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Version 5.0 for EMBOSS tools fuzztran, getorf and isochore

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Chinmay Rao
2007-12-11 21:01:52 +00:00
parent 523323ccd5
commit 73e52be7a0
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tools/emboss_5/emboss_fuzztran.xml
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<tool id="EMBOSS_fuzztran39" name="fuzztran">
<description>Protein pattern search after translation</description>
<command>fuzztran -sequence $input1 -outfile $out_file1 -pattern "$pattern" -pmismatch $mismatch -frame $frame -table $table -rformat2 $out_format1 -auto</command>
<inputs>
<param format="fasta" name="input1" type="data">
<label>Sequences</label>
</param>
<param name="pattern" size="5" type="text" value="">
<label>Search pattern</label>
</param>
<param name="mismatch" size="5" type="text" value="0">
<label>Number of mismatches</label>
</param>
<param name="frame" type="select">
<label>Frame(s) to translate</label>
<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</label>
<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 Report File Format</label>
<option value="table">Table</option>
<option value="embl">EMBL</option>
<option value="genbank">GENBANK</option>
<option value="gff">GFF</option>
<option value="pir">PIR</option>
<option value="swiss">SwissProt</option>
<option value="dbmotif">DbMotif</option>
<option value="diffseq">Diffseq</option>
<option value="excel">Excel (tab delimited)</option>
<option value="feattable">FeatTable</option>
<option value="motif">Motif</option>
<option value="regions">Regions</option>
<option value="seqtable">SeqTable</option>
<option value="simple">SRS Simple</option>
<option value="srs">SRS</option>
<option value="tagseq">TagSeq</option>
</param>
</inputs>
<outputs>
<data format="fuzztran" name="out_file1" />
</outputs>
<tests>
<test>
<param name="input1" value="1.fasta"/>
<param name="pattern" value="AA"/>
<param name="mismatch" value="0"/>
<param name="frame" value="6"/>
<param name="table" value="0"/>
<param name="out_format1" value="excel"/>
<output name="out_file1" file="emboss_fuzztran_out.tabular"/>
</test>
</tests>
<code file="emboss_format_corrector.py" />
<help>
.. class:: warningmark
The input dataset needs to be sequences.
-----
You can view the original documentation here_.
.. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/fuzztran.html
</help>
</tool>
tools/emboss_5/emboss_getorf.xml
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<tool id="EMBOSS_getorf42" name="getorf">
<description>Finds and extracts open reading frames (ORFs)</description>
<command>getorf -sequence $input1 -outseq $out_file1 -table $table -minsize $minsize -maxsize $maxsize -find $find -methionine $methionine -circular $circular -reverse $reverse -flanking $flanking
-osformat2 $out_format1 -auto</command>
<inputs>
<param format="fasta" name="input1" type="data">
<label>Sequences</label>
</param>
<param name="table" type="select">
<label>Code to use</label>
<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="minsize" size="10" type="text" value="30">
<label>Minimum nucleotide size of ORF to report</label>
</param>
<param name="maxsize" size="10" type="text" value="1000000">
<label>Maximum nucleotide size of ORF to report</label>
</param>
<param name="find" type="select">
<label>What to output</label>
<option value="0">Translation of regions between STOP codons</option>
<option value="1">Translation of regions between START and STOP codons</option>
<option value="2">Nucleic sequences between STOP codons</option>
<option value="3">Nucleic sequences between START and STOP codons</option>
<option value="4">Nucleotides flanking START codons</option>
<option value="5">Nucleotides flanking initial STOP codons</option>
<option value="6">Nucleotides flanking ending STOP codons</option>
</param>
<param name="methionine" type="select">
<label>All START codons to code for Methionine</label>
<option value="yes">Yes</option>
<option value="no">No</option>
</param>
<param name="circular" type="select">
<label>Circular sequence</label>
<option value="no">No</option>
<option value="yes">Yes</option>
</param>
<param name="reverse" type="select">
<label>Find ORFs in the reverse complement</label>
<option value="yes">Yes</option>
<option value="no">No</option>
</param>
<param name="flanking" size="10" type="text" value="100">
<label>Number of flanking nucleotides to output</label>
</param>
<param name="out_format1" type="select">
<label>Output Sequence File Format</label>
<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 format="fasta" name="out_file1" />
</outputs>
<tests>
<test>
<param name="input1" value="2.fasta"/>
<param name="minsize" value="30"/>
<param name="maxsize" value="1000000"/>
<param name="find" value="0"/>
<param name="methionine" value="yes"/>
<param name="circular" value="no"/>
<param name="reverse" value="yes"/>
<param name="table" value="0"/>
<param name="flanking" value="100"/>
<param name="out_format1" value="fasta"/>
<output name="out_file1" file="emboss_getorf_out.fasta"/>
</test>
</tests>
<code file="emboss_format_corrector.py" />
<help>
.. class:: warningmark
The input dataset needs to be sequences.
