[2] | 1 | <tool id="EMBOSS: cpgreport16" name="cpgreport" version="5.0.0">
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| 2 | <description>Reports all CpG rich regions</description>
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| 3 | <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
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| 4 | <command>cpgreport -sequence $input1 -outfile $out_file1 -outfeat $out_file2 -offormat3 $out_format2 -score $score -auto</command>
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| 5 | <inputs>
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| 6 | <param format="fasta" name="input1" type="data">
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| 7 | <label>On query</label>
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| 8 | </param>
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| 9 | <param name="score" size="4" type="text" value="17">
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| 10 | <label>Score for each CG sequence found (1-200)</label>
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| 11 | </param>
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| 12 | <param name="out_format2" type="select">
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| 13 | <label>Output Feature File Format</label>
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| 14 | <option value="gff">GFF</option>
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| 15 | <option value="embl">EMBL</option>
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| 16 | <option value="swiss">SwissProt</option>
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| 17 | </param>
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| 18 | </inputs>
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| 19 | <outputs>
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| 20 | <data format="cpgreport" name="out_file1" />
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| 21 | <data format="gff" name="out_file2" />
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| 22 | </outputs> |
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| 23 | <tests> |
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| 24 | <test> |
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| 25 | <param name="input1" value="2.fasta"/> |
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| 26 | <param name="score" value="17"/> |
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| 27 | <param name="out_format2" value="gff"/> |
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| 28 | <output name="out_file2" file="emboss_cpgreport_out2.cpgreport"/> |
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| 29 | </test> |
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| 30 | <!-- <test> |
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| 31 | <param name="input1" value="2.fasta"/> |
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| 32 | <param name="score" value="17"/> |
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| 33 | <param name="out_format2" value="gff"/> |
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| 34 | <output name="out_file1" file="emboss_cpgreport_out1.gff"/> |
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| 35 | </test> --> |
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| 36 | </tests>
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| 37 | <code file="emboss_format_corrector.py" />
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| 38 | <help> |
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| 39 | .. class:: warningmark |
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| 40 | |
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| 41 | The input dataset needs to be sequences. |
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| 42 | |
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| 43 | ----- |
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| 44 | |
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| 45 | You can view the original documentation here_. |
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| 46 | |
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| 47 | .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/cpgreport.html |
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| 48 | </help> |
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| 49 | </tool> |
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