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comparison emboss_codcmp.xml @ 11:0e2484b6829b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
author iuc
date Mon, 30 Jan 2017 13:27:40 -0500
parents 9b98d3d903c6
children 27c43fb015f0
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10:9b98d3d903c6 11:0e2484b6829b
1 <tool id="EMBOSS: codcmp12" name="codcmp" version="5.0.0"> 1 <tool id="EMBOSS: codcmp12" name="codcmp" version="5.0.0">
2 <description>Codon usage table comparison</description> 2 <description>Codon usage table comparison</description>
3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> 3 <macros>
4 <command>codcmp -first $cfile1 -second $cfile2 -outfile $out_file1 -auto</command> 4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <command>codcmp -first $cfile1 -second $cfile2 -outfile '$out_file1' -auto</command>
5 <inputs> 8 <inputs>
6 <param name="cfile1" type="select"> 9 <param name="cfile1" type="select" label="Codon usage file 1">
7 <label>Codon Usage File 1</label>
8 <option value="Ehum.cut">Ehum.cut</option> 10 <option value="Ehum.cut">Ehum.cut</option>
9 <option value="Eacc.cut">Eacc.cut</option> 11 <option value="Eacc.cut">Eacc.cut</option>
10 <option value="Eadenovirus5.cut">Eadenovirus5.cut</option> 12 <option value="Eadenovirus5.cut">Eadenovirus5.cut</option>
11 <option value="Eadenovirus7.cut">Eadenovirus7.cut</option> 13 <option value="Eadenovirus7.cut">Eadenovirus7.cut</option>
12 <option value="Eaidlav.cut">Eaidlav.cut</option> 14 <option value="Eaidlav.cut">Eaidlav.cut</option>
155 <option value="Eyscmt.cut">Eyscmt.cut</option> 157 <option value="Eyscmt.cut">Eyscmt.cut</option>
156 <option value="Eysp.cut">Eysp.cut</option> 158 <option value="Eysp.cut">Eysp.cut</option>
157 <option value="Ezebrafish.cut">Ezebrafish.cut</option> 159 <option value="Ezebrafish.cut">Ezebrafish.cut</option>
158 <option value="Ezma.cut">Ezma.cut</option> 160 <option value="Ezma.cut">Ezma.cut</option>
159 </param> 161 </param>
160 <param name="cfile2" type="select"> 162 <param name="cfile2" type="select" label="Codon usage file 2">
161 <label>Codon Usage File 2</label>
162 <option value="Ehum.cut">Ehum.cut</option> 163 <option value="Ehum.cut">Ehum.cut</option>
163 <option value="Eacc.cut">Eacc.cut</option> 164 <option value="Eacc.cut">Eacc.cut</option>
164 <option value="Eadenovirus5.cut">Eadenovirus5.cut</option> 165 <option value="Eadenovirus5.cut">Eadenovirus5.cut</option>
165 <option value="Eadenovirus7.cut">Eadenovirus7.cut</option> 166 <option value="Eadenovirus7.cut">Eadenovirus7.cut</option>
166 <option value="Eaidlav.cut">Eaidlav.cut</option> 167 <option value="Eaidlav.cut">Eaidlav.cut</option>
311 <option value="Ezebrafish.cut">Ezebrafish.cut</option> 312 <option value="Ezebrafish.cut">Ezebrafish.cut</option>
312 <option value="Ezma.cut">Ezma.cut</option> 313 <option value="Ezma.cut">Ezma.cut</option>
313 </param> 314 </param>
314 </inputs> 315 </inputs>
315 <outputs> 316 <outputs>
316 <data format="codcmp" name="out_file1" /> 317 <data name="out_file1" format="codcmp" />
317 </outputs> 318 </outputs>
318 <tests> 319 <tests>
319 <test> 320 <test>
320 <param name="cfile1" value="Ehum.cut"/> 321 <param name="cfile1" value="Ehum.cut"/>
321 <param name="cfile2" value="Eacc.cut"/> 322 <param name="cfile2" value="Eacc.cut"/>
322 <output name="out_file1" file="emboss_codcmp_out.codcmp"/> 323 <output name="out_file1" file="emboss_codcmp_out.codcmp"/>
323 </test> 324 </test>
324 </tests> 325 </tests>
325 <help> 326 <help>
326 You can view the original documentation here_. 327 You can view the original documentation here_.
327
328 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/codcmp.html
329 328
330 ------ 329 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/codcmp.html
331
332 **Citation**
333
334 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;`_
335
336 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;`_
337 </help> 330 </help>
331 <expand macro="citations" />
338 </tool> 332 </tool>