Mercurial > repos > devteam > emboss_5
changeset 12:832c20329690 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
| author | iuc |
|---|---|
| date | Mon, 23 Apr 2018 13:05:09 -0400 |
| parents | 1b6538ec8b56 |
| children | 8992d258e42f |
| files | 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 |
| diffstat | 6 files changed, 211 insertions(+), 204 deletions(-) [+] |
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--- a/emboss_iep.xml Thu Feb 23 09:43:47 2017 -0500 +++ b/emboss_iep.xml Mon Apr 23 13:05:09 2018 -0400 @@ -15,7 +15,7 @@ </param> </inputs> <outputs> - <data name="out_file1" format="iep" /> + <data name="out_file1" format="txt" /> </outputs> <tests> <test>
--- a/emboss_tranalign.xml Thu Feb 23 09:43:47 2017 -0500 +++ b/emboss_tranalign.xml Mon Apr 23 13:05:09 2018 -0400 @@ -1,82 +1,90 @@ <tool id="EMBOSS: tranalign100" name="tranalign" version="5.0.0"> - <description>Align nucleic coding regions given the aligned proteins</description> - <macros> - <import>macros.xml</import> - </macros> - <expand macro="requirements" /> - <code file="emboss_format_corrector.py" /> - <command>tranalign -asequence '$input1' -bsequence '$input2' -outseq '$out_file1' -table $table -osformat3 $out_format1 -auto</command> - <inputs> - <param name="input1" type="data" format="fasta" label="Nucleic sequences" /> - <param name="input2" type="data" format="data" label="Protein sequences" /> - <param name="table" type="select" label="Code to use"> - <option value="0">Standard</option> - <option value="1">Standard (with alternative initiation codons)</option> - <option value="2">Vertebrate Mitochondrial</option> - <option value="3">Yeast Mitochondrial</option> - <option value="4">Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma</option> - <option value="5">Invertebrate Mitochondrial</option> - <option value="6">Ciliate Macronuclear and Dasycladacean</option> - <option value="9">Echinoderm Mitochondrial</option> - <option value="10">Euplotid Nuclear</option> - <option value="11">Bacterial</option> - <option value="12">Alternative Yeast Nuclear</option> - <option value="13">Ascidian Mitochondrial</option> - <option value="14">Flatworm Mitochondrial</option> - <option value="15">Blepharisma Macronuclear</option> - <option value="16">Chlorophycean Mitochondrial</option> - <option value="21">Trematode Mitochondrial</option> - <option value="22">Scenedesmus obliquus</option> - <option value="23">Thraustochytrium Mitochondrial</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="fasta" /> - </outputs> - <tests> - <test> - <param name="input1" value="3.fasta"/> - <param name="input2" value="2.pep"/> - <param name="table" value="0"/> - <param name="out_format1" value="fasta"/> - <output name="out_file1" file="emboss_tranalign_out.fasta"/> - </test> - </tests> - <help> - You can view the original documentation here_. + <description>Align nucleic coding regions given the aligned proteins</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <code file="emboss_format_corrector.py" /> + <command detect_errors="aggressive"><![CDATA[ +tranalign +-asequence '$input1' +-bsequence '$input2' +-outseq '$out_file1' +-table $table +-osformat3 $out_format1 +-auto + ]]></command> + <inputs> + <param name="input1" argument="-asequence" type="data" format="fasta" label="Nucleic sequences" /> + <param name="input2" argument="-bsequence" type="data" format="data" label="Protein sequences" /> + <param argument="-table" type="select" label="Code to use"> + <option value="0">Standard</option> + <option value="1">Standard (with alternative initiation codons)</option> + <option value="2">Vertebrate Mitochondrial</option> + <option value="3">Yeast Mitochondrial</option> + <option value="4">Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma</option> + <option value="5">Invertebrate Mitochondrial</option> + <option value="6">Ciliate Macronuclear and Dasycladacean</option> + <option value="9">Echinoderm Mitochondrial</option> + <option value="10">Euplotid Nuclear</option> + <option value="11">Bacterial</option> + <option value="12">Alternative Yeast Nuclear</option> + <option value="13">Ascidian Mitochondrial</option> + <option value="14">Flatworm Mitochondrial</option> + <option value="15">Blepharisma Macronuclear</option> + <option value="16">Chlorophycean