Mercurial > repos > bioinformatics_lab_ufsc > test_tools
changeset 6:b50cdb7d7997 draft default tip
Deleted selected files
| author | bioinformatics_lab_ufsc |
|---|---|
| date | Mon, 22 Mar 2021 14:32:19 +0000 |
| parents | e2c6dd900183 |
| children | |
| files | predict_antibody_epitope.xml test.rar |
| diffstat | 2 files changed, 0 insertions(+), 173 deletions(-) [+] |
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--- a/predict_antibody_epitope.xml Mon Mar 08 21:15:05 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,173 +0,0 @@ -<tool id="anti_ep_pred" name="IEDB BCELL Antibody Epitope Prediction" version="v3.0"> - <description>BCELL IEDB Tool</description> - <requirements> - <requirement type="package" version="3.0">IEDB_BCELL</requirement> - <requirement type="package" version="1.0d">Netsurfp</requirement> - <requirement type="package">hh-suite</requirement> - <requirement type="package">MM-seqs2</requirement> - <requirement type="package">nunpy</requirement> - <requirement type="package" version="2.0.0">matplotlib</requirement> - <requirement type="package" version="0.18">scikit-learn</requirement> - <requirement type="package">scipy</requirement> - <requirement type="package" version=">2.7">Python</requirement> - </requirements> - <command interpreter="python"> - #if $input_type.choice == "fchoice": - #if $win_size.cutoff != "def": - predict_antibody_epitope.py -m $method -f $input_type.file $png > prediction.txt - #else: - predict_antibody_epitope.py -m $method -f $input_type.file -w $win_size.threshold $png > prediction.txt - #end if - #else: - #if $win_size.cutoff != "def": - predict_antibody_epitope.py -m $method -s $input_type.swissid $png > prediction.txt - #else: - predict_antibody_epitope.py -m $method -s $input_type.swissid -w $win_size.threshold $png > prediction.txt - #end if - #end if - </command> - <inputs> - <conditional name="input_type"> - <param name="choice" type="select" display="radio" label="File or Swissprot ID?" > - <option value="fchoice" selected="true">File</option> - <option value="schoice">Swissprot ID</option> - </param> - <when value="fchoice"> - <param name="file" type="data" format="fasta" label="Fasta File" help="Fasta or multifasta with protein(s) sequênce(s)" /> - </when> - <when value="schoice"> - <param name="swissid" type="text" label="SwissprotID"/> - </when> - </conditional> - <param name="method" type="select" display="radio" label="Prediction method"> - <option value="Chou-Fasman" selected="true">Chou-Fasman</option> - <option value="Emini">Emini</option> - <option value="Karplus-Schulz">Karplus-Schulz</option> - <option value="Kolaskar-Tongaonkar">Kolaskar-Tongaonkar</option> - <option value="Parker">Parker</option> - <option value="Bepipred">Bepipred</option> - <option value="Bepipred-2.0">Bepipred-2.0</option> - </param> - <conditional name="win_size" > - <param name="cutoff" type="select" display="radio" label="Window Size" > - <option value="" selected="true">Default, defined by method</option> - <option value="def">Set threshold</option> - </param> - <when value="def"> - <param name="threshold" type="integer" value="6" label="Threshold"/> - </when> - </conditional> - <param name="png" type="select" display="radio" label="Plot png graph?"> - <option value="--plot .">Yes</option> - <option value=" " selected="true">No</option> - </param> - </inputs> - <outputs> - <data name="pred" format="txt" from_work_dir="prediction.txt" label="Antibody Epitope prediction with $method - ${on_string}" /> - <data name="png_out" format="png" label="${tool.name} Plot png: ${on_string}" > - <discover_datasets pattern="plot_" ext="png" visible="true" assign_primary_output="true" /> - <filter>png == "--plot ."</filter> - </data> - </outputs> -<tests> - <test> - <!-- Testing Chou-Fasman method --> - <param name="method" value="Chou-Fasman" /> - <param name="file" value="test/single_sequence.txt" /> - <output name="pred" value="test/result_chou.txt" /> - <output name="png_out" value="test/png_chou.png" /> - </test> - <test> - <!-- Testing Emini method --> - <param name="method" value="Emini" /> - <param name="file" value="test/single_sequence.txt" /> - <output name="pred" value="test/result_emiini.txt" /> - <output name="png_out" value="test/png_emini.png" /> - </test> - <test> - <!-- Testing Karplus-Schulz method --> - <param name="method" value="Karplus-Schulz" /> - <param name="file" value="test/multiple_sequence.txt" /> - <output name="pred" value="test/result_karplus.txt" /> - <output name="png_out" value="test/png_karplus.png" /> - </test> - <test> - <!-- Testing Kolaskar-Tongaonkar method --> - <param name="method" value="Kolaskar-Tongaonkar" /> - <param name="file" value="test/single_sequence.txt" /> - <output name="pred" value="test/result_kolaskar.txt" /> - <output name="png_out" value="test/png_kolaskar.png" /> - </test> - <test> - <!-- Testing Parker method --> - <param name="method" value="Parker" /> - <param name="file" value="test/single_sequence.txt" /> - <output name="pred" value="test/result_parker.txt" /> - <output name="png_out" value="test/png_parker.png" /> - </test> - <test> - <!-- Testing Bepipred method --> - <param name="method" value="Bepipred" /> - <param name="file" value="test/single_sequence.txt" /> - <output name="pred" value="test/result_bepipred1.0.txt" /> - <output name="png_out" value="test/png_bepipred1.0.png" /> - </test> - <test> - <!-- Testing Bepipred 2.0 method --> - <param name="method" value="Bepipred-2.0" /> - <param name="file" value="test/single_sequence.txt" /> - <output name="pred" value="test/result_bepipred2.0.txt" /> - <output name="png_out" value="test/png_bepipred2.0.png" /> - </test> - -</tests> - - <help> -**How it works** - ------ - -**This is only bcell interface, need bcell installed on your Galaxy server** - ------ - -This package contains a collection of methods to predict linear B cell epitopes based on - -sequence characteristics of the antigen using amino acid scales and HMMs. The collection - -is a mixture of pythons scripts and linux environment specific binaries for Bepipred method. - ------ - -**WARNING: It's allowed only aminoacid sequences without (*) X and U, please remove it from your sequence before run.** - - ------ - -**Outputs** - - - **Antibody Epitope prediction** - Prediction with method and parameters informed; - - **Plot png** - Graphical representation of results; - ------ - -| We can go on forever with the darkness so far away -| Laboratory of Bioinformatics- UFSC - 2021 - </help> -<citations> - <citation type="doi">10.1093/nar/gkx346</citation> - <citation type="doi">10.1110/ps.062405906</citation> - <citation type="doi">10.1186/1472-6807-7-64</citation> - <citation type="doi">10.1186/1745-7580-2-2</citation> - <citation type="doi">10.1021/bi00367a013</citation> - <citation type="doi">10.1016/0014-5793(90)80535-q</citation> - <citation type="doi">10.1002/9780470122921.ch2</citation> - <citation type="bibtex">@ARTICLE{Kim07aninterior-point, - author = {Emini EA, Hughes JV, Perlow DS, Boger J.}, - title = {Induction of hepatitis A virus-neutralizing antibody by a virus-specific synthetic peptide.}, - journal = {Journal of virology vol.}, - year = {1985 }, - volume = {8}, - }</citation> -</citations> -</tool>