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/tools/emboss_5/emboss_sirna.xml

https://bitbucket.org/cistrome/cistrome-harvard/
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  1<tool id="EMBOSS: sirna89" name="sirna" version="5.0.0">
  2  <description>Finds siRNA duplexes in mRNA</description>
  3  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
  4  <command>sirna -sequence $input1 -outfile $ofile1 -outseq $ofile2 -poliii $poliii -aa $aa -tt $tt -polybase $polybase -context $context -rformat2 $out_format1 -osformat3 $out_format2
  5  -auto</command>
  6  <inputs>
  7    <param format="fasta" name="input1" type="data">
  8      <label>Sequences</label>
  9    </param>
 10    <param name="poliii" type="select">
 11      <label>Select only the 21 base probes that start with a purine (Pol III expression vectors)</label>
 12      <option value="no">No</option>
 13      <option value="yes">Yes</option>
 14    </param>
 15    <param name="aa" type="select">
 16      <label>Select only those 23 base regions that start with AA</label>
 17      <option value="no">No</option>
 18      <option value="yes">Yes</option>
 19    </param>
 20    <param name="tt" type="select">
 21      <label>Select only those 23 base regions that end with TT</label>
 22      <option value="no">No</option>
 23      <option value="yes">Yes</option>
 24    </param>
 25    <param name="polybase" type="select">
 26      <label>Report more than those 23 base regions that have no repeat of 4 or more of any bases in a row</label>
 27      <option value="yes">Yes</option>
 28      <option value="no">No</option>
 29    </param>
 30    <param name="context" type="select">
 31      <label>Displays the whole 23 bases of the region with the first two bases in brackets</label>
 32      <option value="no">No</option>
 33      <option value="yes">Yes</option>
 34    </param>
 35    <param name="out_format1" type="select">
 36      <label>Output Report File Format</label>
 37      <option value="table">Table</option>
 38      <option value="embl">EMBL</option>
 39      <option value="genbank">GENBANK</option>
 40      <option value="gff">GFF</option>
 41      <option value="pir">PIR</option>
 42      <option value="swiss">SwissProt</option>
 43      <option value="dbmotif">DbMotif</option>
 44      <option value="diffseq">Diffseq</option>
 45      <option value="excel">Excel (tab delimited)</option>
 46      <option value="feattable">FeatTable</option>
 47      <option value="motif">Motif</option>
 48      <option value="regions">Regions</option>
 49      <option value="seqtable">SeqTable</option>
 50      <option value="simple">SRS Simple</option>
 51      <option value="srs">SRS</option>
 52      <option value="tagseq">TagSeq</option>
 53    </param>
 54    <param name="out_format2" type="select">
 55      <label>Output Sequence File Format</label>
 56      <option value="fasta">FASTA (m)</option>
 57      <option value="acedb">ACeDB (m)</option>
 58      <option value="asn1">ASN.1 (m)</option>
 59      <option value="clustal">Clustal (m)</option>
 60      <option value="codata">CODATA (m)</option>
 61      <option value="embl">EMBL (m)</option>
 62      <option value="fitch">Fitch (m)</option>
 63      <option value="gcg">Wisconsin Package GCG 9.x and 10.x (s)</option>
 64      <option value="genbank">GENBANK (m)</option>
 65      <option value="gff">GFF (m)</option>
 66      <option value="hennig86">Hennig86 (m)</option>
 67      <option value="ig">Intelligenetics (m)</option>
 68      <option value="jackknifer">Jackknifer (m)</option>
 69      <option value="jackknifernon">Jackknifernon (m)</option>
 70      <option value="mega">Mega (m)</option>
 71      <option value="meganon">Meganon (m)</option>
 72      <option value="msf">Wisconsin Package GCG's MSF (m)</option>
 73      <option value="pir">NBRF (PIR) (m)</option>
 74      <option value="ncbi">NCBI style FASTA (m)</option>
 75      <option value="nexus">Nexus/PAUP (m)</option>
 76      <option value="nexusnon">Nexusnon/PAUPnon (m)</option>
 77      <option value="phylip">PHYLIP interleaved (m)</option>
 78      <option value="phylipnon">PHYLIP non-interleaved (m)</option>
 79      <option value="selex">SELEX (m)</option>
 80      <option value="staden">Staden (s)</option>
 81      <option value="strider">DNA strider (m)</option>
 82      <option value="swiss">SwisProt entry (m)</option>
 83      <option value="text">Plain sequence (s)</option>
 84      <option value="treecon">Treecon (m)</option>
 85    </param>
 86  </inputs>
 87  <outputs>
 88    <data format="table" name="ofile1" />
 89    <data format="fasta" name="ofile2" />
 90  </outputs>
 91  <tests>
 92    <test>
 93      <param name="input1" value="2.fasta"/>
 94      <param name="poliii" value="no"/>
 95      <param name="aa" value="no"/>
 96      <param name="tt" value="no"/>
 97      <param name="polybase" value="yes"/>
 98      <param name="context" value="no"/>
 99      <param name="mismatchpercent" value="0"/>
100      <param name="out_format1" value="gff"/>
101      <param name="out_format2" value="fasta"/>
102      <output name="ofile2" file="emboss_sirna_out.fasta"/>
103    </test>
104  </tests>
105  <code file="emboss_format_corrector.py" />
106  <help>
107
108.. class:: warningmark
109
110The input dataset needs to be sequences.
111
112-----
113
114    You can view the original documentation here_.
115    
116    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/sirna.html
117
118------
119
120**Citation**
121
122If 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;`_
123  </help>
124</tool>