Mercurial > repos > devteam > emboss_5

changeset 15:dc492eb6a4fc draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 431486be049407b094d495ae4a68bf76d27fa522
author iuc
date Mon, 28 Jan 2019 14:50:36 -0500
parents 2e0fb4bc860e
children dba489bfcd62
files emboss_backtranseq.xml test-data/emboss_backtranseq_out.fasta test-data/emboss_backtranseq_out2.fasta
diffstat 3 files changed, 319 insertions(+), 241 deletions(-) [+]
line wrap: on
line diff
--- a/emboss_backtranseq.xml	Mon Jan 28 11:22:18 2019 -0500
+++ b/emboss_backtranseq.xml	Mon Jan 28 14:50:36 2019 -0500
@@ -1,219 +1,228 @@
-<tool id="EMBOSS: backtranseq2" name="backtranseq" version="@VERSION@">
-  <description>Back translate a protein sequence</description>
-  <macros>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="requirements" />
-  <code file="emboss_format_corrector.py" />
-  <command>backtranseq -sequence '$input1' -outfile '$out_file1' -cfile $cfile -osformat2 $out_format1 -auto</command>
-  <inputs>
-    <param name="input1" type="data" format="fasta" label="On query" />
-    <param name="cfile" type="select" label="Codon usage file">
-      <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="out_format1" type="select" label="Output sequence file format">
-      <option value="fasta">FASTA (m)</option>
-      <option value="acedb">ACeDB (m)</option>
-      <option value="asn1">ASN.1 (m)</option>
-      <option value="clustal">Clustal (m)</option>
-      <option value="codata">CODATA (m)</option>
-      <option value="embl">EMBL (m)</option>
-      <option value="fitch">Fitch (m)</option>
-      <option value="gcg">Wisconsin Package GCG 9.x and 10.x (s)</option>
-      <option value="genbank">GENBANK (m)</option>
-      <option value="gff">GFF (m)</option>
-      <option value="hennig86">Hennig86 (m)</option>
-      <option value="ig">Intelligenetics (m)</option>
-      <option value="jackknifer">Jackknifer (m)</option>
-      <option value="jackknifernon">Jackknifernon (m)</option>
-      <option value="mega">Mega (m)</option>
-      <option value="meganon">Meganon (m)</option>
-      <option value="msf">Wisconsin Package GCG's MSF (m)</option>
-      <option value="pir">NBRF (PIR) (m)</option>
-      <option value="ncbi">NCBI style FASTA (m)</option>
-      <option value="nexus">Nexus/PAUP (m)</option>
-      <option value="nexusnon">Nexusnon/PAUPnon (m)</option>
-      <option value="phylip">PHYLIP interleaved (m)</option>
-      <option value="phylipnon">PHYLIP non-interleaved (m)</option>
-      <option value="selex">SELEX (m)</option>
-      <option value="staden">Staden (s)</option>
-      <option value="strider">DNA strider (m)</option>
-      <option value="swiss">SwisProt entry (m)</option>
-      <option value="text">Plain sequence (s)</option>
-      <option value="treecon">Treecon (m)</option>
-    </param>
-  </inputs>
-  <outputs>
-    <data name="out_file1" format="txt" />
-  </outputs>
-  <tests>
-    <test>
-      <param name="input1" value="2.fasta"/>
-      <param name="cfile" value="Ehum.cut"/>
-      <param name="out_format1" value="fasta"/>
-      <output name="out_file1" file="emboss_backtranseq_out.fasta"/>
-    </test>
-  </tests>
-  <help>
+<tool id="EMBOSS: backtranseq2" name="backtranseq" version="6.6.0">
+    <description>Back translate a protein sequence</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <requirements>
+        <requirement type="package" version="6.6.0">emboss</requirement>
+    </requirements>
