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Committing EMBOSS v5.0 tools tcode textsearch tmap twofeat vectorstrip wordmatch with associated functional test files

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Chinmay Rao
2007-12-17 14:38:16 +00:00
parent f955d77ec3
commit 7a366bcec4
6 changed files with 421 additions and 0 deletions
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tools/emboss_5/emboss_tcode.xml
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<tool id="EMBOSS_tcode97" name="tcode">
<description>Fickett TESTCODE statistic to identify protein-coding DNA</description>
<command>tcode -sequence $input1 -outfile $out_file1 -window "$window" -step "$step" -rformat $out_format1 -auto</command>
<inputs>
<param format="data" name="input1" type="data">
<label>Sequence</label>
</param>
<param name="window" size="5" type="text" value="200">
<label>Window size</label>
</param>
<param name="step" size="5" type="text" value="3">
<label>Step size</label>
</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="table" name="out_file1" />
</outputs>
<code file="emboss_format_corrector.py" />
<help>
You can view the original documentation here_.
.. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/tcode.html
</help>
</tool>
tools/emboss_5/emboss_textsearch.xml
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<tool id="EMBOSS_textsearch98" name="textsearch">
<description>Search sequence documentation. Slow, use SRS and Entrez!</description>
<command>textsearch -sequence $input1 -outfile $out_file1 -pattern "$pattern" -casesensitive -heading $heading -usa $usa -accession $accession -name $search_name -description $description -html
$html_out1 -auto</command>
<inputs>
<param format="data" name="input1" type="data">
<label>Sequence</label>
</param>
<param name="pattern" size="50" type="text" value="">
<label>Pattern to search for</label>
</param>
<param name="casesensitive" type="select">
<label>Do a case-sensitive search</label>
<option value="no">No</option>
<option value="yes">Yes</option>
</param>
<param name="heading" type="select">
<label>Display column headings</label>
<option value="yes">Yes</option>
<option value="no">No</option>
</param>
<param name="usa" type="select">
<label>Display the USA of the sequence</label>
<option value="yes">Yes</option>
<option value="no">No</option>
</param>
<param name="accession" type="select">
<label>Display accession column</label>
<option value="yes">Yes</option>
<option value="no">No</option>
</param>
<param name="search_name" type="select">
<label>Display name column</label>
<option value="yes">Yes</option>
<option value="no">No</option>
</param>
<param name="description" type="select">
<label>Display description column</label>
<option value="yes">Yes</option>
<option value="no">No</option>
</param>
<param name="html_out1" type="select">
<label>Format output as an HTML table</label>
<option value="no">No</option>
<option value="yes">Yes</option>
</param>
</inputs>
<outputs>
<data format="textsearch" name="out_file1" />
</outputs>
<code file="emboss_format_corrector.py" />
<help>
You can view the original documentation here_.
.. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/textsearch.html
</help>
</tool>
tools/emboss_5/emboss_tmap.xml
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<tool id="EMBOSS_tmap99" name="tmap">
<description>Displays membrane spanning regions</description>
<command interpreter="perl">emboss_single_outputfile_wrapper.pl tmap -sequences $input1 -outfile $out_file1 -goutfile $out_file2 -graph png -rformat $out_format1 -auto</command>
<inputs>
<param format="data" name="input1" type="data">
<label>Sequence</label>
</param>
<param name="out_format1" type="select">
<label>Output Report File Format</label>
<option value="seqtable ">SeqTable</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="simple">SRS Simple</option>
<option value="srs">SRS</option>
<option value="table">Table</option>
<option value="tagseq">TagSeq</option>
</param>
</inputs>
<outputs>
<data format="seqtable" name="out_file1" />
<data format="png" name="out_file2" />
</outputs>
<code file="emboss_format_corrector.py" />
<help>
You can view the original documentation here_.
.. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/tmap.html
</help>
</tool>
tools/emboss_5/emboss_twofeat.xml
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<tool id="EMBOSS: twofeat104" name="twofeat">
<description>Finds neighbouring pairs of features in sequences</description>
<command>twofeat -sequence $input1 -outfile $out_file1 -atype "$atype" -btype "$btype" -minrange "$minrange" -maxrange "$maxrange" -asource "$asource" -asense $asense -aminscore "$aminscore"
-amaxscore "$amaxscore" -atag "$atag" -avalue "$avalue" -bsource "$bsource" -bsense "$bsense" -bminscore "$bminscore" -bmaxscore "$bmaxscore" -btag "$btag" -bvalue "$bvalue" -overlap $overlap
-rangetype $rangetype -sense $sense -order $order -twoout $twoout -typeout "$typeout" -rformat2 $out_format1 -auto</command>
<inputs>
<param format="data" name="input1" type="data">
<label>Sequences</label>
</param>
<param name="atype" size="50" type="text" value="*">
<label>Feature type you wish to allow. Feature 1</label>
</param>
<param name="btype" size="50" type="text" value="*">
<label>Feature type you wish to allow. Feature 2</label>
</param>
<param name="minrange" size="5" type="text" value="0">
<label>Minimun range</label>
</param>
<param name="maxrange" size="5" type="text" value="0">
<label>Maximum range</label>
</param>
<param name="asource" size="50" type="text" value="*">
<label>Feature source 1</label>
</param>
<param name="asense" type="select">
<label>Feature sense 1</label>
<option value="0">Any sense</option>
<option value="+">Forward sense</option>
<option value="-">Reverse sense</option>
</param>
<param name="aminscore" size="5" type="text" value="0.0">
<label>Feature 1 minimum score</label>
</param>
<param name="amaxscore" size="5" type="text" value="0.0">
<label>Feature1 maxiumum score</label>
</param>
<param name="atag" size="50" type="text" value="*">
<label>Feature 1 tag</label>
</param>
<param name="avalue" size="50" type="text" value="*">
<label>Tag 1 value</label>
</param>
<param name="bsource" size="50" type="text" value="*">
<label>Feature 2 source</label>
</param>
<param name="bsense" type="select">
<label>Feature 2 sense</label>
<option value="0">Any sense</option>
<option value="+">Forward sense</option>
<option value="-">Reverse sense</option>
</param>
<param name="bminscore" size="5" type="text" value="0.0">
<label>Feature 2 miniumum score</label>
</param>
<param name="bmaxscore" size="5" type="text" value="0.0">
<label>Feature 2 maximum score</label>
</param>
<param name="btag" size="50" type="text" value="*">
<label>Feature 2 tag</label>
</param>
<param name="bvalue" size="50" type="text" value="*">
<label>Feature 2 tag value</label>
</param>
<param name="overlap" type="select">
<label>opverlaps allowed</label>
<option value="A">Any</option>
<option value="O">Overlap required but not within</option>
<option value="NO">No overlaps are allowed</option>
<option value="NW:">Overlap required but not within</option>
<option value="AW">A must be all within B</option>
<option value="BW">B must be all within A</option>
</param>
<param name="rangetype" type="select">
<label>How to determine range</label>
<option value="N">From nearest ends</option>
<option value="L">From left ends</option>
<option value="R">From right ends</option>
<option value="F">From furthest ends</option>
</param>
<param name="sense" type="select">
<label>Required sense</label>
<option value="A">Any sense</option>
<option value="S">Same sense</option>
<option value="O">Opposite sense</option>
</param>
<param name="order" type="select">
<label>Required order of the two features</label>
<option value="A">Any</option>
<option value="AB">Feature A then feature B</option>
<option value="BA">Feature B then feature A</option>
</param>
<param name="twoout" type="select">
<label>Write out the two features themselves</label>
<option value="no">No</option>
<option value="yes">Yes</option>
</param>
<param name="typeout" size="50" type="text" value="misc_feature">
<label>New feature type</label>
</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="table" name="out_file1" />
</outputs>
<code file="emboss_format_corrector.py" />
<help>
You can view the original documentation here_.
.. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/twofeat.html
</help>
</tool>
tools/emboss_5/emboss_vectorstrip.xml
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<tool id="EMBOSS_vectorstrip106" name="vectorstrip">
<description>Strips out DNA between a pair of vector sequences</description>
<command>vectorstrip -sequence $input1 -vectorsfile $input2 -outseq $ofile1 -outfile $ofile2 -vectorfile yes -mismatch "$mismatch" -besthits $besthits -linkera "$linkera" -linkerb
"$linkerb" -osformat4 $out_format1 -auto</command>
<inputs>
<param format="fasta" name="input1" type="data">
<label>Sequences</label>
</param>
<param format="data" name="input2" type="data">
<label>Vector file</label>
</param>
<param name="mismatch" size="4" type="text" value="10">
<label>Max allowed percent mismatch</label>
</param>
<param name="besthits" type="select">
<label>Show only the best hits (minimize mismatches)</label>
<option value="yes">Yes</option>
<option value="no">No</option>
</param>
<param name="linkera" size="50" type="text" value="">
<label>The 5' sequence</label>
</param>
<param name="linkerb" size="50" type="text" value="">
<label>The 3' sequence</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="ofile1" />
<data format="vectorstrip" name="ofile2" />
</outputs>
<!-- <tests>
<test>
<param name="input1" value="1.fasta"/>
<param name="input2" value="2.fasta"/>
<param name="mismatch" value="10"/>
<param name="besthits" value="yes"/>
<param name="linkera" value=""/>
<param name="linkerb" value=""/>
<param name="out_format1" value="fasta"/>
<output name="ofile1" file="emboss_vectorstrip_out.fasta"/>
</test>
</tests> -->
<code file="emboss_format_corrector.py" />
<help>
You can view the original documentation here_.
.. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/vectorstrip.html
</help>
</tool>
tools/emboss_5/emboss_wordmatch.xml
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<tool id="EMBOSS_wordmatch110" name="wordmatch">
<description>Finds all exact matches of a given size between 2 sequences</description>
<command>wordmatch -asequence $input1 -bsequence $input2 -outfile $out_file1 -aoutfeat $out_file2 -boutfeat $out_file3 -wordsize "$wordsize" -aformat3 $out_format1 -offormat4 $out_format2
-offormat5 $out_format3 -auto</command>
<inputs>
<param format="fasta" name="input1" type="data">
<label>Sequence 1</label>
</param>
<param format="fasta" name="input2" type="data">
<label>Sequence 2</label>
</param>
<param name="wordsize" size="5" type="text" value="4">
<label>Word size</label>
</param>
<param name="out_format1" type="select">
<label>Output Alignment File Format</label>
<option value="match">Match (m)</option>
<option value="simple">Simple (m)</option>
<option value="fasta">FASTA (m)</option>
<option value="msf">MSF (m)</option>
<option value="srs">SRS (m)</option>
<option value="pair">Pair (p)</option>
<option value="markx0">Markx0 (p)</option>
<option value="markx1">Markx1 (p)</option>
<option value="markx2">Markx2 (p)</option>
<option value="markx3">Markx3 (p)</option>
<option value="markx10">Markx10 (p)</option>
<option value="srspair">SRS pair (p)</option>
<option value="score">Score (p)</option>
</param>
<param name="out_format2" type="select">
<label>Output Feature 1 File Format</label>
<option value="gff">GFF</option>
<option value="embl">EMBL</option>
<option value="swiss">SwissProt</option>
</param>
<param name="out_format3" type="select">
<label>Output Feature 2 File Format</label>
<option value="gff">GFF</option>
<option value="embl">EMBL</option>
<option value="swiss">SwissProt</option>
</param>
</inputs>
<outputs>
<data format="match" name="out_file1" />
<data format="gff" name="out_file2" />
<data format="gff" name="out_file3" />
</outputs>
<!-- <tests>
<test>
<param name="input1" value="2.fasta"/>
<param name="input2" value="1.fasta"/>
<param name="wordsize" value="4"/>
<param name="out_format1" value="fasta"/>
<param name="out_format2" value="gff"/>
<param name="out_format3" value="gff"/>
<output name="ofile2" file="emboss_wordmatch_out.embl"/>
</test>
</tests> test takes a long time to run-->
<code file="emboss_format_corrector.py" />
<help>
.. class:: warningmark
The input datasets need to be sequences.
-----
You can view the original documentation here_.
.. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/wordmatch.html
</help>
</tool>