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comparison emboss_patmatdb.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: patmatdb67" name="patmatdb" version="5.0.0"> 1 <tool id="EMBOSS: patmatdb67" name="patmatdb" version="5.0.0">
2 <description>Search a protein sequence with a motif</description> 2 <description>Search a protein sequence with a motif</description>
3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> 3 <macros>
4 <command>patmatdb -sequence $input1 -outfile $out_file1 -motif "$motif" -rformat3 $out_format1 -auto</command> 4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <code file="emboss_format_corrector.py" />
8 <command>patmatdb -sequence '$input1' -outfile '$out_file1' -motif '$motif' -rformat3 $out_format1 -auto</command>
5 <inputs> 9 <inputs>
6 <param format="data" name="input1" type="data"> 10 <param name="input1" type="data" format="data" label="Main sequence" />
7 <label>Main sequence</label> 11 <param name="motif" type="text" value="" label="Motif to search for" />
8 </param> 12 <param name="out_format1" type="select" label="Output report file format">
9 <param name="motif" type="text" value="">
10 <label>Motif to search for</label>
11 </param>
12 <param name="out_format1" type="select">
13 <label>Output Report File Format</label>
14 <option value="dbmotif">DbMotif</option> 13 <option value="dbmotif">DbMotif</option>
15 <option value="embl">EMBL</option> 14 <option value="embl">EMBL</option>
16 <option value="genbank">GENBANK</option> 15 <option value="genbank">GENBANK</option>
17 <option value="gff">GFF</option> 16 <option value="gff">GFF</option>
18 <option value="pir">PIR</option> 17 <option value="pir">PIR</option>
28 <option value="table">Table</option> 27 <option value="table">Table</option>
29 <option value="tagseq">TagSeq</option> 28 <option value="tagseq">TagSeq</option>
30 </param> 29 </param>
31 </inputs> 30 </inputs>
32 <outputs> 31 <outputs>
33 <data format="dbmotif" name="out_file1" /> 32 <data name="out_file1" format="dbmotif" />
34 </outputs> 33 </outputs>
35 <tests> 34 <tests>
36 <test> 35 <test>
37 <param name="input1" value="2.fasta"/> 36 <param name="input1" value="2.fasta"/>
38 <param name="motif" value="aa"/> 37 <param name="motif" value="aa"/>
39 <param name="out_format1" value="excel"/> 38 <param name="out_format1" value="excel"/>
40 <output name="out_file1" file="emboss_patmatdb_out.tabular"/> 39 <output name="out_file1" file="emboss_patmatdb_out.tabular"/>
41 </test> 40 </test>
42 </tests> 41 </tests>
43 <code file="emboss_format_corrector.py" />
44 <help> 42 <help>
45 You can view the original documentation here_. 43 You can view the original documentation here_.
46
47 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/patmatdb.html
48 44
49 ------ 45 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/patmatdb.html
50
51 **Citation**
52
53 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;`_
54
55 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;`_
56 </help> 46 </help>
47 <expand macro="citations" />
57 </tool> 48 </tool>