Mercurial > repos > devteam > emboss_5
comparison emboss_syco.xml @ 10:9b98d3d903c6 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
| author | devteam |
|---|---|
| date | Fri, 12 Aug 2016 19:17:10 -0400 |
| parents | |
| children | 0e2484b6829b |
comparison
equal
deleted
inserted
replaced
| 9:18a63c800a4d | 10:9b98d3d903c6 |
|---|---|
| 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" 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" 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 | |
| 201 For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ | |
| 202 | |
| 203 If 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. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ | |
| 204 </help> | |
| 205 </tool> |