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comparison emboss_supermatcher.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: supermatcher95" name="supermatcher" version="5.0.0"> 1 <tool id="EMBOSS: supermatcher95" name="supermatcher" version="5.0.0.1">
2 <!-- puts file information in output report --> 2 <!-- puts file information in output report -->
3 <description>Match large sequences against one or more other sequences</description> 3 <description>Match large sequences against one or more other sequences</description>
4 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> 4 <macros>
5 <command>supermatcher -asequence $input1 -bsequence $input2 -gapopen "$gapopen" -gapextend "$gapextend" -width "$width" -wordlen "$wordlen" -outfile $ofile1 -errorfile $ofile2 -aformat3 5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements" />
8 <code file="emboss_format_corrector.py" />
9 <command>supermatcher -asequence '$input1' -bsequence '$input2' -gapopen $gapopen -gapextend $gapextend -width $width -wordlen $wordlen -outfile '$ofile1' -errorfile '$ofile2' -aformat3
6 $out_format1 -auto</command> 10 $out_format1 -auto</command>
7 <inputs> 11 <inputs>
8 <param format="fasta" name="input1" type="data"> 12 <param name="input1" type="data" format="fasta" label="Large sequences" />
9 <label>Large sequences</label> 13 <param name="input2" type="data" format="data" label="Sequences to match" />
10 </param> 14 <param name="gapopen" type="float" value="10.0" label="Gap opening penalty" />
11 <param format="data" name="input2" type="data"> 15 <param name="gapextend" type="float" value="0.5" label="Gap extension penalty" />
12 <label>Sequences to match</label> 16 <param name="width" type="integer" value="16" label="Alignment width" />
13 </param> 17 <param name="wordlen" type="integer" value="6" label="Word length for initial matching" />
14 <param name="gapopen" type="text" value="10.0"> 18 <param name="out_format1" type="select" label="Output alignment file format">
15 <label>Gap opening penalty</label>
16 </param>
17 <param name="gapextend" type="text" value="0.5">
18 <label>Gap extension penalty</label>
19 </param>
20 <param name="width" type="text" value="16">
21 <label>Alignment width</label>
22 </param>
23 <param name="wordlen" type="text" value="6">
24 <label>Word length for initial matching</label>
25 </param>
26 <param name="out_format1" type="select">
27 <label>Output Alignment File Format</label>
28 <option value="simple">Simple (m)</option> 19 <option value="simple">Simple (m)</option>
29 <option value="fasta">FASTA (m)</option> 20 <option value="fasta">FASTA (m)</option>
30 <option value="msf">MSF (m)</option> 21 <option value="msf">MSF (m)</option>
31 <option value="srs">SRS (m)</option> 22 <option value="srs">SRS (m)</option>
32 <option value="pair">Pair (p)</option> 23 <option value="pair">Pair (p)</option>
38 <option value="srspair">SRS pair (p)</option> 29 <option value="srspair">SRS pair (p)</option>
39 <option value="score">Score (p)</option> 30 <option value="score">Score (p)</option>
40 </param> 31 </param>
41 </inputs> 32 </inputs>
42 <outputs> 33 <outputs>
43 <data format="simple" name="ofile1" /> 34 <data name="ofile1" format="simple" />
44 <data format="supermatcher" name="ofile2" /> 35 <data name="ofile2" format="supermatcher" />
45 </outputs> 36 </outputs>
46 <!-- <tests> 37 <!-- <tests>
47 <test> 38 <test>
48 <param name="input1" value="2.fasta"/> 39 <param name="input1" value="2.fasta"/>
49 <param name="input2" value="1.fasta"/> 40 <param name="input2" value="1.fasta"/>
53 <param name="wordlen" value="6"/> 44 <param name="wordlen" value="6"/>
54 <param name="out_format1" value="fasta"/> 45 <param name="out_format1" value="fasta"/>
55 <output name="ofile1" file="emboss_supermatcher_out.fasta"/> 46 <output name="ofile1" file="emboss_supermatcher_out.fasta"/>
56 </test> 47 </test>
57 </tests> --> 48 </tests> -->
58 <code file="emboss_format_corrector.py" />
59 <help> 49 <help>
60 You can view the original documentation here_. 50 You can view the original documentation here_.
61
62 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/supermatcher.html
63 51
64 ------ 52 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/supermatcher.html
65
66 **Citation**
67
68 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;`_
69
70 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;`_
71 </help> 53 </help>
54 <expand macro="citations" />
72 </tool> 55 </tool>