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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115 |
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modified:
emboss_iep.xml emboss_tranalign.xml emboss_transeq.xml test-data/emboss_cai_out.cai test-data/emboss_newcpgseek_out.newcpgseek test-data/emboss_tranalign_out.fasta |
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| diff -r 1b6538ec8b56 -r 832c20329690 emboss_iep.xml --- a/emboss_iep.xml Thu Feb 23 09:43:47 2017 -0500 +++ b/emboss_iep.xml Mon Apr 23 13:05:09 2018 -0400 |
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| @@ -15,7 +15,7 @@ </param> </inputs> <outputs> - <data name="out_file1" format="iep" /> + <data name="out_file1" format="txt" /> </outputs> <tests> <test> |
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| diff -r 1b6538ec8b56 -r 832c20329690 emboss_tranalign.xml --- a/emboss_tranalign.xml Thu Feb 23 09:43:47 2017 -0500 +++ b/emboss_tranalign.xml Mon Apr 23 13:05:09 2018 -0400 |
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| b'@@ -1,82 +1,90 @@\n <tool id="EMBOSS: tranalign100" name="tranalign" version="5.0.0">\n- <description>Align nucleic coding regions given the aligned proteins</description>\n- <macros>\n- <import>macros.xml</import>\n- </macros>\n- <expand macro="requirements" />\n- <code file="emboss_format_corrector.py" />\n- <command>tranalign -asequence \'$input1\' -bsequence \'$input2\' -outseq \'$out_file1\' -table $table -osformat3 $out_format1 -auto</command>\n- <inputs>\n- <param name="input1" type="data" format="fasta" label="Nucleic sequences" />\n- <param name="input2" type="data" format="data" label="Protein sequences" />\n- <param name="table" type="select" label="Code to use">\n- <option value="0">Standard</option>\n- <option value="1">Standard (with alternative initiation codons)</option>\n- <option value="2">Vertebrate Mitochondrial</option>\n- <option value="3">Yeast Mitochondrial</option>\n- <option value="4">Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma</option>\n- <option value="5">Invertebrate Mitochondrial</option>\n- <option value="6">Ciliate Macronuclear and Dasycladacean</option>\n- <option value="9">Echinoderm Mitochondrial</option>\n- <option value="10">Euplotid Nuclear</option>\n- <option value="11">Bacterial</option>\n- <option value="12">Alternative Yeast Nuclear</option>\n- <option value="13">Ascidian Mitochondrial</option>\n- <option value="14">Flatworm Mitochondrial</option>\n- <option value="15">Blepharisma Macronuclear</option>\n- <option value="16">Chlorophycean Mitochondrial</option>\n- <option value="21">Trematode Mitochondrial</option>\n- <option value="22">Scenedesmus obliquus</option>\n- <option value="23">Thraustochytrium Mitochondrial</option>\n- </param>\n- <param name="out_format1" type="select" label="Output sequence file format">\n- <option value="fasta">FASTA (m)</option>\n- <option value="acedb">ACeDB (m)</option>\n- <option value="asn1">ASN.1 (m)</option>\n- <option value="clustal">Clustal (m)</option>\n- <option value="codata">CODATA (m)</option>\n- <option value="embl">EMBL (m)</option>\n- <option value="fitch">Fitch (m)</option>\n- <option value="gcg">Wisconsin Package GCG 9.x and 10.x (s)</option>\n- <option value="genbank">GENBANK (m)</option>\n- <option value="gff">GFF (m)</option>\n- <option value="hennig86">Hennig86 (m)</option>\n- <option value="ig">Intelligenetics (m)</option>\n- <option value="jackknifer">Jackknifer (m)</option>\n- <option value="jackknifernon">Jackknifernon (m)</option>\n- <option value="mega">Mega (m)</option>\n- <option value="meganon">Meganon (m)</option>\n- <option value="msf">Wisconsin Package GCG\'s MSF (m)</option>\n- <option value="pir">NBRF (PIR) (m)</option>\n- <option value="ncbi">NCBI style FASTA (m)</option>\n- <option value="nexus">Nexus/PAUP (m)</option>\n- <option value="nexusnon">Nexusnon/PAUPnon (m)</option>\n- <option value="phylip">PHYLIP interleaved (m)</option>\n- <option value="phylipnon">PHYLIP non-interleaved (m)</option>\n- <option value="selex">SELEX (m)</option>\n- <option value="staden">Staden (s)</option>\n- <option value="strider">DNA strider (m)</option>\n- <option value="swiss">SwisProt entry (m)</option>\n- <option value="text">Plain sequence (s)</option>\n- <option value="treecon">Treecon (m)</option>\n- </param>\n- </inputs>\n- <outputs>\n- <data name="out_file1" format="fasta" />\n- </outputs>\n- <tests>\n- <test>\n- <param name="input1" value="3.fasta"/>\n- <param name="input2" value="2.pep"/>\n- <param name="table" value="0"/>\n- <param name="out_format1" value="fasta"/>\n- <output name="out_file1" file="emboss_tranalign_out.fasta"/>\n- </test>\n- </tests>\n- <help>\n- You can view the original documentation here_.