[2] | 1 | <tool id="EMBOSS: cai6" name="cai" version="5.0.0">
|
---|
| 2 | <description>CAI codon adaptation index</description>
|
---|
| 3 | <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
|
---|
| 4 | <command>cai -seqall $input1 -outfile $out_file1 -cfile $cfile -auto</command>
|
---|
| 5 | <inputs>
|
---|
| 6 | <param format="fasta" name="input1" type="data">
|
---|
| 7 | <label>On query</label>
|
---|
| 8 | </param>
|
---|
| 9 | <param name="cfile" type="select">
|
---|
| 10 | <label>Codon Usage File</label>
|
---|
| 11 | <option value="Eyeastcai.cut">Eyeastcai.cut</option>
|
---|
| 12 | <option value="Ehum.cut">Ehum.cut</option>
|
---|
| 13 | <option value="Eacc.cut">Eacc.cut</option>
|
---|
| 14 | <option value="Eadenovirus5.cut">Eadenovirus5.cut</option>
|
---|
| 15 | <option value="Eadenovirus7.cut">Eadenovirus7.cut</option>
|
---|
| 16 | <option value="Eaidlav.cut">Eaidlav.cut</option>
|
---|
| 17 | <option value="Eanasp.cut">Eanasp.cut</option>
|
---|
| 18 | <option value="Eani.cut">Eani.cut</option>
|
---|
| 19 | <option value="Eani_h.cut">Eani_h.cut</option>
|
---|
| 20 | <option value="Eanidmit.cut">Eanidmit.cut</option>
|
---|
| 21 | <option value="Easn.cut">Easn.cut</option>
|
---|
| 22 | <option value="Eath.cut">Eath.cut</option>
|
---|
| 23 | <option value="Eatu.cut">Eatu.cut</option>
|
---|
| 24 | <option value="Eavi.cut">Eavi.cut</option>
|
---|
| 25 | <option value="Ebja.cut">Ebja.cut</option>
|
---|
| 26 | <option value="Ebly.cut">Ebly.cut</option>
|
---|
| 27 | <option value="Ebme.cut">Ebme.cut</option>
|
---|
| 28 | <option value="Ebmo.cut">Ebmo.cut</option>
|
---|
| 29 | <option value="Ebna.cut">Ebna.cut</option>
|
---|
| 30 | <option value="Ebov.cut">Ebov.cut</option>
|
---|
| 31 | <option value="Ebovsp.cut">Ebovsp.cut</option>
|
---|
| 32 | <option value="Ebst.cut">Ebst.cut</option>
|
---|
| 33 | <option value="Ebsu.cut">Ebsu.cut</option>
|
---|
| 34 | <option value="Ebsu_h.cut">Ebsu_h.cut</option>
|
---|
| 35 | <option value="Ecac.cut">Ecac.cut</option>
|
---|
| 36 | <option value="Ecal.cut">Ecal.cut</option>
|
---|
| 37 | <option value="Eccr.cut">Eccr.cut</option>
|
---|
| 38 | <option value="Ecel.cut">Ecel.cut</option>
|
---|
| 39 | <option value="Echi.cut">Echi.cut</option>
|
---|
| 40 | <option value="Echicken.cut">Echicken.cut</option>
|
---|
| 41 | <option value="Echisp.cut">Echisp.cut</option>
|
---|
| 42 | <option value="Echk.cut">Echk.cut</option>
|
---|
| 43 | <option value="Echmp.cut">Echmp.cut</option>
|
---|
| 44 | <option value="Echnt.cut">Echnt.cut</option>
|
---|
| 45 | <option value="Echos.cut">Echos.cut</option>
|
---|
| 46 | <option value="Echzm.cut">Echzm.cut</option>
|
---|
| 47 | <option value="Echzmrubp.cut">Echzmrubp.cut</option>
|
---|
| 48 | <option value="Ecpx.cut">Ecpx.cut</option>
|
---|
| 49 | <option value="Ecre.cut">Ecre.cut</option>
|
---|
| 50 | <option value="Ecrisp.cut">Ecrisp.cut</option>
|
---|
| 51 | <option value="Ectr.cut">Ectr.cut</option>
|
---|
| 52 | <option value="Edayhoff.cut">Edayhoff.cut</option>
|
---|
| 53 | <option value="Eddi.cut">Eddi.cut</option>
|
---|
| 54 | <option value="Eddi_h.cut">Eddi_h.cut</option>
|
---|
| 55 | <option value="Edog.cut">Edog.cut</option>
|
---|
| 56 | <option value="Edro.cut">Edro.cut</option>
|
---|
| 57 | <option value="Edro_h.cut">Edro_h.cut</option>
|
---|
| 58 | <option value="Edrosophila.cut">Edrosophila.cut</option>
|
---|
| 59 | <option value="Eeca.cut">Eeca.cut</option>