+    <code file="emboss_format_corrector.py" />
+    <command>backtranseq -sequence '$input1' -outfile '$out_file1' -cfile $cfile -osformat2 $out_format1 -auto</command>
+    <inputs>
+        <param name="input1" type="data" format="fasta" label="Protein sequence" help="In FASTA format" />
+        <param name="cfile" type="select" label="Codon usage file">
+            <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="out_format1" type="select" label="Output sequence file format">
+            <option value="fasta">FASTA (m)</option>
+            <option value="acedb">ACeDB (m)</option>
+            <option value="asn1">ASN.1 (m)</option>
+            <option value="clustal">Clustal (m)</option>
+            <option value="codata">CODATA (m)</option>
+            <option value="embl">EMBL (m)</option>
+            <option value="fitch">Fitch (m)</option>
+            <option value="gcg">Wisconsin Package GCG 9.x and 10.x (s)</option>
+            <option value="genbank">GENBANK (m)</option>
+            <option value="gff">GFF (m)</option>
+            <option value="hennig86">Hennig86 (m)</option>
+            <option value="ig">Intelligenetics (m)</option>
+            <option value="jackknifer">Jackknifer (m)</option>
+            <option value="jackknifernon">Jackknifernon (m)</option>
+            <option value="mega">Mega (m)</option>
+            <option value="meganon">Meganon (m)</option>
+            <option value="msf">Wisconsin Package GCG's MSF (m)</option>
+            <option value="pir">NBRF (PIR) (m)</option>
+            <option value="ncbi">NCBI style FASTA (m)</option>
+            <option value="nexus">Nexus/PAUP (m)</option>
+            <option value="nexusnon">Nexusnon/PAUPnon (m)</option>
+            <option value="phylip">PHYLIP interleaved (m)</option>
+            <option value="phylipnon">PHYLIP non-interleaved (m)</option>
+            <option value="selex">SELEX (m)</option>
+            <option value="staden">Staden (s)</option>
+            <option value="strider">DNA strider (m)</option>
+            <option value="swiss">SwisProt entry (m)</option>
+            <option value="text">Plain sequence (s)</option>
+            <option value="treecon">Treecon (m)</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="out_file1" format="txt" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input1" value="emboss_transeq_out.fasta"/>
+            <param name="cfile" value="Ehum.cut"/>
+            <param name="out_format1" value="fasta"/>
+            <output name="out_file1" file="emboss_backtranseq_out.fasta" ftype="fasta" />
+        </test>
+        <!-- Test with multiple sequence FASTA input -->
+        <test>
+            <param name="input1" value="emboss_getorf_out.fasta" />
+            <param name="cfile" value="Ehum.cut"/>
+            <param name="out_format1" value="fasta"/>
+            <output name="out_file1" file="emboss_backtranseq_out2.fasta" ftype="fasta" />
+        </test>
+    </tests>
+    <help>
 .. class:: warningmark
 
-The input dataset needs to be sequences.
+Back-translate a protein sequence to the nucleic acid sequence it is most likely to have come from. ``backtranseq`` uses a codon usage table which gives the frequency of usage of each codon for each amino acid. For each amino acid in the input sequence, the corresponding most frequently occuring codon is used in the nucleic acid sequence that is output.
 
 -----
 
     You can view the original documentation here_.
