Mercurial > repos > xuebing > sharplabtool
comparison tools/emboss_5/emboss_cpgreport.xml @ 0:9071e359b9a3
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| author | xuebing |
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| date | Fri, 09 Mar 2012 19:37:19 -0500 |
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| -1:000000000000 | 0:9071e359b9a3 |
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| 1 <tool id="EMBOSS: cpgreport16" name="cpgreport" version="5.0.0"> | |
| 2 <description>Reports all CpG rich regions</description> | |
| 3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> | |
| 4 <command>cpgreport -sequence $input1 -outfile $out_file1 -outfeat $out_file2 -offormat3 $out_format2 -score $score -auto</command> | |
| 5 <inputs> | |
| 6 <param format="fasta" name="input1" type="data"> | |
| 7 <label>On query</label> | |
| 8 </param> | |
| 9 <param name="score" size="4" type="text" value="17"> | |
| 10 <label>Score for each CG sequence found (1-200)</label> | |
| 11 </param> | |
| 12 <param name="out_format2" type="select"> | |
| 13 <label>Output Feature File Format</label> | |
| 14 <option value="gff">GFF</option> | |
| 15 <option value="embl">EMBL</option> | |
| 16 <option value="swiss">SwissProt</option> | |
| 17 </param> | |
| 18 </inputs> | |
| 19 <outputs> | |
| 20 <data format="cpgreport" name="out_file1" /> | |
| 21 <data format="gff" name="out_file2" /> | |
| 22 </outputs> | |
| 23 <tests> | |
| 24 <test> | |
| 25 <param name="input1" value="2.fasta"/> | |
| 26 <param name="score" value="17"/> | |
| 27 <param name="out_format2" value="gff"/> | |
| 28 <output name="out_file2" file="emboss_cpgreport_out2.cpgreport"/> | |
| 29 </test> | |
| 30 <!-- <test> | |
| 31 <param name="input1" value="2.fasta"/> | |
| 32 <param name="score" value="17"/> | |
| 33 <param name="out_format2" value="gff"/> | |
| 34 <output name="out_file1" file="emboss_cpgreport_out1.gff"/> | |
| 35 </test> --> | |
| 36 </tests> | |
| 37 <code file="emboss_format_corrector.py" /> | |
| 38 <help> | |
| 39 .. class:: warningmark | |
| 40 | |
| 41 The input dataset needs to be sequences. | |
| 42 | |
| 43 ----- | |
| 44 | |
| 45 You can view the original documentation here_. | |
| 46 | |
| 47 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/cpgreport.html | |
| 48 </help> | |
| 49 </tool> |