|
---|
| 60 | <option value="Eeco.cut">Eeco.cut</option>
|
---|
| 61 | <option value="Eeco_h.cut">Eeco_h.cut</option>
|
---|
| 62 | <option value="Eecoli.cut">Eecoli.cut</option>
|
---|
| 63 | <option value="Ef1.cut">Ef1.cut</option>
|
---|
| 64 | <option value="Efish.cut">Efish.cut</option>
|
---|
| 65 | <option value="Efmdvpolyp.cut">Efmdvpolyp.cut</option>
|
---|
| 66 | <option value="Eham.cut">Eham.cut</option>
|
---|
| 67 | <option value="Ehha.cut">Ehha.cut</option>
|
---|
| 68 | <option value="Ehin.cut">Ehin.cut</option>
|
---|
| 69 | <option value="Ehma.cut">Ehma.cut</option>
|
---|
| 70 | <option value="Ehuman.cut">Ehuman.cut</option>
|
---|
| 71 | <option value="Ekla.cut">Ekla.cut</option>
|
---|
| 72 | <option value="Ekpn.cut">Ekpn.cut</option>
|
---|
| 73 | <option value="Ella.cut">Ella.cut</option>
|
---|
| 74 | <option value="Emac.cut">Emac.cut</option>
|
---|
| 75 | <option value="Emaize.cut">Emaize.cut</option>
|
---|
| 76 | <option value="Emam_h.cut">Emam_h.cut</option>
|
---|
| 77 | <option value="Emixlg.cut">Emixlg.cut</option>
|
---|
| 78 | <option value="Emouse.cut">Emouse.cut</option>
|
---|
| 79 | <option value="Emsa.cut">Emsa.cut</option>
|
---|
| 80 | <option value="Emse.cut">Emse.cut</option>
|
---|
| 81 | <option value="Emta.cut">Emta.cut</option>
|
---|
| 82 | <option value="Emtu.cut">Emtu.cut</option>
|
---|
| 83 | <option value="Emus.cut">Emus.cut</option>
|
---|
| 84 | <option value="Emussp.cut">Emussp.cut</option>
|
---|
| 85 | <option value="Emva.cut">Emva.cut</option>
|
---|
| 86 | <option value="Emze.cut">Emze.cut</option>
|
---|
| 87 | <option value="Emzecp.cut">Emzecp.cut</option>
|
---|
| 88 | <option value="Encr.cut">Encr.cut</option>
|
---|
| 89 | <option value="Eneu.cut">Eneu.cut</option>
|
---|
| 90 | <option value="Engo.cut">Engo.cut</option>
|
---|
| 91 | <option value="Eoncsp.cut">Eoncsp.cut</option>
|
---|
| 92 | <option value="Epae.cut">Epae.cut</option>
|
---|
| 93 | <option value="Epea.cut">Epea.cut</option>
|
---|
| 94 | <option value="Epet.cut">Epet.cut</option>
|
---|
| 95 | <option value="Epfa.cut">Epfa.cut</option>
|
---|
| 96 | <option value="Ephix174.cut">Ephix174.cut</option>
|
---|
| 97 | <option value="Ephv.cut">Ephv.cut</option>
|
---|
| 98 | <option value="Ephy.cut">Ephy.cut</option>
|
---|
| 99 | <option value="Epig.cut">Epig.cut</option>
|
---|
| 100 | <option value="Epolyomaa2.cut">Epolyomaa2.cut</option>
|
---|
| 101 | <option value="Epombe.cut">Epombe.cut</option>
|
---|
| 102 | <option value="Epombecai.cut">Epombecai.cut</option>
|
---|
| 103 | <option value="Epot.cut">Epot.cut</option>
|
---|
| 104 | <option value="Eppu.cut">Eppu.cut</option>
|
---|
| 105 | <option value="Epse.cut">Epse.cut</option>
|
---|
| 106 | <option value="Epsy.cut">Epsy.cut</option>
|
---|
| 107 | <option value="Epvu.cut">Epvu.cut</option>
|
---|
| 108 | <option value="Erab.cut">Erab.cut</option>
|
---|
| 109 | <option value="Erabbit.cut">Erabbit.cut</option>
|
---|
| 110 | <option value="Erabsp.cut">Erabsp.cut</option>
|
---|
| 111 | <option value="Erat.cut">Erat.cut</option>
|
---|
| 112 | <option value="Eratsp.cut">Eratsp.cut</option>
|
---|
| 113 | <option value="Erca.cut">Erca.cut</option>
|
---|
| 114 | <option value="Erhm.cut">Erhm.cut</option>
|
---|
| 115 | <option value="Eric.cut">Eric.cut</option>
|
---|
| 116 | <option value="Erle.cut">Erle.cut</option>
|
---|
| 117 | <option value="Erme.cut">Erme.cut</option>