 
-    .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/backtranseq.html
-  </help>
-  <expand macro="citations" />
+    .. _here: http://emboss.open-bio.org/rel/rel6/apps/backtranseq.html
+    </help>
+    <expand macro="citations" />
 </tool>
--- a/test-data/emboss_backtranseq_out.fasta	Mon Jan 28 11:22:18 2019 -0500
+++ b/test-data/emboss_backtranseq_out.fasta	Mon Jan 28 14:50:36 2019 -0500
@@ -1,30 +1,11 @@
->Sequence 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
-GGCACCACCTGCGGCGCCACCGGCTGCTGCACCGCCGCCGCCGCCACCGCCTGCTGCACC
-ACCTGCACCACCACCACCGGCACCTGCTGCTGCACCGCCTGCGCCTGCGCCGGCGCCTGC
-TGCGCCTGCGCCGGCACCACCACCACCTGCTGCACCGCCGCCACCGGCGGCTGCACCACC
-ACCGCCTGCGCCTGCTGCGGCGCCTGCACCGCCGGCGCCGCCGCCACCACCTGCACCACC
-GGCACCGGCTGCGCCGCCGGCTGCGCCTGCACCGCCGCCACCACCGGCGCCGCCGCCGGC
-TGCGGCGGCACCACCGGCGGCTGCTGCACCGCCGGCGCCGGCACCGGCACCACCGCCTGC
-TGCGGCGGCACCACCACCGGCACCGCCACCGCCGGCTGCACCGGCGCCGGCTGCGGCTGC
-GGCACCTGCACCTGCACCACCGGCTGCTGCTGCACCGGCGCCACCTGCGCCGCCGCCGGC
-GGCACCACCTGCGCCACCACCACCACCTGCACCTGCACCGCCTGCACCACCACCGGCGGC
-GCCGCCGGCGCCTGCGGCACCACCGGCACCGGCGGCGCCGCCGGCGCCGCCACCGCCTGC
-GCCGCCTGCGCCGCCGGCACCGCCTGCGGCGCCGGCACCTGCACCTGCACCTGCTGCTGC
-TGCTGCTGCACCGGCGGCACCACCACCGGCTGCACCGGCGCCACCACCGCCTGCACCGGC
-GGCGCCACCGCCTGCGCCGGCACCACCGGCACCGCCGCCACCGCCTGCTGCTGCACCACC
-TGCGGCTGCGCCGCCTGCGCCTGCTGCGGCTGCGGCACCGCCGCCTGCACCGCCACCTGC
-ACCGCCACCGCCACCGGCGCCGCCACCACCGCCACCACCACCACCTGCTGCTGCACCACC
-ACCGCCACCACCGCCACCGCCACCGGCACCGCCGGCACCGCCGGCGGCACCACCTGCGGC
-ACCTGCACCACCACCGCCGCCACCTGCACCACCTGCTGCACCACCACCGCCGGCTGCGCC
-GCCGGCACCTGCACCACCACCACCGCCTGCACCGGCACCACCACCACCTGCGGCGCCTGC
-TGCACCTGCGCCGCCACCGGCACCACCTGCGCCACCGGCACCACCTGCACCACCGCCGGC
-GGCACCACCGGCACCACCACCACCGGCGGCGCCACCGCCGCCACCGCCACCGGCTGCGGC
-GGCACCTGCGCCGGCACCACCACCGCCGCCACCTGCACCACCTGCGGCACCACCGGCACC
-ACCACCTGCACCACCTGCACCACCGCCGCCGCCGCCACCGCCACCACCACCGCCACCACC
-TGCGCCACCGGCGGCACCACCACCGCCGCCACCACCACCACCACCGGCGGCACCACCACC
-GGCACCGCCTGCACCACCGGCACCACCTGCGCCGGCGGCGGCGGCTGCTGCGCCGGCACC
-ACCTGCGCCACCACCGCCACCACCACCGCCTGCACCTGCACCGGCACCACCACCGGCACC
-GCCACCGCCTGCGCCGGCTGCGCCGGCACCACCTGCACCACCACCACCGCCACCACCACC
-ACCACCGCCGGCACCGCCACCGGCGCCACCACCACCACCGCCGCCACCACCACCGCCGCC
-GCCGCCTGCGCCGCCACCACCTGCACCGCCGCCACCGGCGGCACCTGCGCCGCCGCCGCC
-GCC
+>Sequence_1 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+GTGAGATGCCTGAAGTACCTGCTGCTGAGCCTGCACAGACCCCAGTTCAGCTGATGGCTG
+TACACCGACTGAAAGTTCCTGTGCAAGCACTGACTGAAGGCCGTGGGCCTGGAGTGCTAC
+AGATTCGTGTGACTGAGCGCCAGCCTGGCCCTGATCAAGGGCAGCTTCAGCCTGCTGTGG
+AAGACCCTGTGGAAGAACACCACCAGCACCAGCCTGAGCCCCCTGGTGTGCTGACTGCTG
+GACACCGTGGTGATCCCCTTCGCCACCCCCAGAAACTACCTGTACGAGCTGTTCAGCCTG
+TACTACATGTGATGAGTGAGACTGTGAAGCAGCTTCAGCAAGAGCTTCACCGTGTTCGAC
+CTGAACGTGCACGTGCTGAGACTGTTCTGGATCATCTGCGGCCAGTTCAACCTGAGATGC
