diff emboss_water.xml @ 10:9b98d3d903c6 draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/emboss_water.xml	Fri Aug 12 19:17:10 2016 -0400
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+<tool id="EMBOSS: water107" name="water" version="5.0.0">
+  <description>Smith-Waterman local alignment</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
+  <command>water -asequence $input1 -bsequence $input2 -outfile $out_file1 -gapopen "$gapopen" -gapextend "$gapextend" -brief $brief -aformat3 $out_format1 -auto</command>
+  <inputs>
+    <param format="fasta" name="input1" type="data">
+      <label>Sequence 1</label>
+    </param>
+    <param format="fasta" name="input2" type="data">
+      <label>Sequence 2</label>
+    </param>
+    <param name="gapopen" type="text" value="10.0">
+      <label>Gap open penalty</label>
+    </param>
+    <param name="gapextend" type="text" value="0.5">
+      <label>Gap extension penalty</label>
+    </param>
+    <param name="brief" type="select">
+      <label>Brief identity and similarity</label>
+      <option value="yes">Yes</option>
+      <option value="no">No</option>
+    </param>
+    <param name="out_format1" type="select">
+      <label>Output Alignment File Format</label>
+      <option value="srs">SRS (m)</option>
+      <option value="simple">Simple (m)</option>
+      <option value="fasta">FASTA (m)</option>
+      <option value="msf">MSF (m)</option>
+      <option value="pair">Pair (p)</option>
+      <option value="markx0">Markx0 (p)</option>
+      <option value="markx1">Markx1 (p)</option>
+      <option value="markx2">Markx2 (p)</option>
+      <option value="markx3">Markx3 (p)</option>
+      <option value="markx10">Markx10 (p)</option>
+      <option value="srspair">SRS pair (p)</option>
+      <option value="score">Score (p)</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="srs" name="out_file1" />
+  </outputs>
+  <tests>
+    <test>
+      <param name="input1" value="2.fasta"/>
+      <param name="input2" value="1.fasta"/>
+      <param name="gapopen" value="10.0"/>
+      <param name="gapextend" value="0.5"/>
+      <param name="brief" value="no"/>
+      <param name="out_format1" value="score"/>
+      <output name="out_file1" file="emboss_water_out.score"/>
+    </test>
+  </tests>
+  <code file="emboss_format_corrector.py" />
+  <help>
+
+.. class:: warningmark 
+
+The input datasets need to be sequences. 
+
+----- 
+
+    You can view the original documentation here_.
+    
+    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/water.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>