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galaxy/tools/emboss_5/emboss_codcmp.xml
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<tool id="EMBOSS_codcmp12" name="codcmp">
<description>Codon usage table comparison</description>
<command>codcmp -first $cfile1 -second $cfile2 -outfile $out_file1 -auto</command>
<inputs>
<param name="cfile1" type="select">
<label>Codon Usage File 1</label>
<option value="Ehum.cut">Ehum.cut</option>
<option value="Eacc.cut">Eacc.cut</option>
<option value="Eadenovirus5.cut">Eadenovirus5.cut</option>
<option value="Eadenovirus7.cut">Eadenovirus7.cut</option>
<option value="Eaidlav.cut">Eaidlav.cut</option>
<option value="Eanasp.cut">Eanasp.cut</option>
<option value="Eani.cut">Eani.cut</option>
<option value="Eani_h.cut">Eani_h.cut</option>
<option value="Eanidmit.cut">Eanidmit.cut</option>
<option value="Easn.cut">Easn.cut</option>
<option value="Eath.cut">Eath.cut</option>
<option value="Eatu.cut">Eatu.cut</option>
<option value="Eavi.cut">Eavi.cut</option>
<option value="Ebja.cut">Ebja.cut</option>
<option value="Ebly.cut">Ebly.cut</option>
<option value="Ebme.cut">Ebme.cut</option>
<option value="Ebmo.cut">Ebmo.cut</option>
<option value="Ebna.cut">Ebna.cut</option>
<option value="Ebov.cut">Ebov.cut</option>
<option value="Ebovsp.cut">Ebovsp.cut</option>
<option value="Ebst.cut">Ebst.cut</option>
<option value="Ebsu.cut">Ebsu.cut</option>
<option value="Ebsu_h.cut">Ebsu_h.cut</option>
<option value="Ecac.cut">Ecac.cut</option>
<option value="Ecal.cut">Ecal.cut</option>
<option value="Eccr.cut">Eccr.cut</option>
<option value="Ecel.cut">Ecel.cut</option>
<option value="Echi.cut">Echi.cut</option>
<option value="Echicken.cut">Echicken.cut</option>
<option value="Echisp.cut">Echisp.cut</option>
<option value="Echk.cut">Echk.cut</option>
<option value="Echmp.cut">Echmp.cut</option>
<option value="Echnt.cut">Echnt.cut</option>
<option value="Echos.cut">Echos.cut</option>
<option value="Echzm.cut">Echzm.cut</option>
<option value="Echzmrubp.cut">Echzmrubp.cut</option>
<option value="Ecpx.cut">Ecpx.cut</option>
<option value="Ecre.cut">Ecre.cut</option>
<option value="Ecrisp.cut">Ecrisp.cut</option>
<option value="Ectr.cut">Ectr.cut</option>
<option value="Edayhoff.cut">Edayhoff.cut</option>
<option value="Eddi.cut">Eddi.cut</option>
<option value="Eddi_h.cut">Eddi_h.cut</option>
<option value="Edog.cut">Edog.cut</option>
<option value="Edro.cut">Edro.cut</option>
<option value="Edro_h.cut">Edro_h.cut</option>
<option value="Edrosophila.cut">Edrosophila.cut</option>
<option value="Eeca.cut">Eeca.cut</option>
<option value="Eeco.cut">Eeco.cut</option>
<option value="Eeco_h.cut">Eeco_h.cut</option>
<option value="Eecoli.cut">Eecoli.cut</option>
<option value="Ef1.cut">Ef1.cut</option>
<option value="Efish.cut">Efish.cut</option>
<option value="Efmdvpolyp.cut">Efmdvpolyp.cut</option>
<option value="Eham.cut">Eham.cut</option>
<option value="Ehha.cut">Ehha.cut</option>
<option value="Ehin.cut">Ehin.cut</option>
<option value="Ehma.cut">Ehma.cut</option>
<option value="Ehuman.cut">Ehuman.cut</option>
<option value="Ekla.cut">Ekla.cut</option>
<option value="Ekpn.cut">Ekpn.cut</option>
<option value="Ella.cut">Ella.cut</option>
<option value="Emac.cut">Emac.cut</option>
<option value="Emaize.cut">Emaize.cut</option>
<option value="Emam_h.cut">Emam_h.cut</option>
<option value="Emixlg.cut">Emixlg.cut</option>
<option value="Emouse.cut">Emouse.cut</option>
<option value="Emsa.cut">Emsa.cut</option>
<option value="Emse.cut">Emse.cut</option>
<option value="Emta.cut">Emta.cut</option>
<option value="Emtu.cut">Emtu.cut</option>
