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comparison emboss_cai.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: cai6" name="cai" version="5.0.0"> 1 <tool id="EMBOSS: cai6" name="cai" version="5.0.0">
2 <description>CAI codon adaptation index</description> 2 <description>CAI codon adaptation index</description>
3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> 3 <macros>
4 <command>cai -seqall '$input1' -outfile '$out_file1' -cfile '$cfile' -auto</command> 4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <command>cai -seqall '$input1' -outfile '$out_file1' -cfile $cfile -auto</command>
5 <inputs> 8 <inputs>
6 <param format="fasta" name="input1" type="data"> 9 <param name="input1" type="data" format="fasta" label="On query" />
7 <label>On query</label> 10 <param name="cfile" type="select" label="Codon usage file">
8 </param>
9 <param name="cfile" type="select">
10 <label>Codon Usage File</label>
11 <option value="Eyeastcai.cut">Eyeastcai.cut</option> 11 <option value="Eyeastcai.cut">Eyeastcai.cut</option>
12 <option value="Ehum.cut">Ehum.cut</option> 12 <option value="Ehum.cut">Ehum.cut</option>
13 <option value="Eacc.cut">Eacc.cut</option> 13 <option value="Eacc.cut">Eacc.cut</option>
14 <option value="Eadenovirus5.cut">Eadenovirus5.cut</option> 14 <option value="Eadenovirus5.cut">Eadenovirus5.cut</option>
15 <option value="Eadenovirus7.cut">Eadenovirus7.cut</option> 15 <option value="Eadenovirus7.cut">Eadenovirus7.cut</option>
160 <option value="Ezebrafish.cut">Ezebrafish.cut</option> 160 <option value="Ezebrafish.cut">Ezebrafish.cut</option>
161 <option value="Ezma.cut">Ezma.cut</option> 161 <option value="Ezma.cut">Ezma.cut</option>
162 </param> 162 </param>
163 </inputs> 163 </inputs>
164 <outputs> 164 <outputs>
165 <data format="cai" name="out_file1" /> 165 <data name="out_file1" format="cai" />
166 </outputs> 166 </outputs>
167 <tests> 167 <tests>
168 <test> 168 <test>
169 <param name="input1" value="2.fasta"/> 169 <param name="input1" value="2.fasta"/>
170 <param name="cfile" value="Eyeastcai.cut"/> 170 <param name="cfile" value="Eyeastcai.cut"/>
177 The input dataset needs to be sequences. 177 The input dataset needs to be sequences.
178 178
179 ----- 179 -----
180 180
181 You can view the original documentation here_. 181 You can view the original documentation here_.
182
183 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/cai.html
184 182
185 ------ 183 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/cai.html
186
187 **Citation**
188
189 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;`_
190
191 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;`_
192 </help> 184 </help>
185 <expand macro="citations" />
193 </tool> 186 </tool>