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/tools/emboss_5/emboss_syco.xml

https://bitbucket.org/cistrome/cistrome-harvard/
XML | 203 lines | 187 code | 5 blank | 11 comment | 0 complexity | de0709dc84a841d995612766f7fdb191 MD5 | raw file
  1<tool id="EMBOSS: syco96" name="syco" version="5.0.0">
  2  <!-- graphics output -->
  3  <description>Synonymous codon usage Gribskov statistic plot</description>
  4  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
  5  <command interpreter="perl">emboss_single_outputfile_wrapper.pl syco -sequence $input1 -graph png -goutfile $ofile1 -outfile $ofile2 -cfile $cfile -window "$window" -uncommon $uncommon -minimum "$minimum"
  6  -auto</command>
  7  <inputs>
  8    <param format="fasta" name="input1" type="data">
  9      <label>Sequence</label>
 10    </param>
 11    <param name="cfile" type="select">
 12      <label>Codon Usage File</label>
 13      <option value="Ehum.cut">Ehum.cut</option>
 14      <option value="Eyeastcai.cut">Eyeastcai.cut</option>
 15      <option value="Eacc.cut">Eacc.cut</option>
 16      <option value="Eadenovirus5.cut">Eadenovirus5.cut</option>
 17      <option value="Eadenovirus7.cut">Eadenovirus7.cut</option>
 18      <option value="Eaidlav.cut">Eaidlav.cut</option>
 19      <option value="Eanasp.cut">Eanasp.cut</option>
 20      <option value="Eani.cut">Eani.cut</option>
 21      <option value="Eani_h.cut">Eani_h.cut</option>
 22      <option value="Eanidmit.cut">Eanidmit.cut</option>
 23      <option value="Easn.cut">Easn.cut</option>
 24      <option value="Eath.cut">Eath.cut</option>
 25      <option value="Eatu.cut">Eatu.cut</option>
 26      <option value="Eavi.cut">Eavi.cut</option>
 27      <option value="Ebja.cut">Ebja.cut</option>
 28      <option value="Ebly.cut">Ebly.cut</option>
 29      <option value="Ebme.cut">Ebme.cut</option>
 30      <option value="Ebmo.cut">Ebmo.cut</option>
 31      <option value="Ebna.cut">Ebna.cut</option>
 32      <option value="Ebov.cut">Ebov.cut</option>
 33      <option value="Ebovsp.cut">Ebovsp.cut</option>
 34      <option value="Ebst.cut">Ebst.cut</option>
 35      <option value="Ebsu.cut">Ebsu.cut</option>
 36      <option value="Ebsu_h.cut">Ebsu_h.cut</option>
 37      <option value="Ecac.cut">Ecac.cut</option>
 38      <option value="Ecal.cut">Ecal.cut</option>
 39      <option value="Eccr.cut">Eccr.cut</option>
 40      <option value="Ecel.cut">Ecel.cut</option>
 41      <option value="Echi.cut">Echi.cut</option>
 42      <option value="Echicken.cut">Echicken.cut</option>
 43      <option value="Echisp.cut">Echisp.cut</option>
 44      <option value="Echk.cut">Echk.cut</option>
 45      <option value="Echmp.cut">Echmp.cut</option>
 46      <option value="Echnt.cut">Echnt.cut</option>
 47      <option value="Echos.cut">Echos.cut</option>
 48      <option value="Echzm.cut">Echzm.cut</option>
 49      <option value="Echzmrubp.cut">Echzmrubp.cut</option>
 50      <option value="Ecpx.cut">Ecpx.cut</option>
 51      <option value="Ecre.cut">Ecre.cut</option>
 52      <option value="Ecrisp.cut">Ecrisp.cut</option>
 53      <option value="Ectr.cut">Ectr.cut</option>
 54      <option value="Edayhoff.cut">Edayhoff.cut</option>
 55      <option value="Eddi.cut">Eddi.cut</option>
 56      <option value="Eddi_h.cut">Eddi_h.cut</option>
 57      <option value="Edog.cut">Edog.cut</option>
 58      <option value="Edro.cut">Edro.cut</option>