-----
You can view the original documentation here_.
.. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/getorf.html
</help>
</tool>
tools/emboss_5/emboss_isochore.xml
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<tool id="EMBOSS_isochore47" name="isochore">
<description>Plots isochores in large DNA sequences</description>
<command interpreter="perl">emboss_single_outputfile_wrapper.pl isochore -sequence $input1 -outfile $ofile2 -goutfile $ofile1 -graph png -window $window -shift $shift -auto</command>
<!-- <command interpreter="perl">emboss_single_outputfile_wrapper.pl isochore -sequence $input1 -goutfile $ofile1 -graph png -window $window -shift $shift -auto</command>-->
<inputs>
<param format="fasta" name="input1" type="data">
<label>Sequences</label>
</param>
<param name="window" size="4" type="text" value="1000">
<label>Window size</label>
</param>
<param name="shift" size="4" type="text" value="100">
<label>Shift increment</label>
</param>
</inputs>
<outputs>
<data format="png" name="ofile1" />
<data format="isochore" name="ofile2" />
</outputs>
<!-- <tests>
<test>
<param name="input1" value="2.fasta"/>
<param name="window" value="1000"/>
<param name="shift" value="100"/>
<output name="ofile1" file="emboss_isochore_out.isochore"/>
<output name="ofile2" file="emboss_isochore_out.isochore"/>
</test>
<test>
<param name="input1" value="2.fasta"/>
<param name="window" value="1000"/>
<param name="shift" value="100"/>
<output name="ofile2" file="emboss_isochore_out.isochore"/>
</test>
</tests>-->
<help>
.. class:: warningmark
The input dataset needs to be sequences.
-----
**Syntax**
This application plots GC content over a sequence. It is intended for large sequences such as complete chromosomes or large genomic contigs, although interesting results can also be obtained from shorter sequences. You can view the original documentation here_.
.. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/isochore.html
- Both **Window size** and **Shift increment** are intergers.
-----
**Example**
- Input sequences::
>hg18_dna range=chrX:151073054-151073376 5'pad=0 3'pad=0 revComp=FALSE strand=? repeatMasking=none
TTTATGTCTATAATCCTTACCAAAAGTTACCTTGGAATAAGAAGAAGTCA
GTAAAAAGAAGGCTGTTGTTCCGTGAAATACTGTCTTTATGCCTCAGATT
TGGAGTGCTCAGAGCCTCTGCAGCAAAGATTTGGCATGTGTCCTAGGCCT
GCTCAGAGCAGCAAATCCCACCCTCTTGGAGAATGAGACTCATAGAGGGA
CAGCTCCCTCCTCAGAGGCTTCTCTAATGGGACTCCAAAGAGCAAACACT
CAGCCCCATGAGGACTGGCCAGGCCAAGTGGTGTGTGGGAACAGGGAGCA
GCGGTTTCCAAGAGGATACAGTA
- Output data file::
Position Percent G+C 1 .. 323
80 0.422
112 0.460
144 0.509
176 0.534
208 0.553
240 0.553
- Output graphics file:
.. image:: ../static/emboss_icons/isochore.png
</help>
</tool>