+TTCTTCCTGAAGTACCTGTTCATGGTGTGATTCCTGGTGTGCACCTGCAGCGGCGCCAGC
+AGCCTGTTCACCCTGTTCGTGTACAGCAGCAGCTTCATCTTCAGCATGATCCTGATCTGA
+AACAACAGCAACGGCCAGAAG
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/emboss_backtranseq_out2.fasta	Mon Jan 28 14:50:36 2019 -0500
@@ -0,0 +1,88 @@
+>Sequence_1 [1 - 51] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+GTGAGATGCCTGAAGTACCTGCTGCTGAGCCTGCACAGACCCCAGTTCAGC
+>Sequence_2 [14 - 94] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+AACACCTTCTTCTGCCCCTACACCGACCACAGCTTCCCCAACGGCTTCACCCCCACCAGA
+AACAGCTGCGCCAGCACCAAC
+>Sequence_3 [94 - 129] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+CTGAAGGCCGTGGGCCTGGAGTGCTACAGATTCGTG
+>Sequence_4 [133 - 231] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+CTGAGCGCCAGCCTGGCCCTGATCAAGGGCAGCTTCAGCCTGCTGTGGAAGACCCTGTGG
+AAGAACACCACCAGCACCAGCCTGAGCCCCCTGGTGTGC
+>Sequence_5 [155 - 250] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+AGCAAGGTGCACTTCCTGTACTTCGGCAGAAGATGCGGCAGAATCCAGCAGGTGAGAGTG
+AGCCCCCCCTGGTTCGCCGACTACTGGATCCAGCTG
+>Sequence_6 [3 - 272] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+AGCATGCCCAAGATCCCCAGCTTCGTGCCCACCCAGACCACCGTGTTCCTGATGGCCCTG
+CACAGACTGGAGATCCTGGTGCAGGCCCTGATCGAGAGCGGCTGGCCCAGAGTGCTGCCC
+GTGTGCATCGCCGAGAGAGTGAGCTGCCCCGACCAGAGATTCATCTTCAGCACCCTGGAG
+GACGTGGTGGAGGAGTACAACAAGTACGAGAGCCTGCCCCCCGGCCTGCTGATCACCGGC
+TACAGCTGCAACACCCTGAGAAACACCGCC
+>Sequence_7 [235 - 309] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+CTGCTGGACACCGTGGTGATCCCCTTCGCCACCCCCAGAAACTACCTGTACGAGCTGTTC
+AGCCTGTACTACATG
+>Sequence_8 [288 - 335] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+ATCATCTTCCCCCTGCTGTACGTGGTGGGCAGCAGCCTGATCTTCCTG
+>Sequence_9 [339 - 377] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+CAGGTGTTCTACTGCTTCAGACCCCAGTGCAGCTGCAGC
+>Sequence_10 [254 - 391] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+TACCCCAGCCAGCACAGAGTGACCATCTACATGAACTACTTCCCCTTCATCATCTGCAGC
+AGATTCGTGTTCAACCTGCCCCTGGCCAGCCTGCTGCTGTTCAGCACCAGCATGTTCATG
+TTCCTGGGCTGCTTCGGC
+>Sequence_11 [395 - 427] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+TACGCCGTGAGCCTGATCTTCGTGGTGAGCAGC
+>Sequence_12 [328 - 447] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+AGCAGCTTCAGCAAGAGCTTCACCGTGTTCGACCTGAACGTGCACGTGCTGAGACTGTTC
+TGGATCATCTGCGGCCAGTTCAACCTGAGATGCTTCTTCCTGAAGTACCTGTTCATGGTG
+>Sequence_13 [411 - 521] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+AGCAGCCTGTTCCTGCTGAAGATCTTCATCCACGGCCTGATCTTCGGCCTGTACCTGTTC
+AGAGGCCAGTTCATCATCTACAGCGTGTGCATCCAGCAGTTCTTCTACTTC
+>Sequence_14 [431 - 526] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+AACATCTACAGCTGGTTCAACTTCTGGTTCGTGCTGGTGCAGGGCCCCGTGCACTACCTG
+CTGTGCCTGTACACCGCCGTGCTGCTGTTCCTGGTG