Mitochondrial</option> + <option value="21">Trematode Mitochondrial</option> + <option value="22">Scenedesmus obliquus</option> + <option value="23">Thraustochytrium Mitochondrial</option> + </param> + <param name="out_format1" argument="-osformat3" 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="fasta" /> + </outputs> + <tests> + <test> + <param name="input1" value="3.fasta"/> + <param name="input2" value="2.pep"/> + <param name="table" value="0"/> + <param name="out_format1" value="fasta"/> + <output name="out_file1" file="emboss_tranalign_out.fasta"/> + </test> + </tests> + <help><![CDATA[ +You can view the original documentation here_. - .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/tranalign.html - </help> - <expand macro="citations" /> +.. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/tranalign.html + ]]></help> + <expand macro="citations" /> </tool>
--- a/emboss_transeq.xml Thu Feb 23 09:43:47 2017 -0500 +++ b/emboss_transeq.xml Mon Apr 23 13:05:09 2018 -0400 @@ -1,130 +1,129 @@ <tool id="EMBOSS: transeq101" name="transeq" version="5.0.0"> - <description>Translate nucleic acid sequences</description> - <macros> - <import>macros.xml</import> - </macros> - <expand macro="requirements" /> - <code file="emboss_format_corrector.py" /> - <command><![CDATA[ - transeq - -sequence '$input1' - -outseq '$out_file1' - -frame $frame - -table $table - #if str($regions).strip(): - -regions '$regions' - #end if - -trim $trim - -clean $clean - -alternative $alternative - -osformat2 '$out_format1' - -auto - ]]> - </command> - <inputs> - <param name="input1" type="data" format="fasta" label="Sequences" /> - <param name="frame" type="select" label="Frame(s) to translate"> - <option value="1">Frame 1</option> - <option value="2">Frame 2</option> - <option value="3">Frame 3</option> - <option value="F">Forward three frames</option> - <option value="-1">Frame -1</option> - <option value="-2">Frame -2</option> - <option value="-3">Frame -3</option> - <option value="R">Reverse three frames</option> - <option value="6">All six frames</option> - </param> - <param name="table" type="select" label="Code to use"> - <option value="0">Standard</option> - <option value="1">Standard (with alternative initiation codons)</option> - <option value="2">Vertebrate Mitochondrial</option> - <option value="3">Yeast Mitochondrial</option> - <option value="4">Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma</option> - <option value="5">Invertebrate Mitochondrial</option> - <option value="6">Ciliate Macronuclear and Dasycladacean</option> - <option value="9">Echinoderm Mitochondrial</option> - <option value="10">Euplotid Nuclear</option> - <option value="11">Bacterial</option> - <option value="12">Alternative Yeast Nuclear</option> - <option value="13">Ascidian Mitochondrial</option> - <option value="14">Flatworm Mitochondrial</option> - <option value="15">Blepharisma Macronuclear</option> - <option value="16">Chlorophycean Mitochondrial</option> - <option value="21">Trematode Mitochondrial</option> - <option value="22">Scenedesmus obliquus</option> - <option value="23">Thraustochytrium Mitochondrial</option> - </param> - <param name="regions" type="text" value="" label="Regions to translate" /> - <param name="trim" type="select" label="Remove all 'X' and '*' characters from the right end of the translation"> - <option value="no">No</option> - <option value="yes">Yes</option> - </param> - <param name="clean" type="select" label="Change all STOP codon positions from the '*' character to 'X'"> - <option value="no">No</option> - <option value="yes">Yes</option> - </param> - <param name="alternative" type="select" label="Define frame '-1' as using the set of codons starting with the last codon of the sequence"> - <option value="no">No</option> - <option value="yes">Yes</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="fasta" /> - </outputs> - <tests> - <test> - <param name="input1" value="2.fasta"/> - <param name="frame" value="1"/> - <param name="table" value="0"/> - <param name="regions" value=""/> - <param name="trim" value="no"/> - <param name="clean" value="no"/> - <param name="alternative" value="no"/> - <param name="out_format1" value="fasta"/> - <output name="out_file1" file="emboss_transeq_out.fasta"/> - </test> - </tests> - <help> + <description>Translate