<option value="Emus.cut">Emus.cut</option>
<option value="Emussp.cut">Emussp.cut</option>
<option value="Emva.cut">Emva.cut</option>
<option value="Emze.cut">Emze.cut</option>
<option value="Emzecp.cut">Emzecp.cut</option>
<option value="Encr.cut">Encr.cut</option>
<option value="Eneu.cut">Eneu.cut</option>
<option value="Engo.cut">Engo.cut</option>
<option value="Eoncsp.cut">Eoncsp.cut</option>
<option value="Epae.cut">Epae.cut</option>
<option value="Epea.cut">Epea.cut</option>
<option value="Epet.cut">Epet.cut</option>
<option value="Epfa.cut">Epfa.cut</option>
<option value="Ephix174.cut">Ephix174.cut</option>
<option value="Ephv.cut">Ephv.cut</option>
<option value="Ephy.cut">Ephy.cut</option>
<option value="Epig.cut">Epig.cut</option>
<option value="Epolyomaa2.cut">Epolyomaa2.cut</option>
<option value="Epombe.cut">Epombe.cut</option>
<option value="Epombecai.cut">Epombecai.cut</option>
<option value="Epot.cut">Epot.cut</option>
<option value="Eppu.cut">Eppu.cut</option>
<option value="Epse.cut">Epse.cut</option>
<option value="Epsy.cut">Epsy.cut</option>
<option value="Epvu.cut">Epvu.cut</option>
<option value="Erab.cut">Erab.cut</option>
<option value="Erabbit.cut">Erabbit.cut</option>
<option value="Erabsp.cut">Erabsp.cut</option>
<option value="Erat.cut">Erat.cut</option>
<option value="Eratsp.cut">Eratsp.cut</option>
<option value="Erca.cut">Erca.cut</option>
<option value="Erhm.cut">Erhm.cut</option>
<option value="Eric.cut">Eric.cut</option>
<option value="Erle.cut">Erle.cut</option>
<option value="Erme.cut">Erme.cut</option>
<option value="Ersp.cut">Ersp.cut</option>
<option value="Esalsp.cut">Esalsp.cut</option>
<option value="Esau.cut">Esau.cut</option>
<option value="Esco.cut">Esco.cut</option>
<option value="Esgi.cut">Esgi.cut</option>
<option value="Eshp.cut">Eshp.cut</option>
<option value="Eshpsp.cut">Eshpsp.cut</option>
<option value="Esli.cut">Esli.cut</option>
<option value="Eslm.cut">Eslm.cut</option>
<option value="Esma.cut">Esma.cut</option>
<option value="Esmi.cut">Esmi.cut</option>
<option value="Esmu.cut">Esmu.cut</option>
<option value="Esoy.cut">Esoy.cut</option>
<option value="Espi.cut">Espi.cut</option>
<option value="Espn.cut">Espn.cut</option>
<option value="Espo.cut">Espo.cut</option>
<option value="Espo_h.cut">Espo_h.cut</option>
<option value="Espu.cut">Espu.cut</option>
<option value="Esta.cut">Esta.cut</option>
<option value="Esty.cut">Esty.cut</option>
<option value="Esus.cut">Esus.cut</option>
<option value="Esv40.cut">Esv40.cut</option>
<option value="Esyhsp.cut">Esyhsp.cut</option>
<option value="Esynsp.cut">Esynsp.cut</option>
<option value="Etbr.cut">Etbr.cut</option>
<option value="Etcr.cut">Etcr.cut</option>
<option value="Eter.cut">Eter.cut</option>
<option value="Etetsp.cut">Etetsp.cut</option>
<option value="Etob.cut">Etob.cut</option>
<option value="Etobcp.cut">Etobcp.cut</option>
<option value="Etom.cut">Etom.cut</option>
<option value="Etrb.cut">Etrb.cut</option>
<option value="Evco.cut">Evco.cut</option>
<option value="Ewht.cut">Ewht.cut</option>
<option value="Exel.cut">Exel.cut</option>
<option value="Exenopus.cut">Exenopus.cut</option>
<option value="Eyeast.cut">Eyeast.cut</option>
<option value="Eyeastcai.cut">Eyeastcai.cut</option>
<option value="Eyen.cut">Eyen.cut</option>
<option value="Eysc.cut">Eysc.cut</option>
<option value="Eysc_h.cut">Eysc_h.cut</option>
<option value="Eyscmt.cut">Eyscmt.cut</option>
<option value="Eysp.cut">Eysp.cut</option>
<option value="Ezebrafish.cut">Ezebrafish.cut</option>
<option value="Ezma.cut">Ezma.cut</option>
</param>
<param name="cfile2" type="select">