 59      <option value="Edro_h.cut">Edro_h.cut</option>
 60      <option value="Edrosophila.cut">Edrosophila.cut</option>
 61      <option value="Eeca.cut">Eeca.cut</option>
 62      <option value="Eeco.cut">Eeco.cut</option>
 63      <option value="Eeco_h.cut">Eeco_h.cut</option>
 64      <option value="Eecoli.cut">Eecoli.cut</option>
 65      <option value="Ef1.cut">Ef1.cut</option>
 66      <option value="Efish.cut">Efish.cut</option>
 67      <option value="Efmdvpolyp.cut">Efmdvpolyp.cut</option>
 68      <option value="Eham.cut">Eham.cut</option>
 69      <option value="Ehha.cut">Ehha.cut</option>
 70      <option value="Ehin.cut">Ehin.cut</option>
 71      <option value="Ehma.cut">Ehma.cut</option>
 72      <option value="Ehuman.cut">Ehuman.cut</option>
 73      <option value="Ekla.cut">Ekla.cut</option>
 74      <option value="Ekpn.cut">Ekpn.cut</option>
 75      <option value="Ella.cut">Ella.cut</option>
 76      <option value="Emac.cut">Emac.cut</option>
 77      <option value="Emaize.cut">Emaize.cut</option>
 78      <option value="Emam_h.cut">Emam_h.cut</option>
 79      <option value="Emixlg.cut">Emixlg.cut</option>
 80      <option value="Emouse.cut">Emouse.cut</option>
 81      <option value="Emsa.cut">Emsa.cut</option>
 82      <option value="Emse.cut">Emse.cut</option>
 83      <option value="Emta.cut">Emta.cut</option>
 84      <option value="Emtu.cut">Emtu.cut</option>
 85      <option value="Emus.cut">Emus.cut</option>
 86      <option value="Emussp.cut">Emussp.cut</option>
 87      <option value="Emva.cut">Emva.cut</option>
 88      <option value="Emze.cut">Emze.cut</option>
 89      <option value="Emzecp.cut">Emzecp.cut</option>
 90      <option value="Encr.cut">Encr.cut</option>
 91      <option value="Eneu.cut">Eneu.cut</option>
 92      <option value="Engo.cut">Engo.cut</option>
 93      <option value="Eoncsp.cut">Eoncsp.cut</option>
 94      <option value="Epae.cut">Epae.cut</option>
 95      <option value="Epea.cut">Epea.cut</option>
 96      <option value="Epet.cut">Epet.cut</option>
 97      <option value="Epfa.cut">Epfa.cut</option>
 98      <option value="Ephix174.cut">Ephix174.cut</option>
 99      <option value="Ephv.cut">Ephv.cut</option>
100      <option value="Ephy.cut">Ephy.cut</option>
101      <option value="Epig.cut">Epig.cut</option>
102      <option value="Epolyomaa2.cut">Epolyomaa2.cut</option>
103      <option value="Epombe.cut">Epombe.cut</option>
104      <option value="Epombecai.cut">Epombecai.cut</option>
105      <option value="Epot.cut">Epot.cut</option>
106      <option value="Eppu.cut">Eppu.cut</option>
107      <option value="Epse.cut">Epse.cut</option>
108      <option value="Epsy.cut">Epsy.cut</option>
109      <option value="Epvu.cut">Epvu.cut</option>
110      <option value="Erab.cut">Erab.cut</option>
111      <option value="Erabbit.cut">Erabbit.cut</option>
112      <option value="Erabsp.cut">Erabsp.cut</option>
113      <option value="Erat.cut">Erat.cut</option>
114      <option value="Eratsp.cut">Eratsp.cut</option>
115      <option value="Erca.cut">Erca.cut</option>
116      <option value="Erhm.cut">Erhm.cut</option>
117      <option value="Eric.cut">Eric.cut</option>
118      <option value="Erle.cut">Erle.cut</option>
119      <option value="Erme.cut">Erme.cut</option>
120      <option value="Ersp.cut">Ersp.cut</option>
121      <option value="Esalsp.cut">Esalsp.cut</option>
122      <option value="Esau.cut">Esau.cut</option>
