diff emboss_fuzztran.xml @ 10:d49956b87f7e draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/emboss_fuzztran.xml	Wed Feb 08 12:42:22 2017 -0500
@@ -0,0 +1,89 @@
+<tool id="EMBOSS: fuzztran39" name="fuzztran" version="5.0.0.1">
+  <description>Protein pattern search after translation</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements" />
+  <code file="emboss_format_corrector.py" />
+  <command>fuzztran -sequence '$input1' -outfile '$out_file1' -pattern '$pattern' -pmismatch $mismatch -frame $frame -table $table -rformat2 $out_format1 -auto</command>
+  <inputs>
+    <param name="input1" type="data" format="fasta" label="Sequences" />
+    <param name="pattern" type="text" value="" label="Search pattern" />
+    <param name="mismatch" type="integer" value="0" label="Number of mismatches" />
+    <param name="frame" type="select" label="Frame(s) to translate">
+      <option value="1">Frame 1</option>
+      <option value="2">Frame 2</option>
+      <option value="3">Frame 3</option>
+      <option value="F">Forward three frames</option>
+      <option value="-1">Frame -1</option>
+      <option value="-2">Frame -2</option>
+      <option value="-3">Frame -3</option>
+      <option value="R">Reverse three frames</option>
+      <option value="6">All six frames</option>
+    </param>
+    <param name="table" type="select" label="Code to use">
+      <option value="0">Standard</option>
+      <option value="1">Standard (with alternative initiation codons)</option>
+      <option value="2">Vertebrate Mitochondrial</option>
+      <option value="3">Yeast Mitochondrial</option>
+      <option value="4">Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma</option>
+      <option value="5">Invertebrate Mitochondrial</option>
+      <option value="6">Ciliate Macronuclear and Dasycladacean</option>
+      <option value="9">Echinoderm Mitochondrial</option>
+      <option value="10">Euplotid Nuclear</option>
+      <option value="11">Bacterial</option>
+      <option value="12">Alternative Yeast Nuclear</option>
+      <option value="13">Ascidian Mitochondrial</option>
+      <option value="14">Flatworm Mitochondrial</option>
+      <option value="15">Blepharisma Macronuclear</option>
+      <option value="16">Chlorophycean Mitochondrial</option>
+      <option value="21">Trematode Mitochondrial</option>
+      <option value="22">Scenedesmus obliquus</option>
+      <option value="23">Thraustochytrium Mitochondrial</option>
+    </param>
+    <param name="out_format1" type="select" label="Output report file format">
+      <option value="table">Table</option>
+      <option value="embl">EMBL</option>
+      <option value="genbank">GENBANK</option>
+      <option value="gff">GFF</option>
+      <option value="pir">PIR</option>
+      <option value="swiss">SwissProt</option>
+      <option value="dbmotif">DbMotif</option>
+      <option value="diffseq">Diffseq</option>
+      <option value="excel">Excel (tab delimited)</option>
+      <option value="feattable">FeatTable</option>
+      <option value="motif">Motif</option>
+      <option value="regions">Regions</option>
+      <option value="seqtable">SeqTable</option>
+      <option value="simple">SRS Simple</option>
+      <option value="srs">SRS</option>
+      <option value="tagseq">TagSeq</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data name="out_file1" format="fuzztran" />
+  </outputs>
+  <tests>
+    <test>
+      <param name="input1" value="1.fasta"/>
+      <param name="pattern" value="AA"/>
+      <param name="mismatch" value="0"/>
+      <param name="frame" value="6"/>
+      <param name="table" value="0"/>
+      <param name="out_format1" value="excel"/>
+      <output name="out_file1" file="emboss_fuzztran_out.tabular"/>
+    </test>
+  </tests>
+  <help>
+.. class:: warningmark
+
+The input dataset needs to be sequences.
+
+-----
+
+    You can view the original documentation here_.
+
+    .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/fuzztran.html
+  </help>
+  <expand macro="citations" />
+</tool>