option value="CCT" selected="false">CCT</option> + <option value="CAC" selected="false">CAC</option> + <option value="CAT" selected="false">CAT</option> + <option value="CAA" selected="false">CAA</option> + <option value="CAG" selected="false">CAG</option> + <option value="CGA" selected="false">CGA</option> + <option value="CGC" selected="false">CGC</option> + <option value="CGG" selected="false">CGG</option> + <option value="CGT" selected="false">CGT</option> + <option value="GTA" selected="false">GTA</option> + <option value="GTC" selected="false">GTC</option> + <option value="GTG" selected="false">GTG</option> + <option value="GTT" selected="false">GTT</option> + <option value="GCA" selected="false">GCA</option> + <option value="GCC" selected="false">GCC</option> + <option value="GCG" selected="false">GCG</option> + <option value="GCT" selected="false">GCT</option> + <option value="GAC" selected="false">GAC</option> + <option value="GAT" selected="false">GAT</option> + <option value="GAA" selected="false">GAA</option> + <option value="GAG" selected="false">GAG</option> + <option value="GGA" selected="false">GGA</option> + <option value="GGC" selected="false">GGC</option> + <option value="GGG" selected="false">GGG</option> + <option value="GGT" selected="false">GGT</option> + <option value="TCA" selected="false">TCA</option> + <option value="TCC" selected="false">TCC</option> + <option value="TCG" selected="false">TCG</option> + <option value="TCT" selected="false">TCT</option> + <option value="TTC" selected="false">TTC</option> + <option value="TTT" selected="false">TTT</option> + <option value="TTA" selected="false">TTA</option> + <option value="TTG" selected="false">TTG</option> + <option value="TAC" selected="false">TAC</option> + <option value="TAT" selected="false">TAT</option> + <option value="TAA" selected="false">TAA</option> + <option value="TAG" selected="false">TAG</option> + <option value="TGC" selected="false">TGC</option> + <option value="TGT" selected="false">TGT</option> + <option value="TGA" selected="false">TGA</option> + <option value="TGG" selected="false">TGG</option> + </param> + <param name="minimum" type="float" value="0.0" label="Minimum codon content (cutoff)"/> + </inputs> + <outputs> + <data format="txt" name="resultfile"/> + </outputs> + + <help> + **What it does** + **GeCos** is a tool that calculates the codon composition of any given DNA sequence. + + **Input** + + - If more than one sequence is analyzed at a time, a **cutoff value** can be used to filter the output. Only the sequences with a higher total score than the cutoff value will be displayed in the output. + + - The DNA sequence(s), that are supposed to be analyzed with GeCoS need to be formatted as fasta. + + Example:: + + >CCE57618 cdna plasmid:HUSEC2011CHR1:pHUSEC2011-2:166:1143:1 gene:HUS2011_pII0001 description:replication initiation protein RepFIB + GTGGATAAGTC ... TCTTCAAATCCCGCTGA + >CCE57620 cdna plasmid:HUSEC2011CHR1:pHUSEC2011-2:1422:2162:-1 gene:HUS2011_pII0003 description:site-specific recombinase + ATGAACAATG ... CTCCCCTGAAGTAA + >CCE57621 cdna plasmid:HUSEC2011CHR1:pHUSEC2011-2:2531:2692:-1 gene:HUS2011_pII0004 description:plasmid stabilisation system family protein + ATGAGTAATCA ... ATTTCAACTGA + >CCE57622 cdna plasmid:HUSEC2011CHR1:pHUSEC2011-2:2894:3076:-1 gene:HUS2011_pII0005 description:putative transcriptional regulator + ATGGCCAG ... AGAAGGCT + + **Output** + + - GeCoS produces a matrix containing the identifier used in the input, the combined score of the sequence and the number of each of the chosen codons. + + - **Total Score** = sum of codon occurences / sequence length * number of analyzed codons + + - The output is sorted from low to high (Total Score: 0 to 1). + + Example:: + + [['Gene_ID' 'Total Score' 'AGG' 'AGC' 'CCC' 'TGC' 'GCG'] + ['CCE57562' 0.0190476 1 3 1 2 1] + ['CCQ29559' 0.0190476 0 1 2 2 1] + ... + ['CCQ31238' 0.0328358 0 3 0 6 2] + ['CCE57539' 0.05 2 0 4 3 3]] + + </help> + +</tool>