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annotate emboss_cpgreport.xml @ 10:9b98d3d903c6 draft

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author devteam
date Fri, 12 Aug 2016 19:17:10 -0400
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10
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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><![CDATA[
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5 cpgreport
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6 -sequence '$input1'
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7 -outfile '$out_file1'
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8 -outfeat '$out_file2'
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9 -offormat3 '$out_format2'
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10 -score '$score'
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11 -auto
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12 ]]>
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13 </command>
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14 <inputs>
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15 <param format="fasta" name="input1" type="data">
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16 <label>On query</label>
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17 </param>
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18 <param name="score" type="text" value="17">
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19 <label>Score for each CG sequence found (1-200)</label>
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20 </param>
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21 <param name="out_format2" type="select" label="Output Feature File Format">
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22 <option value="gff">GFF</option>
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23 <option value="embl">EMBL</option>
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24 <option value="swiss">SwissProt</option>
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25 </param>
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26 </inputs>
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27 <outputs>
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28 <data format="cpgreport" name="out_file1" />
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29 <data format="gff" name="out_file2" />
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30 </outputs>
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31 <tests>
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32 <test>
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33 <param name="input1" value="2.fasta"/>
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34 <param name="score" value="17"/>
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35 <param name="out_format2" value="embl"/>
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36 <output name="out_file1" file="emboss_cpgreport_out2.cpgreport"/>
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37 </test>
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38 <!-- <test>
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39 <param name="input1" value="2.fasta"/>
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40 <param name="score" value="17"/>
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41 <param name="out_format2" value="gff"/>
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42 <output name="out_file1" file="emboss_cpgreport_out1.gff"/>
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43 </test> -->
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44 </tests>
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45 <code file="emboss_format_corrector.py" />
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46 <help>
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47 .. class:: warningmark
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48
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49 The input dataset needs to be sequences.
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50
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51 -----
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52
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53 You can view the original documentation here_.
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54
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55 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/cpgreport.html
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56
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57 ------
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58
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59 **Citation**
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60
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61 For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
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62
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63 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
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64 </help>
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65 </tool>