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README.rst phage_promoter.xml |
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| diff -r 2d0e8418e8ea -r 9c150558ea72 README.rst --- a/README.rst Mon Sep 10 05:18:46 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,29 +0,0 @@ -=============== -PhagePromoters -=============== - -Get promoters of phage genomes - -PhagePromoters is a python script that predicts promoter sequences in phage genomes, using a machine learning SVM model. This model was built from a train dataset with 25 features and 3200 examples (800 positives and 2400 negatives), each representing a 65 bp sequence of a phage genome. The positive cases represent the phage sequences that are already identified as promoters. - -**Inputs:** - -* genome format: fasta vs genbank; -* genome file: acepts both genbank and fasta formats; -* both strands (yes or no): allows the search in both DNA strands; -* threshold: represents the probability of the test sequence be a promoter (float between 0 and 1)" -* family: The family of the testing phage - Podoviridae, Siphoviridae or Myoviridae; -* Bacteria: The host of the phage. The train dataset include the following hosts: Bacillus, EColi, Salmonella, Pseudomonas, Yersinia, Klebsiella, Pectobacterium, Morganella, Cronobacter, Staphylococcus, Streptococcus, Streptomyces, Lactococcus. If the testing phage has a different host, select the option 'other', and it is recommended the use of a higher threshold value for more accurate results. -* phage type: The type of the phage, according to its lifecycle: virulent or temperate; - -**Outputs:** -This tool outputs two files: a FASTA file and a table in HTML, with the locations, sequence, score and type (recognized by host or phage RNAP) of the predicted promoters. - -**Requirements:** - -* Biopython -* Sklearn -* Numpy -* Pandas - - |
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| diff -r 2d0e8418e8ea -r 9c150558ea72 phage_promoter.xml --- a/phage_promoter.xml Mon Sep 10 05:18:46 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,104 +0,0 @@ -<tool id="get_proms" name="PhagePromoter" version="0.1.0"> - <description> -Get promoters of phage genomes - </description> - <requirements> - <requirement type="package">biopython</requirement> - <requirement type="package">scikit-learn</requirement> - <requirement type="package"> numpy</requirement> - <requirement type="package">pandas</requirement> - </requirements> - <command detect_errors="exit_code" interpreter="python"><![CDATA[ - phage_promoter.py "$input_type.genome_format" "$genome" "$both" "$threshold" "$family" "$bacteria" "$lifecycle" - ]]> - </command> - <inputs> - <conditional name="input_type"> - <param type="select" name="genome_format" label='file format'> - <option value="genbank" selected="yes">genbank</option> - <option value="fasta">fasta</option> - </param> - <when value="genbank"> - <param type="data" name="genome" format="genbank" label='genome'/> - </when> - <when value="fasta"> - <param type="data" name="genome" format="fasta" label='genome'/> - </when> - </conditional> - <param type="boolean" name="both" label='Search both strands' checked="false" truevalue="-both" falsevalue="" /> - <param name="threshold" type="float" value="0.50" label="Threshold" help="Probabilty of being a promoter (float between 0 and 1)" /> - <param type="select" name="family" label='Phage family'> - <option value="Podoviridae" selected="yes">Podoviridae</option> - <option value="Siphoviridae">Siphoviridae</option> - <option value="Myoviridae">Myoviridae</option> - </param> - <param type="select" name="bacteria" label='Host bacteria Genus'> - <option value="Escherichia coli" selected="yes">Escherichia coli</option> - <option value="Salmonella">Salmonella</option> - <option value="Pseudomonas">Pseudomonas</option> - <option value="Yersinia">Yersinia</option> - <option value="Morganella">Morganella</option> - <option value="Cronobacter">Cronobacter</option> - <option value="Staphylococcus">Staphylococcus</option> - <option value="Streptococcus">Streptococcus</option> - <option value="Lactococcus">Lactococcus</option> - <option value="Streptomyces">Streptomyces</option> - <option value="Klebsiella">Klebsiella</option> - <option value="Bacillus">Bacillus</option> - <option value="Pectobacterium">Pectobacterium</option> - <option value="other">other</option> - </param> - <param type="select" name="lifecycle" label='Phage type'> - <option value="virulent" selected="yes">virulent</option> - <option value="temperate">temperate</option> - </param> - </inputs> - <outputs> - <data name="output1" format="html" from_work_dir="output.html" /> - <data name="output2" format="fasta" from_work_dir="output.fasta" /> - </outputs> - <tests> - <test> - <param name="genome_format" value="genbank"/> - <param name="genome" value="NC_015264.gb"/> - <param name="both" value="False"/> - <param name="threshold" value="0.50"/> - <param name="family" value="Podoviridae"/> - <param name="bacteria" value="Pseudomonas"/> - <param name="lifecycle" value="virulent"/> - <output name="output1" file="output.html"/> - <output name="output2" file="output.fasta"/> - </test> - </tests> - <help><![CDATA[ - -=============== -PhagePromoters -=============== - -Get promoters of phage genomes - -PhagePromoters is a python script that predicts promoter sequences in phage genomes, using a machine learning SVM model. This model was built from a train dataset with 19 features and 3200 examples (800 positives and 2400 negatives), each representing a 65 bp sequence of a phage genome. The positive cases represent the phage sequences that are already identified as promoters. - -**Inputs:** - -* genome format: fasta vs genbank; -* genome file: acepts both genbank and fasta formats; -* both strands (yes or no): allows the search in both DNA strands; -* threshold: represents the probability of the test sequence being a promoter (float between 0 and 1, default 0.50)". For example, if threshold=0.90, the model only returns the predicted sequences with more than 90% probability of being a promoter. The larger the genome, the higher the threshold should be. -* family: The family of the testing phage - Podoviridae, Siphoviridae or Myoviridae; -* Bacteria: The host of the phage. The train dataset include the following hosts: Bacillus, EColi, Salmonella, Pseudomonas, Yersinia, Klebsiella, Pectobacterium, Morganella, Cronobacter, Staphylococcus, Streptococcus, Streptomyces, Lactococcus. If the testing phage has a different host, select the option 'other', and it is recommended the use of a higher threshold value for more accurate results. -* phage type: The type of the phage, according to its lifecycle: virulent or temperate; - -**Outputs:** -This tool outputs two files: a FASTA file and a table in HTML, with the locations, sequence, score and type (recognized by host or phage RNAP) of the predicted promoters. - -**Requirements:** - -* Biopython -* Sklearn -* Numpy -* Pandas - - ]]></help> -</tool> |