+>Sequence_15 [451 - 537] 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+TTCCTGGTGTGCACCTGCAGCGGCGCCAGCAGCCTGTTCACCCTGTTCGTGTACAGCAGC
+AGCTTCATCTTCAGCATGATCCTGATC
+>Sequence_16 [531 - 487] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+AACCACACCAAGAACAAGAGAACCGCCGTGTACAAGCAGAGCAAG
+>Sequence_17 [536 - 450] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+ATCAAGATCATCCTGAAGATCAAGGAGCTGCTGTACACCAACAGAGTGAACAACGAGCTG
+GCCCCCGAGCAGGTGCAGACCAAGAAC
+>Sequence_18 [487 - 443] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+ATCATGAACTGGCCCCTGAACAAGTACAAGCCCAAGATCAAGCCC
+>Sequence_19 [468 - 439] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+ACCAGCACCAACCAGAAGCTGAACCACGAG
+>Sequence_20 [439 - 410] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+ATCAACATCCTGAGAAGAAACAACGAGGAC
+>Sequence_21 [446 - 405] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+ACCATGAACAAGTACTTCAAGAAGAAGCAGAGAAGACTGAAC
+>Sequence_22 [401 - 372] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+CCCCACATCATCCAGAACAACCTGAGAACC
+>Sequence_23 [368 - 327] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+ACCCTGAGAAGCAAGACCGTGAAGGACCTGCTGAAGGAGGAC
+>Sequence_24 [426 - 292] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+GAGGAGACCACCAAGATCAAGCTGACCGCCTACTACCCCAAGCAGCCCAAGAACATGAAC
+ATCGAGGTGGAGAACAGCAAGAGACTGGCCAAGGGCAGACTGAAGACCAACCTGCTGCAC
+ATCATCAAGGGCAAG
+>Sequence_25 [279 - 238] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+ATCGTGACCAGATGCTGCGAGGGCTACTACAACTGCATCCAG
+>Sequence_26 [234 - 175] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+AGCGCCAACCAGGGCGGCGAGACCAGAACCTGCTGCATCCTGCCCCAGAGACTGCCCAAG
+>Sequence_27 [334 - 158] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+AGAAAGATCAAGGACGAGCCCACCACCTACAACAAGGGCAAGATCATCCACATCGACAGC
+TACGCCGTGCTGAGAAGAGTGCTGCAGCTGTACCCCGTGATCAGCAAGCCCGGCGGCAGA
+GACAGCTACCTGCTGTACAGCAGCACCACCAGCAGCAAGGTGGAGAAGATGAACCTG
+>Sequence_28 [275 - 120] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+CTGAGAGGCGTGGCCAAGGGCATCACCACCGTGAGCAGCAACCAGCAGACCAGAGGCGAG
+AGACTGGTGCTGGTGGTGTTCTTCCACAACGTGTTCCAGAGCAGAGAGAACGAGCCCCTG
+ATCAGAGCCAGAGACGCCCTGAGCTACACCAACAGA
+>Sequence_29 [162 - 112] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+ACCTTCGACCAGGGCAAGAGAAGAGCCCAGCTGTACAAGCCCGTGACCCTG
+>Sequence_30 [108 - 34] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+GCCAACAGATTCCAGCTGGTGCTGGCCCAGGAGTTCCTGGTGGGCGTGAAGCCCCTGGGC
+AAGCTGTGGAGCGTG
+>Sequence_31 [50 - 3] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+GAGAACTGCGGCCTGTGCAGAGACAAGAGAAGATACTTCAGACACAGA
+>Sequence_32 [154 - 2] (REVERSE SENSE) 561 BP; 135 A; 106 C; 98 G; 222 T; 0 other;
+AGCGGCCAGGAGACCAGAAGCGCCATCCAGACCGGCAACACCCTGGGCCAGCCCCTGAGC
+ATCAGCGCCTGCACCAGAATCAGCAGCAGATGCAAGGCCATCAGAAAGACCGTGGTGTGC
+GTGGGCACCAAGGAGGGCATCCTGGGCATCGAG