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/tools/emboss_5/emboss_twofeat.xml

https://bitbucket.org/cistrome/cistrome-harvard/
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  1<tool id="EMBOSS: twofeat104" name="twofeat" version="5.0.0">
  2  <description>Finds neighbouring pairs of features in sequences</description>
  3  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
  4  <command>twofeat -sequence $input1 -outfile $out_file1 -atype "$atype" -btype "$btype" -minrange "$minrange" -maxrange "$maxrange" -asource "$asource" -asense $asense -aminscore "$aminscore"
  5  -amaxscore "$amaxscore" -atag "$atag" -avalue "$avalue" -bsource "$bsource" -bsense "$bsense" -bminscore "$bminscore" -bmaxscore "$bmaxscore" -btag "$btag" -bvalue "$bvalue" -overlap $overlap
  6  -rangetype $rangetype -sense $sense -order $order -twoout $twoout -typeout "$typeout" -rformat2 $out_format1 -auto</command>
  7  <inputs>
  8    <param format="data" name="input1" type="data">
  9      <label>Sequences</label>
 10    </param>
 11    <param name="atype" size="50" type="text" value="*">
 12      <label>Feature type you wish to allow. Feature 1</label>
 13    </param>
 14    <param name="btype" size="50" type="text" value="*">
 15      <label>Feature type you wish to allow. Feature 2</label>
 16    </param>
 17    <param name="minrange" size="5" type="text" value="0">
 18      <label>Minimun range</label>
 19    </param>
 20    <param name="maxrange" size="5" type="text" value="0">
 21      <label>Maximum range</label>
 22    </param>
 23    <param name="asource" size="50" type="text" value="*">
 24      <label>Feature source 1</label>
 25    </param>
 26    <param name="asense" type="select">
 27      <label>Feature sense 1</label>
 28      <option value="0">Any sense</option>
 29      <option value="+">Forward sense</option>
 30      <option value="-">Reverse sense</option>
 31    </param>
 32    <param name="aminscore" size="5" type="text" value="0.0">
 33      <label>Feature 1 minimum score</label>
 34    </param>
 35    <param name="amaxscore" size="5" type="text" value="0.0">
 36      <label>Feature1 maxiumum score</label>
 37    </param>
 38    <param name="atag" size="50" type="text" value="*">
 39      <label>Feature 1 tag</label>
 40    </param>
 41    <param name="avalue" size="50" type="text" value="*">
 42      <label>Tag 1 value</label>
 43    </param>
 44    <param name="bsource" size="50" type="text" value="*">
 45      <label>Feature 2 source</label>
 46    </param>
 47    <param name="bsense" type="select">
 48      <label>Feature 2 sense</label>
 49      <option value="0">Any sense</option>
 50      <option value="+">Forward sense</option>
 51      <option value="-">Reverse sense</option>
 52    </param>
 53    <param name="bminscore" size="5" type="text" value="0.0">
 54      <label>Feature 2 miniumum score</label>
 55    </param>
 56    <param name="bmaxscore" size="5" type="text" value="0.0">
 57      <label>Feature 2 maximum score</label>
 58    </param>
 59    <param name="btag" size="50" type="text" value="*">
 60      <label>Feature 2 tag</label>
 61    </param>
 62    <param name="bvalue" size="50" type="text" value="*">
 63      <label>Feature 2 tag value</label>
 64    </param>
 65    <param name="overlap" type="select">
 66      <label>opverlaps allowed</label>
 67      <option value="A">Any</option>
 68      <option value="O">Overlap required but not within</option>
 69      <option value="NO">No overlaps are allowed</option>
 70      <option value="NW:">Overlap required but not within</option>
 71      <option value="AW">A must be all within B</option>
 72      <option value="BW">B must be all within A</option>
 73    </param>
 74    <param name="rangetype" type="select">
 75      <label>How to determine range</label>
 76      <option value="N">From nearest ends</option>
 77      <option value="L">From left ends</option>
 78      <option value="R">From right ends</option>
 79      <option value="F">From furthest ends</option>
 80    </param>
 81    <param name="sense" type="select">
 82      <label>Required sense</label>
 83      <option value="A">Any sense</option>
 84      <option value="S">Same sense</option>
 85      <option value="O">Opposite sense</option>
 86    </param>
 87    <param name="order" type="select">
 88      <label>Required order of the two features</label>
 89      <option value="A">Any</option>
 90      <option value="AB">Feature A then feature B</option>
 91      <option value="BA">Feature B then feature A</option>
 92    </param>
 93    <param name="twoout" type="select">
 94      <label>Write out the two features themselves</label>
 95      <option value="no">No</option>
 96      <option value="yes">Yes</option>
 97    </param>
 98    <param name="typeout" size="50" type="text" value="misc_feature">
 99      <label>New feature type</label>
100    </param>
101    <param name="out_format1" type="select">
102      <label>Output Report File Format</label>
103      <option value="table">Table</option>
104      <option value="embl">EMBL</option>
105      <option value="genbank">GENBANK</option>
106      <option value="gff">GFF</option>
107      <option value="pir">PIR</option>
108      <option value="swiss">SwissProt</option>
109      <option value="dbmotif">DbMotif</option>
110      <option value="diffseq">Diffseq</option>
111      <option value="excel">Excel (tab delimited)</option>
112      <option value="feattable">FeatTable</option>
113      <option value="motif">Motif</option>
114      <option value="regions">Regions</option>
115      <option value="seqtable">SeqTable</option>
116      <option value="simple">SRS Simple</option>
117      <option value="srs">SRS</option>
118      <option value="tagseq">TagSeq</option>
119    </param>
120  </inputs>
121  <outputs>
122    <data format="table" name="out_file1" />
123  </outputs>
124  <code file="emboss_format_corrector.py" />
125  <help>
126    You can view the original documentation here_.
127    
128    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/twofeat.html
129
130------
131
132**Citation**
133
134If 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;`_
135  </help>
136</tool>