123      <option value="Esco.cut">Esco.cut</option>
124      <option value="Esgi.cut">Esgi.cut</option>
125      <option value="Eshp.cut">Eshp.cut</option>
126      <option value="Eshpsp.cut">Eshpsp.cut</option>
127      <option value="Esli.cut">Esli.cut</option>
128      <option value="Eslm.cut">Eslm.cut</option>
129      <option value="Esma.cut">Esma.cut</option>
130      <option value="Esmi.cut">Esmi.cut</option>
131      <option value="Esmu.cut">Esmu.cut</option>
132      <option value="Esoy.cut">Esoy.cut</option>
133      <option value="Espi.cut">Espi.cut</option>
134      <option value="Espn.cut">Espn.cut</option>
135      <option value="Espo.cut">Espo.cut</option>
136      <option value="Espo_h.cut">Espo_h.cut</option>
137      <option value="Espu.cut">Espu.cut</option>
138      <option value="Esta.cut">Esta.cut</option>
139      <option value="Esty.cut">Esty.cut</option>
140      <option value="Esus.cut">Esus.cut</option>
141      <option value="Esv40.cut">Esv40.cut</option>
142      <option value="Esyhsp.cut">Esyhsp.cut</option>
143      <option value="Esynsp.cut">Esynsp.cut</option>
144      <option value="Etbr.cut">Etbr.cut</option>
145      <option value="Etcr.cut">Etcr.cut</option>
146      <option value="Eter.cut">Eter.cut</option>
147      <option value="Etetsp.cut">Etetsp.cut</option>
148      <option value="Etob.cut">Etob.cut</option>
149      <option value="Etobcp.cut">Etobcp.cut</option>
150      <option value="Etom.cut">Etom.cut</option>
151      <option value="Etrb.cut">Etrb.cut</option>
152      <option value="Evco.cut">Evco.cut</option>
153      <option value="Ewht.cut">Ewht.cut</option>
154      <option value="Exel.cut">Exel.cut</option>
155      <option value="Exenopus.cut">Exenopus.cut</option>
156      <option value="Eyeast.cut">Eyeast.cut</option>
157      <option value="Eyen.cut">Eyen.cut</option>
158      <option value="Eysc.cut">Eysc.cut</option>
159      <option value="Eysc_h.cut">Eysc_h.cut</option>
160      <option value="Eyscmt.cut">Eyscmt.cut</option>
161      <option value="Eysp.cut">Eysp.cut</option>
162      <option value="Ezebrafish.cut">Ezebrafish.cut</option>
163      <option value="Ezma.cut">Ezma.cut</option>
164    </param>
165    <param name="window" size="4" type="text" value="30">
166      <label>Averaging window</label>
167    </param>
168    <param name="uncommon" type="select">
169      <label>Show common codon usage</label>
170      <option value="no">No</option>
171      <option value="yes">Yes</option>
172    </param>
173    <param name="minimum" size="4" type="text" value="0.15">
174      <label>Minimum value for a common codon</label>
175    </param>
176  </inputs>
177  <outputs>
178    <data format="png" name="ofile1" />
179    <data format="syco" name="ofile2" />
180  </outputs>
181 <!--   <tests>
182    <test>
183      <param name="input1" value="2.fasta"/>
184      <param name="cfile" value="Ehum.cut"/>
185      <param name="window" value="30"/>
186      <param name="uncommon" value="no"/>
187      <param name="minimum" value="0.15"/>
188      <output name="ofile2" file="emboss_syco_out.syco"/>
189    </test>
190  </tests> -->
191  <help>
192
193    You can view the original documentation here_.
194    
195    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/syco.html
196
197------
198
199**Citation**
200
201If 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;`_
202  </help>
203</tool>