\n+ <description>Align nucleic coding regions given the aligned prote'..b'uence" type="data" format="data" label="Protein sequences" />\n+ <param argument="-table" type="select" label="Code to use">\n+ <option value="0">Standard</option>\n+ <option value="1">Standard (with alternative initiation codons)</option>\n+ <option value="2">Vertebrate Mitochondrial</option>\n+ <option value="3">Yeast Mitochondrial</option>\n+ <option value="4">Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma</option>\n+ <option value="5">Invertebrate Mitochondrial</option>\n+ <option value="6">Ciliate Macronuclear and Dasycladacean</option>\n+ <option value="9">Echinoderm Mitochondrial</option>\n+ <option value="10">Euplotid Nuclear</option>\n+ <option value="11">Bacterial</option>\n+ <option value="12">Alternative Yeast Nuclear</option>\n+ <option value="13">Ascidian Mitochondrial</option>\n+ <option value="14">Flatworm Mitochondrial</option>\n+ <option value="15">Blepharisma Macronuclear</option>\n+ <option value="16">Chlorophycean Mitochondrial</option>\n+ <option value="21">Trematode Mitochondrial</option>\n+ <option value="22">Scenedesmus obliquus</option>\n+ <option value="23">Thraustochytrium Mitochondrial</option>\n+ </param>\n+ <param name="out_format1" argument="-osformat3" type="select" label="Output sequence file format">\n+ <option value="fasta">FASTA (m)</option>\n+ <option value="acedb">ACeDB (m)</option>\n+ <option value="asn1">ASN.1 (m)</option>\n+ <option value="clustal">Clustal (m)</option>\n+ <option value="codata">CODATA (m)</option>\n+ <option value="embl">EMBL (m)</option>\n+ <option value="fitch">Fitch (m)</option>\n+ <option value="gcg">Wisconsin Package GCG 9.x and 10.x (s)</option>\n+ <option value="genbank">GENBANK (m)</option>\n+ <option value="gff">GFF (m)</option>\n+ <option value="hennig86">Hennig86 (m)</option>\n+ <option value="ig">Intelligenetics (m)</option>\n+ <option value="jackknifer">Jackknifer (m)</option>\n+ <option value="jackknifernon">Jackknifernon (m)</option>\n+ <option value="mega">Mega (m)</option>\n+ <option value="meganon">Meganon (m)</option>\n+ <option value="msf">Wisconsin Package GCG\'s MSF (m)</option>\n+ <option value="pir">NBRF (PIR) (m)</option>\n+ <option value="ncbi">NCBI style FASTA (m)</option>\n+ <option value="nexus">Nexus/PAUP (m)</option>\n+ <option value="nexusnon">Nexusnon/PAUPnon (m)</option>\n+ <option value="phylip">PHYLIP interleaved (m)</option>\n+ <option value="phylipnon">PHYLIP non-interleaved (m)</option>\n+ <option value="selex">SELEX (m)</option>\n+ <option value="staden">Staden (s)</option>\n+ <option value="strider">DNA strider (m)</option>\n+ <option value="swiss">SwisProt entry (m)</option>\n+ <option value="text">Plain sequence (s)</option>\n+ <option value="treecon">Treecon (m)</option>\n+ </param>\n+ </inputs>\n+ <outputs>\n+ <data name="out_file1" format="fasta" />\n+ </outputs>\n+ <tests>\n+ <test>\n+ <param name="input1" value="3.fasta"/>\n+ <param name="input2" value="2.pep"/>\n+ <param name="table" value="0"/>\n+ <param name="out_format1" value="fasta"/>\n+ <output name="out_file1" file="emboss_tranalign_out.fasta"/>\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+You can view the original documentation here_.\n \n- .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/tranalign.html\n- </help>\n- <expand macro="citations" />\n+.. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/tranalign.html\n+ ]]></help>\n+ <expand macro="citations" />\n </tool>\n' |
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| diff -r 1b6538ec8b56 -r 832c20329690 emboss_transeq.xml --- a/emboss_transeq.xml Thu Feb 23 09:43:47 2017 -0500 +++ b/emboss_transeq.xml Mon Apr 23 13:05:09 2018 -0400 |
