diff emboss_5/emboss_epestfind.xml @ 0:b94ca591877b

Uploaded emboss_5.tar

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+++ b/emboss_5/emboss_epestfind.xml	Tue Dec 20 14:02:45 2011 -0500
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+<tool id="EMBOSS: epestfind29" name="epestfind" version="5.0.0">
+  <description>Finds PEST motifs as potential proteolytic cleavage sites</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
+  <command interpreter="perl">emboss_single_outputfile_wrapper.pl epestfind -sequence $input1 -goutfile $ofile2 -outfile $ofile1 -window $window -order $order -potential $potential -poor $poor
+  -invalid $invalid -map $map -graph png -auto</command>
+  <inputs>
+    <param format="data" name="input1" type="data">
+      <label>Sequence</label>
+    </param>
+    <param name="window" size="4" type="text" value="10">
+      <label>Minimal distance between positively charged amino acids</label>
+    </param>
+    <param name="order" type="select">
+      <label>Sort by</label>
+      <option value="3">Score</option>
+      <option value="1">Length</option>
+      <option value="2">Position</option>
+    </param>
+    <param name="threshold" size="4" type="text" value="5.0">
+      <label>Threshold value to discriminate weak from potential PEST motifs.</label>
+    </param>
+    <param name="potential" type="select">
+      <label>Decide whether potential PEST motifs should be printed</label>
+      <option value="yes">Yes</option>
+      <option value="no">No</option>
+    </param>
+    <param name="poor" type="select">
+      <label>Decide whether poor PEST motifs should be printed</label>
+      <option value="yes">Yes</option>
+      <option value="no">No</option>
+    </param>
+    <param name="invalid" type="select">
+      <label>Decide whether invalid PEST motifs should be printed</label>
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+    <param name="map" type="select">
+      <label>Decide whether PEST motifs should be mapped to sequence</label>
+      <option value="yes">Yes</option>
+      <option value="no">No</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="png" name="ofile2" />
+    <data format="epestfind" name="ofile1" />
+  </outputs>
+<!--    <tests>
+    <test>
+      <param name="input1" value="2.fasta"/>
+      <param name="window" value="10"/>
+      <param name="order" value="3"/>
+      <param name="threshold" value="5.0"/>
+      <param name="potential" value="yes"/>
+      <param name="poor" value="yes"/>
+      <param name="invalid" value="no"/>
+      <param name="map" value="yes"/>
+      <output name="ofile1" file="emboss_epestfind_out.epestfind"/>
+    </test>
+  </tests>  output file contains file location info  -->
+  <help>
+    You can view the original documentation here_.
+    
+    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/epestfind.html
+
+------
+
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
+If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
+  </help>
+</tool>
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