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Committing EMBOSS v5.0 tools marscan maskfeat maskseq matcher megamerger merger and associated test files.

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Chinmay Rao
2007-12-17 14:16:37 +00:00
parent 3b4bfb49c0
commit 9cbcae2402
7 changed files with 398 additions and 0 deletions
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tools/emboss_5/emboss_marscan.xml
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<tool id="EMBOSS_marscan49" name="marscan">
<description>Finds MAR/SAR sites in nucleic sequences</description>
<command>marscan -sequence $input1 -outfile $out_file1 -rformat2 $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="gff">GFF</option>
<option value="embl">EMBL</option>
<option value="genbank">GENBANK</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="table">Table</option>
<option value="tagseq">TagSeq</option>
</param>
</inputs>
<outputs>
<data format="gff" name="out_file1" />
</outputs>
<tests>
<test>
<param name="input1" value="1.fasta"/>
<param name="out_format1" value="excel"/>
<output name="out_file1" file="emboss_marscan_out.tabular"/>
</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/marscan.html
</help>
</tool>
tools/emboss_5/emboss_maskfeat.xml
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<tool id="EMBOSS_maskfeat50" name="maskfeat">
<description>Mask off features of a sequence</description>
<command>maskfeat -sequence $input1 -outseq $out_file1 -type "$type" -tolower $tolower -maskchar "$maskchar" -osformat2 $out_format1 -auto</command>
<inputs>
<param format="data" name="input1" type="data">
<label>Sequence</label>
</param>
<param name="type" size="50" type="text" value="repeat*">
<label>Feature to mask</label>
</param>
<param name="tolower" type="select">
<label>Mask features by converting to lowercase</label>
<option value="no">No</option>
<option value="yes">Yes</option>
</param>
<param name="maskchar" size="1" type="text" value="N">
<label>Character to mask with</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="type" value="repeat*"/>
<param name="tolower" value="no"/>
<param name="maskchar" value="N"/>
<param name="out_format1" value="fasta"/>
<output name="out_file1" file="emboss_maskfeat_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/maskfeat.html
</help>
</tool>
tools/emboss_5/emboss_maskseq.xml
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<tool id="EMBOSS_maskseq51" name="maskseq">
<description>Mask off regions of a sequence</description>
<command>maskseq -sequence $input1 -outseq $out_file1 -regions "$regions" -tolower $tolower -maskchar "$maskchar" -osformat2 $out_format1 -auto</command>
<inputs>
<param format="data" name="input1" type="data">
<label>Sequence</label>
</param>
<param name="regions" size="50" type="text" value="">
<label>Regions to mask (Example 1-99)</label>
</param>
<param name="tolower" type="select">
<label>mask by converting to lowercase</label>
<option value="no">No</option>
<option value="yes">Yes</option>
</param>
<param name="maskchar" size="1" type="text" value="N">
<label>Character to use when masking</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="regions" value="1-3"/>
<param name="tolower" value="no"/>
<param name="maskchar" value="N"/>
<param name="out_format1" value="fasta"/>
<output name="out_file1" file="emboss_maskseq_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/maskseq.html
</help>
</tool>
tools/emboss_5/emboss_matcher.xml
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<tool id="EMBOSS_matcher52" name="matcher">
<description>Finds the best local alignments between two sequences</description>
<command>matcher -asequence $input1 -bsequence $input2 -outfile $out_file1 -alternatives $alternatives -gapopen $gapopen -gapextend $gapextend -aformat3 $out_format1 -auto</command>
<inputs>
<param format="data" name="input1" type="data">
<label>Sequence 1</label>
</param>
<param format="data" name="input2" type="data">
<label>Sequence 2</label>
</param>
<param name="alternatives" size="4" type="text" value="1">
<label>Number of alternative matches</label>
</param>
<param name="gapopen" size="4" type="text" value="16">
<label>Gap penalty</label>
</param>
<param name="gapextend" size="4" type="text" value="4">
<label>Gap length (extension) penalty</label>
</param>
<param name="out_format1" type="select">
<label>Output Alignment File Format</label>
<option value="markx0">Markx0 (p)</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="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>
</inputs>
<outputs>
<data format="markx0" name="out_file1" />
</outputs>
<tests>
<test>
<param name="input1" value="2.fasta"/>
<param name="input2" value="1.fasta"/>
<param name="alternatives" value="1"/>
<param name="gapopen" value="16"/>
<param name="gapextend" value="4"/>
<param name="out_format1" value="fasta"/>
<output name="out_file1" file="emboss_matcher_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/matcher.html
</help>
</tool>
tools/emboss_5/emboss_megamerger.xml
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<tool id="EMBOSS_megamerger53" name="megamerger">
<description>Merge two large overlapping nucleic acid sequences</description>
<command>megamerger -asequence $input1 -bsequence $input2 -outseq $out_file1 -outfile $out_file2 -wordsize $wordsize -prefer $prefer -osformat3 $out_format1 -auto</command>
<inputs>
<param format="data" name="input1" type="data">
<label>Sequence 1</label>
</param>
<param format="data" name="input2" type="data">
<label>Sequence 2</label>
</param>
<param name="wordsize" size="4" type="text" value="20">
<label>Word size</label>
</param>
<param name="prefer" type="select">
<label>Prefer first sequence when mismatches occur</label>
<option value="no">No</option>
<option value="yes">Yes</option>
</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" />
<data format="txt" 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/megamerger.html
</help>
</tool>
tools/emboss_5/emboss_merger.xml
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<tool id="EMBOSS_merger54" name="merger">
<description>Merge two overlapping nucleic acid sequences</description>
<command>merger -asequence $input1 -bsequence $input2 -outseq $out_file1 -outfile $out_file2 -gapopen $gapopen -gapextend $gapextend -osformat4 $out_format1 -aformat3 $out_format2 -auto</command>
<inputs>
<param format="data" name="input1" type="data">
<label>Sequence 1</label>
</param>
<param format="data" name="input2" type="data">
<label>Sequence 2</label>
</param>
<param name="gapopen" size="4" type="text" value="50.0">
<label>Gap opening penalty</label>
</param>
<param name="gapextend" size="4" type="text" value="5.0">
<label>Gap extension penalty</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>
<param name="out_format2" type="select">
<label>Output Alignment File Format</label>
<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>
</inputs>
<outputs>
<data format="fasta" name="out_file1" />
<data format="simple" 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/merger.html
</help>
</tool>
tools/emboss_5/emboss_multiple_outputfile_wrapper.pl
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#! /usr/bin/perl -w
use strict;
my $cmd_string = join (" ",@ARGV);
my $results = `$cmd_string`;
my @files = split("\n",$results);
foreach my $thisLine (@files)
{
if ($thisLine =~ /Created /)
{
$thisLine =~ /[\w|\.]+$/;
$thisLine =$&;
print "outfile: $thisLine\n";
}
else
{
print $thisLine,"\n";
}
}