nucleic acid sequences</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <code file="emboss_format_corrector.py" /> + <command detect_errors="aggressive"><![CDATA[ +transeq +-sequence '$input1' +-outseq '$out_file1' +-frame $frame +-table $table +#if str($regions).strip(): + -regions '$regions' +#end if +-trim $trim +-clean $clean +-alternative $alternative +-osformat2 '$out_format1' +-auto + ]]></command> + <inputs> + <param name="input1" argument="-sequence" type="data" format="fasta" label="Sequences" /> + <param argument="-frame" type="select" label="Frame(s) to translate"> + <option value="1">Frame 1</option> + <option value="2">Frame 2</option> + <option value="3">Frame 3</option> + <option value="F">Forward three frames</option> + <option value="-1">Frame -1</option> + <option value="-2">Frame -2</option> + <option value="-3">Frame -3</option> + <option value="R">Reverse three frames</option> + <option value="6">All six frames</option> + </param> + <param argument="-table" type="select" label="Code to use"> + <option value="0">Standard</option> + <option value="1">Standard (with alternative initiation codons)</option> + <option value="2">Vertebrate Mitochondrial</option> + <option value="3">Yeast Mitochondrial</option> + <option value="4">Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma</option> + <option value="5">Invertebrate Mitochondrial</option> + <option value="6">Ciliate Macronuclear and Dasycladacean</option> + <option value="9">Echinoderm Mitochondrial</option> + <option value="10">Euplotid Nuclear</option> + <option value="11">Bacterial</option> + <option value="12">Alternative Yeast Nuclear</option> + <option value="13">Ascidian Mitochondrial</option> + <option value="14">Flatworm Mitochondrial</option> + <option value="15">Blepharisma Macronuclear</option> + <option value="16">Chlorophycean Mitochondrial</option> + <option value="21">Trematode Mitochondrial</option> + <option value="22">Scenedesmus obliquus</option> + <option value="23">Thraustochytrium Mitochondrial</option> + </param> + <param argument="-regions" type="text" value="" label="Regions to translate" /> + <param argument="-trim" type="select" label="Remove all 'X' and '*' characters from the right end of the translation"> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + <param argument="-clean" type="select" label="Change all STOP codon positions from the '*' character to 'X'"> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + <param argument="-alternative" type="select" label="Define frame '-1' as using the set of codons starting with the last codon of the sequence"> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + <param name="out_format1" argument="-osformat2" 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="fasta" /> + </outputs> + <tests> + <test> + <param name="input1" value="2.fasta"/> + <param name="frame" value="1"/> + <param name="table" value="0"/> + <param name="regions" value=""/> + <param name="trim" value="no"/> + <param name="clean" value="no"/> + <param name="alternative" value="no"/> + <param name="out_format1" value="fasta"/> + <output name="out_file1" file="emboss_transeq_out.fasta"/> + </test> + </tests> + <help><![CDATA[ .. class:: warningmark The input dataset needs to be sequences. ----- - You can view the original documentation here_. +You can view the original documentation here_. - .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/transeq.html - </help> - <expand macro="citations" /> +.. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/transeq.html + ]]></help> + <expand macro="citations" /> </tool>
--- 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 @@ -1,1 +1,1 @@ -Sequence: Sequence CAI: 0.188 \ No newline at end of file +Sequence: Sequence CAI: 0.188
--- 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 @@ -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 +-------------------------------------------
--- 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 @@ -42,4 +42,4 @@ ctgactaccctggaagtaggccgcatgctttttgga---ggtaaagttcatggttccctg gcccgtgctggaaaagtgagaggtcagactcctaaggtggccaaacaggagaagaagaag aagaagacaggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtg -cccacctttggcaagaagaagggccccaatgccaactct \ No newline at end of file +cccacctttggcaagaagaagggccccaatgccaactct