diff anomaly_wrapper.xml @ 0:9c8ffce71f7c draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/anomaly_wrapper.xml	Mon Sep 09 12:16:17 2013 -0400
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+<tool id="anomaly_wrapper" name="Anomaly" version="0.2">
+  <description></description>
+  <requirements>
+    <requirement type="package" version="3.02">glimmer</requirement>
+  </requirements>
+  <command interpreter="python">
+    anomaly_wrapper.py --anSequence $anSequence --anCoords $anCoords
+    #if $anStartCodons
+      --anStartCodons="$anStartCodons"
+    #end if
+    #if $anCheckFirstCodon
+      --anCheckFirstCodon
+    #end if
+    #if $anCheckStopCodon
+      --anCheckStopCodon
+    #end if
+    #if $anStopCodons
+      --anStopCodons="$anStopCodons"
+    #end if
+    --anOutput $anOutput --logfile $logfile
+ </command>
+
+  <inputs>
+    <param name="anSequence" type="data" format="fasta" label="DNA sequence to be analyzed" help="FASTA format" />
+
+    <param name="anCoords" type="data" format="glimmer_coords" label="Region coordinates" />
+
+    <param name="anStartCodons" type="text" value="" optional="true" label="Specify allowable start codons as a comma-separated list (-A)" help="Sample format: 'atg,gtg' . The default start codons are atg, gtg and ttg." />
+
+    <param name="anCheckFirstCodon" type="boolean" checked="false" label="Omit the check that the first codon is a start codon (-s)" help="" />
+
+    <param name="anCheckStopCodon" type="boolean" checked="false" label="Check whether the codon preceding the start coordinate position is a stop codon (-t)" help="This is useful if the coordinates represent the entire region between stop codons." />
+
+    <param name="anStopCodons" type="text" value="" optional="true" label="Specify allowable stop codons as a comma-separated list (-Z)" help="Sample format: 'tag,tga'. The default stop codons are tag, tga and taa." />
+  </inputs>
+
+  <outputs>
+    <data name="logfile" format="txt" label="${tool.name} on ${on_string}: log" />
+    <data name="anOutput" format="txt" label="${tool.name} on ${on_string}: output" />
+  </outputs>
+
+  <tests>
+
+  </tests>
+  <help>
+**What it does**
+
+Read DNA sequence in "sequence-file" and for each region specified by the coordinates in "coord-file", check whether the region represents a normal gene, i.e., it begins with a start codon, ends with a stop codon, and has no frame shifts.
+
+**License and citation**
+
+This Galaxy tool is Copyright © 2013 `CRS4 Srl.`_ and is released under the `MIT license`_.
+
+.. _CRS4 Srl.: http://www.crs4.it/
+.. _MIT license: http://opensource.org/licenses/MIT
+
+If you use this tool in Galaxy, please cite |Cuccuru2013|_.
+
+.. |Cuccuru2013| replace:: Cuccuru, G., Orsini, M., Pinna, A., Sbardellati, A., Soranzo, N., Travaglione, A., Uva, P., Zanetti, G., Fotia, G. (2013) Orione, a web-based framework for NGS analysis in microbiology. *Submitted*
+.. _Cuccuru2013: http://orione.crs4.it/
+
+This tool uses `Glimmer`_, which is licensed separately. Please cite |Delcher2007|_.
+
+.. _Glimmer: http://ccb.jhu.edu/software/glimmer/index.shtml
+.. |Delcher2007| replace:: Delcher, A. L., Bratke, K. A., Powers, E. C., Salzberg, S. L. (2007) Identifying bacterial genes and endosymbiont DNA with Glimmer. *Bioinformatics* 23(6), 673-679
+.. _Delcher2007: http://bioinformatics.oxfordjournals.org/content/23/6/673
+  </help>
+</tool>