<label>Codon Usage File 2</label>
<option value="Ehum.cut">Ehum.cut</option>
<option value="Eacc.cut">Eacc.cut</option>
<option value="Eadenovirus5.cut">Eadenovirus5.cut</option>
<option value="Eadenovirus7.cut">Eadenovirus7.cut</option>
<option value="Eaidlav.cut">Eaidlav.cut</option>
<option value="Eanasp.cut">Eanasp.cut</option>
<option value="Eani.cut">Eani.cut</option>
<option value="Eani_h.cut">Eani_h.cut</option>
<option value="Eanidmit.cut">Eanidmit.cut</option>
<option value="Easn.cut">Easn.cut</option>
<option value="Eath.cut">Eath.cut</option>
<option value="Eatu.cut">Eatu.cut</option>
<option value="Eavi.cut">Eavi.cut</option>
<option value="Ebja.cut">Ebja.cut</option>
<option value="Ebly.cut">Ebly.cut</option>
<option value="Ebme.cut">Ebme.cut</option>
<option value="Ebmo.cut">Ebmo.cut</option>
<option value="Ebna.cut">Ebna.cut</option>
<option value="Ebov.cut">Ebov.cut</option>
<option value="Ebovsp.cut">Ebovsp.cut</option>
<option value="Ebst.cut">Ebst.cut</option>
<option value="Ebsu.cut">Ebsu.cut</option>
<option value="Ebsu_h.cut">Ebsu_h.cut</option>
<option value="Ecac.cut">Ecac.cut</option>
<option value="Ecal.cut">Ecal.cut</option>
<option value="Eccr.cut">Eccr.cut</option>
<option value="Ecel.cut">Ecel.cut</option>
<option value="Echi.cut">Echi.cut</option>
<option value="Echicken.cut">Echicken.cut</option>
<option value="Echisp.cut">Echisp.cut</option>
<option value="Echk.cut">Echk.cut</option>
<option value="Echmp.cut">Echmp.cut</option>
<option value="Echnt.cut">Echnt.cut</option>
<option value="Echos.cut">Echos.cut</option>
<option value="Echzm.cut">Echzm.cut</option>
<option value="Echzmrubp.cut">Echzmrubp.cut</option>
<option value="Ecpx.cut">Ecpx.cut</option>
<option value="Ecre.cut">Ecre.cut</option>
<option value="Ecrisp.cut">Ecrisp.cut</option>
<option value="Ectr.cut">Ectr.cut</option>
<option value="Edayhoff.cut">Edayhoff.cut</option>
<option value="Eddi.cut">Eddi.cut</option>
<option value="Eddi_h.cut">Eddi_h.cut</option>
<option value="Edog.cut">Edog.cut</option>
<option value="Edro.cut">Edro.cut</option>
<option value="Edro_h.cut">Edro_h.cut</option>
<option value="Edrosophila.cut">Edrosophila.cut</option>
<option value="Eeca.cut">Eeca.cut</option>
<option value="Eeco.cut">Eeco.cut</option>
<option value="Eeco_h.cut">Eeco_h.cut</option>
<option value="Eecoli.cut">Eecoli.cut</option>
<option value="Ef1.cut">Ef1.cut</option>
<option value="Efish.cut">Efish.cut</option>
<option value="Efmdvpolyp.cut">Efmdvpolyp.cut</option>
<option value="Eham.cut">Eham.cut</option>
<option value="Ehha.cut">Ehha.cut</option>
<option value="Ehin.cut">Ehin.cut</option>
<option value="Ehma.cut">Ehma.cut</option>
<option value="Ehuman.cut">Ehuman.cut</option>
<option value="Ekla.cut">Ekla.cut</option>
<option value="Ekpn.cut">Ekpn.cut</option>
<option value="Ella.cut">Ella.cut</option>
<option value="Emac.cut">Emac.cut</option>
<option value="Emaize.cut">Emaize.cut</option>
<option value="Emam_h.cut">Emam_h.cut</option>
<option value="Emixlg.cut">Emixlg.cut</option>
<option value="Emouse.cut">Emouse.cut</option>
<option value="Emsa.cut">Emsa.cut</option>
<option value="Emse.cut">Emse.cut</option>
<option value="Emta.cut">Emta.cut</option>
<option value="Emtu.cut">Emtu.cut</option>
<option value="Emus.cut">Emus.cut</option>
<option value="Emussp.cut">Emussp.cut</option>
<option value="Emva.cut">Emva.cut</option>
<option value="Emze.cut">Emze.cut</option>
<option value="Emzecp.cut">Emzecp.cut</option>
<option value="Encr.cut">Encr.cut</option>
<option value="Eneu.cut">Eneu.cut</option>
<option value="Engo.cut">Engo.cut</option>
<option value="Eoncsp.cut">Eoncsp.cut</option>
