diff emboss_est2genome.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_est2genome.xml	Fri Aug 12 19:17:10 2016 -0400
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+<tool id="EMBOSS: est2genome32" name="est2genome" version="5.0.0">
+  <description>Align EST and genomic DNA sequences</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
+  <command>est2genome -estsequence $input1 -genomesequence $input2 -outfile $out_file1 -match $match -mismatch $mismatch -gappenalty $gappenalty -intronpenalty $intronpenalty -splicepenalty
+  $splicepenalty -minscore $minscore -reverse $reverse -splice $splice -mode $mode -best $best -shuffle $shuffle -seed $seed -align $align -width $width -auto</command>
+  <inputs>
+    <param format="fasta" name="input1" type="data">
+      <label>EST sequence(s)</label>
+    </param>
+    <param format="data" name="input2" type="data">
+      <label>Genomic sequence</label>
+    </param>
+    <param name="match" type="text" value="1">
+      <label>Score for matching two bases</label>
+    </param>
+    <param name="mismatch" type="text" value="1">
+      <label>Cost for mismatching two bases</label>
+    </param>
+    <param name="gappenalty" type="text" value="2">
+      <label>Cost for deleting a single base in either sequence, excluding introns</label>
+    </param>
+    <param name="intronpenalty" type="text" value="40">
+      <label>Cost for an intron, independent of length</label>
+    </param>
+    <param name="splicepenalty" type="text" value="20">
+      <label>Cost for an intron, independent of length and starting/ending on donor-acceptor sites</label>
+    </param>
+    <param name="minscore" type="text" value="30">
+      <label>Exclude alignments with scores below this threshold score</label>
+    </param>
+    <param name="reverse" type="select">
+      <label>Reverse the orientation of the EST sequence</label>
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+    <param name="splice" type="select">
+      <label>Use donor and acceptor splice sites</label>
+      <option value="yes">Yes</option>
+      <option value="no">No</option>
+    </param>
+    <param name="mode" type="select">
+      <label>Comparison mode</label>
+      <option value="both">Both strands</option>
+      <option value="forward">Forward strand only</option>
+      <option value="reverse">Reverse strand only</option>
+    </param>
+    <param name="best" type="select">
+      <label>Only best comparisons</label>
+      <option value="yes">Yes</option>
+      <option value="no">No</option>
+    </param>
+    <param name="shuffle" type="text" value="0">
+      <label>Shuffle</label>
+    </param>
+    <param name="seed" type="text" value="20825">
+      <label>Random number seed</label>
+    </param>
+    <param name="align" type="select">
+      <label>Show the alignment</label>
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+    <param name="width" type="text" value="50">
+      <label>Alignment width</label>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="est2genome" name="out_file1" />
+  </outputs>
+  <tests>
+    <test>
+      <param name="input1" value="2.fasta"/>
+      <param name="input2" value="1.fasta"/>
+      <param name="match" value="1"/>
+      <param name="mismatch" value="1"/>
+      <param name="match" value="1"/>
+      <param name="gappenalty" value="2"/>
+      <param name="intronpenalty" value="40"/>
+      <param name="splicepenalty" value="20"/>
+      <param name="minscore" value="30"/>
+      <param name="reverse" value="no"/>
+      <param name="splice" value="yes"/>
+      <param name="mode" value="both"/>
+      <param name="best" value="yes"/>
+      <param name="shuffle" value="0"/>
+      <param name="seed" value="20825"/>
+      <param name="align" value="no"/>
+      <param name="width" value="50"/>
+      <output name="out_file1" file="emboss_est2genome_out.est2genome"/>
+    </test>
+  </tests>
+  <help>
+.. class:: warningmark
+
+The input dataset needs to be sequences.
+
+-----
+
+    You can view the original documentation here_.
+    
+    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/est2genome.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>