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/tools/emboss_5/emboss_fuzztran.xml

https://bitbucket.org/cistrome/cistrome-harvard/
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  1<tool id="EMBOSS: fuzztran39" name="fuzztran" version="5.0.0">
  2  <description>Protein pattern search after translation</description>
  3  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
  4  <command>fuzztran -sequence $input1 -outfile $out_file1 -pattern "$pattern" -pmismatch $mismatch -frame $frame -table $table -rformat2 $out_format1 -auto</command>
  5  <inputs>
  6    <param format="fasta" name="input1" type="data">
  7      <label>Sequences</label>
  8    </param>
  9    <param name="pattern" size="5" type="text" value="">
 10      <label>Search pattern</label>
 11    </param>
 12    <param name="mismatch" size="5" type="text" value="0">
 13      <label>Number of mismatches</label>
 14    </param>
 15    <param name="frame" type="select">
 16      <label>Frame(s) to translate</label>
 17      <option value="1">Frame 1</option>
 18      <option value="2">Frame 2</option>
 19      <option value="3">Frame 3</option>
 20      <option value="F">Forward three frames</option>
 21      <option value="-1">Frame -1</option>
 22      <option value="-2">Frame -2</option>
 23      <option value="-3">Frame -3</option>
 24      <option value="R">Reverse three frames</option>
 25      <option value="6">All six frames</option>
 26    </param>
 27    <param name="table" type="select">
 28      <label>Code to use</label>
 29      <option value="0">Standard</option>
 30      <option value="1">Standard (with alternative initiation codons)</option>
 31      <option value="2">Vertebrate Mitochondrial</option>
 32      <option value="3">Yeast Mitochondrial</option>
 33      <option value="4">Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma</option>
 34      <option value="5">Invertebrate Mitochondrial</option>
 35      <option value="6">Ciliate Macronuclear and Dasycladacean</option>
 36      <option value="9">Echinoderm Mitochondrial</option>
 37      <option value="10">Euplotid Nuclear</option>
 38      <option value="11">Bacterial</option>
 39      <option value="12">Alternative Yeast Nuclear</option>
 40      <option value="13">Ascidian Mitochondrial</option>
 41      <option value="14">Flatworm Mitochondrial</option>
 42      <option value="15">Blepharisma Macronuclear</option>
 43      <option value="16">Chlorophycean Mitochondrial</option>
 44      <option value="21">Trematode Mitochondrial</option>
 45      <option value="22">Scenedesmus obliquus</option>
 46      <option value="23">Thraustochytrium Mitochondrial</option>
 47    </param>
 48    <param name="out_format1" type="select">
 49      <label>Output Report File Format</label>
 50      <option value="table">Table</option>
 51      <option value="embl">EMBL</option>
 52      <option value="genbank">GENBANK</option>
 53      <option value="gff">GFF</option>
 54      <option value="pir">PIR</option>
 55      <option value="swiss">SwissProt</option>
 56      <option value="dbmotif">DbMotif</option>
 57      <option value="diffseq">Diffseq</option>
 58      <option value="excel">Excel (tab delimited)</option>
 59      <option value="feattable">FeatTable</option>
 60      <option value="motif">Motif</option>
 61      <option value="regions">Regions</option>
 62      <option value="seqtable">SeqTable</option>
 63      <option value="simple">SRS Simple</option>
 64      <option value="srs">SRS</option>
 65      <option value="tagseq">TagSeq</option>
 66    </param>
 67  </inputs>
 68  <outputs>
 69    <data format="fuzztran" name="out_file1" />
 70  </outputs>
 71  <tests>
 72    <test>
 73      <param name="input1" value="1.fasta"/>
 74      <param name="pattern" value="AA"/>
 75      <param name="mismatch" value="0"/>
 76      <param name="frame" value="6"/>
 77      <param name="table" value="0"/>
 78      <param name="out_format1" value="excel"/>
 79      <output name="out_file1" file="emboss_fuzztran_out.tabular"/>
 80    </test>
 81  </tests>
 82  <code file="emboss_format_corrector.py" />
 83  <help>
 84
 85.. class:: warningmark
 86
 87The input dataset needs to be sequences.
 88
 89-----
 90
 91    You can view the original documentation here_.
 92    
 93    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/fuzztran.html
 94
 95------
 96
 97**Citation**
 98
 99If 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;`_
100  </help>
101</tool>