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comparison emboss_est2genome.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: est2genome32" name="est2genome" version="5.0.0"> 1 <tool id="EMBOSS: est2genome32" name="est2genome" version="5.0.0.1">
2 <description>Align EST and genomic DNA sequences</description> 2 <description>Align EST and genomic DNA sequences</description>
3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> 3 <macros>
4 <command>est2genome -estsequence $input1 -genomesequence $input2 -outfile $out_file1 -match $match -mismatch $mismatch -gappenalty $gappenalty -intronpenalty $intronpenalty -splicepenalty 4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <command>est2genome -estsequence '$input1' -genomesequence '$input2' -outfile '$out_file1' -match $match -mismatch $mismatch -gappenalty $gappenalty -intronpenalty $intronpenalty -splicepenalty
5 $splicepenalty -minscore $minscore -reverse $reverse -splice $splice -mode $mode -best $best -shuffle $shuffle -seed $seed -align $align -width $width -auto</command> 8 $splicepenalty -minscore $minscore -reverse $reverse -splice $splice -mode $mode -best $best -shuffle $shuffle -seed $seed -align $align -width $width -auto</command>
6 <inputs> 9 <inputs>
7 <param format="fasta" name="input1" type="data"> 10 <param name="input1" type="data" format="fasta" label="EST sequence(s)" />
8 <label>EST sequence(s)</label> 11 <param name="input2" type="data" format="data" label="Genomic sequence" />
9 </param> 12 <param name="match" type="integer" value="1" label="Score for matching two bases" />
10 <param format="data" name="input2" type="data"> 13 <param name="mismatch" type="integer" value="1" label="Cost for mismatching two bases" />
11 <label>Genomic sequence</label> 14 <param name="gappenalty" type="integer" value="2" label="Cost for deleting a single base in either sequence, excluding introns" />
12 </param> 15 <param name="intronpenalty" type="integer" value="40" label="Cost for an intron, independent of length" />
13 <param name="match" type="text" value="1"> 16 <param name="splicepenalty" type="integer" value="20" label="Cost for an intron, independent of length and starting/ending on donor-acceptor sites" />
14 <label>Score for matching two bases</label> 17 <param name="minscore" type="integer" value="30" label="Exclude alignments with scores below this threshold score" />
15 </param> 18 <param name="reverse" type="select" label="Reverse the orientation of the EST sequence">
16 <param name="mismatch" type="text" value="1">
17 <label>Cost for mismatching two bases</label>
18 </param>
19 <param name="gappenalty" type="text" value="2">
20 <label>Cost for deleting a single base in either sequence, excluding introns</label>
21 </param>
22 <param name="intronpenalty" type="text" value="40">
23 <label>Cost for an intron, independent of length</label>
24 </param>
25 <param name="splicepenalty" type="text" value="20">
26 <label>Cost for an intron, independent of length and starting/ending on donor-acceptor sites</label>
27 </param>
28 <param name="minscore" type="text" value="30">
29 <label>Exclude alignments with scores below this threshold score</label>
30 </param>
31 <param name="reverse" type="select">
32 <label>Reverse the orientation of the EST sequence</label>
33 <option value="no">No</option> 19 <option value="no">No</option>
34 <option value="yes">Yes</option> 20 <option value="yes">Yes</option>
35 </param> 21 </param>
36 <param name="splice" type="select"> 22 <param name="splice" type="select" label="Use donor and acceptor splice sites">
37 <label>Use donor and acceptor splice sites</label>
38 <option value="yes">Yes</option> 23 <option value="yes">Yes</option>
39 <option value="no">No</option> 24 <option value="no">No</option>
40 </param> 25 </param>
41 <param name="mode" type="select"> 26 <param name="mode" type="select" label="Comparison mode">
42 <label>Comparison mode</label>
43 <option value="both">Both strands</option> 27 <option value="both">Both strands</option>
44 <option value="forward">Forward strand only</option> 28 <option value="forward">Forward strand only</option>
45 <option value="reverse">Reverse strand only</option> 29 <option value="reverse">Reverse strand only</option>
46 </param> 30 </param>
47 <param name="best" type="select"> 31 <param name="best" type="select" label="Only best comparisons">
48 <label>Only best comparisons</label>
49 <option value="yes">Yes</option> 32 <option value="yes">Yes</option>
50 <option value="no">No</option> 33 <option value="no">No</option>
51 </param> 34 </param>
52 <param name="shuffle" type="text" value="0"> 35 <param name="shuffle" type="integer" value="0" label="Shuffle" />
53 <label>Shuffle</label> 36 <param name="seed" type="integer" value="20825" label="Random number seed" />
54 </param> 37 <param name="align" type="select" label="Show the alignment">
55 <param name="seed" type="text" value="20825">
56 <label>Random number seed</label>
57 </param>
58 <param name="align" type="select">
59 <label>Show the alignment</label>
60 <option value="no">No</option> 38 <option value="no">No</option>
61 <option value="yes">Yes</option> 39 <option value="yes">Yes</option>
62 </param> 40 </param>
63 <param name="width" type="text" value="50"> 41 <param name="width" type="integer" value="50" label="Alignment width" />
64 <label>Alignment width</label>
65 </param>
66 </inputs> 42 </inputs>
67 <outputs> 43 <outputs>
68 <data format="est2genome" name="out_file1" /> 44 <data name="out_file1" format="est2genome" />
69 </outputs> 45 </outputs>
70 <tests> 46 <tests>
71 <test> 47 <test>
72 <param name="input1" value="2.fasta"/> 48 <param name="input1" value="2.fasta"/>
73 <param name="input2" value="1.fasta"/> 49 <param name="input2" value="1.fasta"/>
95 The input dataset needs to be sequences. 71 The input dataset needs to be sequences.
96 72
97 ----- 73 -----
98 74
99 You can view the original documentation here_. 75 You can view the original documentation here_.
100
101 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/est2genome.html
102 76
103 ------ 77 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/est2genome.html
104
105 **Citation**
106
107 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;`_
108
109 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;`_
110 </help> 78 </help>
79 <expand macro="citations" />
111 </tool> 80 </tool>