<option value="Epae.cut">Epae.cut</option>
<option value="Epea.cut">Epea.cut</option>
<option value="Epet.cut">Epet.cut</option>
<option value="Epfa.cut">Epfa.cut</option>
<option value="Ephix174.cut">Ephix174.cut</option>
<option value="Ephv.cut">Ephv.cut</option>
<option value="Ephy.cut">Ephy.cut</option>
<option value="Epig.cut">Epig.cut</option>
<option value="Epolyomaa2.cut">Epolyomaa2.cut</option>
<option value="Epombe.cut">Epombe.cut</option>
<option value="Epombecai.cut">Epombecai.cut</option>
<option value="Epot.cut">Epot.cut</option>
<option value="Eppu.cut">Eppu.cut</option>
<option value="Epse.cut">Epse.cut</option>
<option value="Epsy.cut">Epsy.cut</option>
<option value="Epvu.cut">Epvu.cut</option>
<option value="Erab.cut">Erab.cut</option>
<option value="Erabbit.cut">Erabbit.cut</option>
<option value="Erabsp.cut">Erabsp.cut</option>
<option value="Erat.cut">Erat.cut</option>
<option value="Eratsp.cut">Eratsp.cut</option>
<option value="Erca.cut">Erca.cut</option>
<option value="Erhm.cut">Erhm.cut</option>
<option value="Eric.cut">Eric.cut</option>
<option value="Erle.cut">Erle.cut</option>
<option value="Erme.cut">Erme.cut</option>
<option value="Ersp.cut">Ersp.cut</option>
<option value="Esalsp.cut">Esalsp.cut</option>
<option value="Esau.cut">Esau.cut</option>
<option value="Esco.cut">Esco.cut</option>
<option value="Esgi.cut">Esgi.cut</option>
<option value="Eshp.cut">Eshp.cut</option>
<option value="Eshpsp.cut">Eshpsp.cut</option>
<option value="Esli.cut">Esli.cut</option>
<option value="Eslm.cut">Eslm.cut</option>
<option value="Esma.cut">Esma.cut</option>
<option value="Esmi.cut">Esmi.cut</option>
<option value="Esmu.cut">Esmu.cut</option>
<option value="Esoy.cut">Esoy.cut</option>
<option value="Espi.cut">Espi.cut</option>
<option value="Espn.cut">Espn.cut</option>
<option value="Espo.cut">Espo.cut</option>
<option value="Espo_h.cut">Espo_h.cut</option>
<option value="Espu.cut">Espu.cut</option>
<option value="Esta.cut">Esta.cut</option>
<option value="Esty.cut">Esty.cut</option>
<option value="Esus.cut">Esus.cut</option>
<option value="Esv40.cut">Esv40.cut</option>
<option value="Esyhsp.cut">Esyhsp.cut</option>
<option value="Esynsp.cut">Esynsp.cut</option>
<option value="Etbr.cut">Etbr.cut</option>
<option value="Etcr.cut">Etcr.cut</option>
<option value="Eter.cut">Eter.cut</option>
<option value="Etetsp.cut">Etetsp.cut</option>
<option value="Etob.cut">Etob.cut</option>
<option value="Etobcp.cut">Etobcp.cut</option>
<option value="Etom.cut">Etom.cut</option>
<option value="Etrb.cut">Etrb.cut</option>
<option value="Evco.cut">Evco.cut</option>
<option value="Ewht.cut">Ewht.cut</option>
<option value="Exel.cut">Exel.cut</option>
<option value="Exenopus.cut">Exenopus.cut</option>
<option value="Eyeast.cut">Eyeast.cut</option>
<option value="Eyeastcai.cut">Eyeastcai.cut</option>
<option value="Eyen.cut">Eyen.cut</option>
<option value="Eysc.cut">Eysc.cut</option>
<option value="Eysc_h.cut">Eysc_h.cut</option>
<option value="Eyscmt.cut">Eyscmt.cut</option>
<option value="Eysp.cut">Eysp.cut</option>
<option value="Ezebrafish.cut">Ezebrafish.cut</option>
<option value="Ezma.cut">Ezma.cut</option>
</param>
</inputs>
<outputs>
<data format="codcmp" name="out_file1" />
</outputs>
<tests>
<test>
<param name="cfile1" value="Ehum.cut"/>
<param name="cfile2" value="Eacc.cut"/>
<output name="out_file1" file="emboss_codcmp_out.codcmp"/>
</test>
</tests>
<help>
You can view the original documentation here_.
.. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/codcmp.html
</help>
</tool>
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