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Fix for EMBOSS 5 cpgplot tool.

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This commit is contained in:
Greg Von Kuster
2008-04-25 19:05:56 +00:00
parent 648c2de5a1
commit 61aa1fe894
2 changed files with 10 additions and 20 deletions
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tools/emboss_5/emboss_cpgplot.xml
+9 -19
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@@ -1,42 +1,32 @@
<tool id="EMBOSS: cpgplot15" name="cpgplot" version="5.0.0">
<description>Plot CpG rich areas</description>
<command interpreter="perl">emboss_cpgplot_wrapper.pl cpgplot -sequence $input1 -window $window -minlen $minlen -minpc $minpc -outfile $out_file1 -graph png -goutfile3 $out_file2
-outfeat $out_file3 -offormat4 $out_format3 -minoe $minoe -auto</command>
<command interpreter="perl">emboss_cpgplot_wrapper.pl /home/universe/linux-i686/EMBOSS-5.0.0/bin/cpgplot -sequence $input1 -window $window -minlen $minlen -minpc $minpc -outfile $outfile -graph png -goutfile $goutfile -outfeat $outfeat -minoe $minoe -auto</command>
<inputs>
<param format="data" name="input1" type="data">
<label>On query</label>
</param>
<param name="window" size="4" type="text" value="100">
<param name="window" size="4" type="integer" value="100">
<label>Window Size</label>
</param>
<!-- <param name="shift" size="4" type="text" value="1">
<label>Step size (shift)</label>
</param> -->
<param name="minlen" size="4" type="text" value="200">
<param name="minlen" size="4" type="integer" value="200">
<label>Minimum length</label>
</param>
<param name="minoe" size="4" type="text" value="0.6">
<param name="minoe" size="4" type="float" value="0.6">
<label>Minimum average observed to expected ratio</label>
</param>
<param name="minpc" size="4" type="text" value="50.0">
<param name="minpc" size="4" type="float" value="50.0">
<label>Minimum average percentage of G plus C</label>
</param>
<param name="out_format3" type="select">
<label>Output Feature File Format</label>
<option value="gff">GFF</option>
<option value="embl">EMBL</option>
<option value="swiss">SwissProt</option>
</param>
</inputs>
<outputs>
<data format="txt" name="out_file1" />
<data format="png" name="out_file2" />
<data format="gff" name="out_file3" />
<data format="cpgplot" name="outfile" />
<data format="png" name="goutfile" />
<data format="gff" name="outfeat" />
</outputs>
<code file="emboss_format_corrector.py" />
<help>
You can view the original documentation here_.
.. _here: http://emboss.sourceforge.net/apps/release/4.0/emboss/apps/cpgplot.html
.. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/cpgplot.html
</help>
</tool>
tools/emboss_5/emboss_cpgplot_wrapper.pl
+1 -1
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@@ -5,5 +5,5 @@ use File::Copy;
my $cmd_string = join (" ",@ARGV);
my $results = `$cmd_string`;
my @files = split("\n",$results);
my $fileNameOut = $ARGV[16];
my $fileNameOut = $ARGV[14];
move($fileNameOut.".1.png",$fileNameOut);