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| b'@@ -1,130 +1,129 @@\n <tool id="EMBOSS: transeq101" name="transeq" version="5.0.0">\n- <description>Translate nucleic acid sequences</description>\n- <macros>\n- <import>macros.xml</import>\n- </macros>\n- <expand macro="requirements" />\n- <code file="emboss_format_corrector.py" />\n- <command><![CDATA[\n- transeq \n- -sequence \'$input1\' \n- -outseq \'$out_file1\' \n- -frame $frame \n- -table $table\n- #if str($regions).strip():\n- -regions \'$regions\'\n- #end if\n- -trim $trim \n- -clean $clean \n- -alternative $alternative \n- -osformat2 \'$out_format1\' \n- -auto\n- ]]>\n- </command>\n- <inputs>\n- <param name="input1" type="data" format="fasta" label="Sequences" />\n- <param name="frame" type="select" label="Frame(s) to translate">\n- <option value="1">Frame 1</option>\n- <option value="2">Frame 2</option>\n- <option value="3">Frame 3</option>\n- <option value="F">Forward three frames</option>\n- <option value="-1">Frame -1</option>\n- <option value="-2">Frame -2</option>\n- <option value="-3">Frame -3</option>\n- <option value="R">Reverse three frames</option>\n- <option value="6">All six frames</option>\n- </param>\n- <param name="table" type="select" label="Code to use">\n- <option value="0">Standard</option>\n- <option value="1">Standard (with alternative initiation codons)</option>\n- <option value="2">Vertebrate Mitochondrial</option>\n- <option value="3">Yeast Mitochondrial</option>\n- <option value="4">Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma</option>\n- <option value="5">Invertebrate Mitochondrial</option>\n- <option value="6">Ciliate Macronuclear and Dasycladacean</option>\n- <option value="9">Echinoderm Mitochondrial</option>\n- <option value="10">Euplotid Nuclear</option>\n- <option value="11">Bacterial</option>\n- <option value="12">Alternative Yeast Nuclear</option>\n- <option value="13">Ascidian Mitochondrial</option>\n- <option value="14">Flatworm Mitochondrial</option>\n- <option value="15">Blepharisma Macronuclear</option>\n- <option value="16">Chlorophycean Mitochondrial</option>\n- <option value="21">Trematode Mitochondrial</option>\n- <option value="22">Scenedesmus obliquus</option>\n- <option value="23">Thraustochytrium Mitochondrial</option>\n- </param>\n- <param name="regions" type="text" value="" label="Regions to translate" />\n- <param name="trim" type="select" label="Remove all \'X\' and \'*\' characters from the right end of the translation">\n- <option value="no">No</option>\n- <option value="yes">Yes</option>\n- </param>\n- <param name="clean" type="select" label="Change all STOP codon positions from the \'*\' character to \'X\'">\n- <option value="no">No</option>\n- <option value="yes">Yes</option>\n- </param>\n- <param name="alternative" type="select" label="Define frame \'-1\' as using the set of codons starting with the last codon of the sequence">\n- <option value="no">No</option>\n- <option value="yes">Yes</option>\n- </param>\n- <param name="out_format1" type="select" label="Output sequence file format">\n- <option value="fasta">FASTA (m)</option>\n- <option value="acedb">ACeDB (m)</option>\n- <option value="asn1">ASN.1 (m)</option>\n- <option value="clustal">Clustal (m)</option>\n- <option value="codata">CODATA (m)</option>\n- <option value="embl">EMBL (m)</option>\n- <option value="fitch">Fitch (m)</option>\n- <option value="gcg">Wisconsin Package GCG 9.x and 10.x (s)</option>\n- <option value="genbank">GENBANK (m)</option>\n- <option value="gff">GFF (m)</option>\n- <option value="hennig86">Hennig86 (m)</option>\n- <option value="ig">Intelligenetics (m)</option>\n- <option value="jackknifer">Jackknifer (m)</option>\n- <option value="jackknifernon">Jackknifernon (m)</option>\n- <option value="mega">Meg'..b'hycean Mitochondrial</option>\n+ <option value="21">Trematode Mitochondrial</option>\n+ <option value="22">Scenedesmus obliquus</option>\n+ <option value="23">Thraustochytrium Mitochondrial</option>\n+ </param>\n+ <param argument="-regions" type="text" value="" label="Regions to translate" />\n+ <param argument="-trim" type="select" label="Remove all \'X\' and \'*\' characters from the right end of the translation">\n+ <option value="no">No</option>\n+ <option value="yes">Yes</option>\n+ </param>\n+ <param argument="-clean" type="select" label="Change all STOP codon positions from the \'*\' character to \'X\'">\n+ <option value="no">No</option>\n+ <option value="yes">Yes</option>\n+ </param>\n+ <param argument="-alternative" type="select" label="Define