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49 lines
1.6 KiB
XML
49 lines
1.6 KiB
XML
<tool id="EMBOSS: cpgreport16" name="cpgreport" version="5.0.0">
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<description>Reports all CpG rich regions</description>
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<command>cpgreport -sequence $input1 -outfile $out_file1 -outfeat $out_file2 -offormat3 $out_format2 -score $score -auto</command>
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<inputs>
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<param format="fasta" name="input1" type="data">
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<label>On query</label>
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</param>
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<param name="score" size="4" type="text" value="17">
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<label>Score for each CG sequence found (1-200)</label>
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</param>
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<param name="out_format2" type="select">
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<label>Output Feature File Format</label>
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<option value="gff">GFF</option>
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<option value="embl">EMBL</option>
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<option value="swiss">SwissProt</option>
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</param>
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</inputs>
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<outputs>
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<data format="cpgreport" name="out_file1" />
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<data format="gff" name="out_file2" />
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</outputs>
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<tests>
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<test>
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<param name="input1" value="2.fasta"/>
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<param name="score" value="17"/>
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<param name="out_format2" value="gff"/>
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<output name="out_file2" file="emboss_cpgreport_out2.cpgreport"/>
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</test>
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<!-- <test>
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<param name="input1" value="2.fasta"/>
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<param name="score" value="17"/>
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<param name="out_format2" value="gff"/>
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<output name="out_file1" file="emboss_cpgreport_out1.gff"/>
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</test> -->
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</tests>
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<code file="emboss_format_corrector.py" />
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<help>
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.. class:: warningmark
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The input dataset needs to be sequences.
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-----
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You can view the original documentation here_.
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.. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/cpgreport.html
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</help>
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</tool>
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