annotate predict_antibody_epitope.xml @ 4:dd573dcdbb03 draft

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<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>