frame \'-1\' as using the set of codons starting with the last codon of the sequence">\n+ <option value="no">No</option>\n+ <option value="yes">Yes</option>\n+ </param>\n+ <param name="out_format1" argument="-osformat2" type="select" label="Output sequence file format">\n+ <option value="fasta">FASTA (m)</option>\n+ <option value="acedb">ACeDB (m)</option>\n+ <option value="asn1">ASN.1 (m)</option>\n+ <option value="clustal">Clustal (m)</option>\n+ <option value="codata">CODATA (m)</option>\n+ <option value="embl">EMBL (m)</option>\n+ <option value="fitch">Fitch (m)</option>\n+ <option value="gcg">Wisconsin Package GCG 9.x and 10.x (s)</option>\n+ <option value="genbank">GENBANK (m)</option>\n+ <option value="gff">GFF (m)</option>\n+ <option value="hennig86">Hennig86 (m)</option>\n+ <option value="ig">Intelligenetics (m)</option>\n+ <option value="jackknifer">Jackknifer (m)</option>\n+ <option value="jackknifernon">Jackknifernon (m)</option>\n+ <option value="mega">Mega (m)</option>\n+ <option value="meganon">Meganon (m)</option>\n+ <option value="msf">Wisconsin Package GCG\'s MSF (m)</option>\n+ <option value="pir">NBRF (PIR) (m)</option>\n+ <option value="ncbi">NCBI style FASTA (m)</option>\n+ <option value="nexus">Nexus/PAUP (m)</option>\n+ <option value="nexusnon">Nexusnon/PAUPnon (m)</option>\n+ <option value="phylip">PHYLIP interleaved (m)</option>\n+ <option value="phylipnon">PHYLIP non-interleaved (m)</option>\n+ <option value="selex">SELEX (m)</option>\n+ <option value="staden">Staden (s)</option>\n+ <option value="strider">DNA strider (m)</option>\n+ <option value="swiss">SwisProt entry (m)</option>\n+ <option value="text">Plain sequence (s)</option>\n+ <option value="treecon">Treecon (m)</option>\n+ </param>\n+ </inputs>\n+ <outputs>\n+ <data name="out_file1" format="fasta" />\n+ </outputs>\n+ <tests>\n+ <test>\n+ <param name="input1" value="2.fasta"/>\n+ <param name="frame" value="1"/>\n+ <param name="table" value="0"/>\n+ <param name="regions" value=""/>\n+ <param name="trim" value="no"/>\n+ <param name="clean" value="no"/>\n+ <param name="alternative" value="no"/>\n+ <param name="out_format1" value="fasta"/>\n+ <output name="out_file1" file="emboss_transeq_out.fasta"/>\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n .. class:: warningmark\n \n The input dataset needs to be sequences.\n \n -----\n \n- You can view the original documentation here_.\n+You can view the original documentation here_.\n \n- .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/transeq.html\n- </help>\n- <expand macro="citations" />\n+.. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/transeq.html\n+ ]]></help>\n+ <expand macro="citations" />\n </tool>\n' |
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| diff -r 1b6538ec8b56 -r 832c20329690 test-data/emboss_cai_out.cai --- a/test-data/emboss_cai_out.cai Thu Feb 23 09:43:47 2017 -0500 +++ b/test-data/emboss_cai_out.cai Mon Apr 23 13:05:09 2018 -0400 |
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| @@ -1,1 +1,1 @@ -Sequence: Sequence CAI: 0.188 \ No newline at end of file +Sequence: Sequence CAI: 0.188 |
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| diff -r 1b6538ec8b56 -r 832c20329690 test-data/emboss_newcpgseek_out.newcpgseek --- a/test-data/emboss_newcpgseek_out.newcpgseek Thu Feb 23 09:43:47 2017 -0500 +++ b/test-data/emboss_newcpgseek_out.newcpgseek Mon Apr 23 13:05:09 2018 -0400 |
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| @@ -6,4 +6,4 @@ Begin End Score CpG %CG CG/GC 121 141 34 3 57.1 1.00 261 272 43 3 75.0 1.00 -------------------------------------------- \ No newline at end of file +------------------------------------------- |
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| diff -r 1b6538ec8b56 -r 832c20329690 test-data/emboss_tranalign_out.fasta --- a/test-data/emboss_tranalign_out.fasta Thu Feb 23 09:43:47 2017 -0500 +++ b/test-data/emboss_tranalign_out.fasta Mon Apr 23 13:05:09 2018 -0400 |
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| @@ -42,4 +42,4 @@ ctgactaccctggaagtaggccgcatgctttttgga---ggtaaagttcatggttccctg gcccgtgctggaaaagtgagaggtcagactcctaaggtggccaaacaggagaagaagaag aagaagacaggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtg -cccacctttggcaagaagaagggccccaatgccaactct \ No newline at end of file +cccacctttggcaagaagaagggccccaatgccaactct |