|
---|
| 118 | <option value="Ersp.cut">Ersp.cut</option>
|
---|
| 119 | <option value="Esalsp.cut">Esalsp.cut</option>
|
---|
| 120 | <option value="Esau.cut">Esau.cut</option>
|
---|
| 121 | <option value="Esco.cut">Esco.cut</option>
|
---|
| 122 | <option value="Esgi.cut">Esgi.cut</option>
|
---|
| 123 | <option value="Eshp.cut">Eshp.cut</option>
|
---|
| 124 | <option value="Eshpsp.cut">Eshpsp.cut</option>
|
---|
| 125 | <option value="Esli.cut">Esli.cut</option>
|
---|
| 126 | <option value="Eslm.cut">Eslm.cut</option>
|
---|
| 127 | <option value="Esma.cut">Esma.cut</option>
|
---|
| 128 | <option value="Esmi.cut">Esmi.cut</option>
|
---|
| 129 | <option value="Esmu.cut">Esmu.cut</option>
|
---|
| 130 | <option value="Esoy.cut">Esoy.cut</option>
|
---|
| 131 | <option value="Espi.cut">Espi.cut</option>
|
---|
| 132 | <option value="Espn.cut">Espn.cut</option>
|
---|
| 133 | <option value="Espo.cut">Espo.cut</option>
|
---|
| 134 | <option value="Espo_h.cut">Espo_h.cut</option>
|
---|
| 135 | <option value="Espu.cut">Espu.cut</option>
|
---|
| 136 | <option value="Esta.cut">Esta.cut</option>
|
---|
| 137 | <option value="Esty.cut">Esty.cut</option>
|
---|
| 138 | <option value="Esus.cut">Esus.cut</option>
|
---|
| 139 | <option value="Esv40.cut">Esv40.cut</option>
|
---|
| 140 | <option value="Esyhsp.cut">Esyhsp.cut</option>
|
---|
| 141 | <option value="Esynsp.cut">Esynsp.cut</option>
|
---|
| 142 | <option value="Etbr.cut">Etbr.cut</option>
|
---|
| 143 | <option value="Etcr.cut">Etcr.cut</option>
|
---|
| 144 | <option value="Eter.cut">Eter.cut</option>
|
---|
| 145 | <option value="Etetsp.cut">Etetsp.cut</option>
|
---|
| 146 | <option value="Etob.cut">Etob.cut</option>
|
---|
| 147 | <option value="Etobcp.cut">Etobcp.cut</option>
|
---|
| 148 | <option value="Etom.cut">Etom.cut</option>
|
---|
| 149 | <option value="Etrb.cut">Etrb.cut</option>
|
---|
| 150 | <option value="Evco.cut">Evco.cut</option>
|
---|
| 151 | <option value="Ewht.cut">Ewht.cut</option>
|
---|
| 152 | <option value="Exel.cut">Exel.cut</option>
|
---|
| 153 | <option value="Exenopus.cut">Exenopus.cut</option>
|
---|
| 154 | <option value="Eyeast.cut">Eyeast.cut</option>
|
---|
| 155 | <option value="Eyen.cut">Eyen.cut</option>
|
---|
| 156 | <option value="Eysc.cut">Eysc.cut</option>
|
---|
| 157 | <option value="Eysc_h.cut">Eysc_h.cut</option>
|
---|
| 158 | <option value="Eyscmt.cut">Eyscmt.cut</option>
|
---|
| 159 | <option value="Eysp.cut">Eysp.cut</option>
|
---|
| 160 | <option value="Ezebrafish.cut">Ezebrafish.cut</option>
|
---|
| 161 | <option value="Ezma.cut">Ezma.cut</option>
|
---|
| 162 | </param>
|
---|
| 163 | </inputs>
|
---|
| 164 | <outputs>
|
---|
| 165 | <data format="cai" name="out_file1" />
|
---|
| 166 | </outputs> |
---|
| 167 | <tests> |
---|
| 168 | <test> |
---|
| 169 | <param name="input1" value="2.fasta"/> |
---|
| 170 | <param name="cfile" value="Eyeastcai.cut"/> |
---|
| 171 | <output name="out_file1" file="emboss_cai_out.cai"/> |
---|
| 172 | </test> |
---|
| 173 | </tests>
|
---|
| 174 | <help> |
---|
| 175 | .. class:: warningmark |
---|
| 176 | |
---|
| 177 | The input dataset needs to be sequences. |
---|
| 178 | |
---|
| 179 | ----- |
---|
| 180 | |
---|
| 181 | You can view the original documentation here_. |
---|
| 182 | |
---|
| 183 | .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/cai.html |
---|
| 184 | </help> |
---|
| 185 | </tool> |
---|