Mercurial > repos > timpalpant > java_genomics_toolkit
comparison galaxy-conf/DNAPropertyCalculator.xml @ 24:a77e126ae856 draft
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author | timpalpant |
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date | Tue, 19 Jun 2012 22:15:09 -0400 |
parents | 9d56b5b85740 |
children | b43c420a6135 |
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23:01d5d20eaadd | 24:a77e126ae856 |
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1 <tool id="DNAPropertyCalculator" name="Calculate sequence-specific DNA properties" version="2.0.0"> | |
2 <description>for a genome</description> | |
3 <command interpreter="sh">galaxyToolRunner.sh dna.DNAPropertyCalculator -i | |
4 #if $refGenomeSource.genomeSource == "history": | |
5 $refGenomeSource.ownFile | |
6 #else | |
7 ${refGenomeSource.index.fields.path} | |
8 #end if | |
9 $N -p $property -o $output | |
10 </command> | |
11 <inputs> | |
12 <conditional name="refGenomeSource"> | |
13 <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options"> | |
14 <option value="indexed">Use a built-in index</option> | |
15 <option value="history">Use one from the history</option> | |
16 </param> | |
17 <when value="indexed"> | |
18 <param name="index" type="select" label="Select a reference genome" help="if your genome of interest is not listed - contact Galaxy team"> | |
19 <options from_data_table="sam_fa_indexes"> | |
20 <filter type="sort_by" column="1" /> | |
21 <validator type="no_options" message="No indexes are available" /> | |
22 </options> | |
23 </param> | |
24 </when> | |
25 <when value="history"> | |
26 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" /> | |
27 </when> <!-- history --> | |
28 </conditional> <!-- refGenomeSource --> | |
29 | |
30 <param name="property" type="select" label="Property to calculate"> | |
31 <option value="ATG-density">ATG</option> | |
32 <option value="G-content">G</option> | |
33 <option value="C-content">C</option> | |
34 <option value="T-content">T</option> | |
35 <option value="A-content">A</option> | |
36 <option value="GC-content">GC</option> | |
37 <option value="AT-content">AT</option> | |
38 <option value="Pyrimidine-content">Pyrimidine</option> | |
39 <option value="Purine-content">Purine</option> | |
40 <option value="Bendability">Bendability</option> | |
41 <option value="zDNA">zDNA</option> | |
42 <option value="DuplexStabilityFreeEnergy">Duplex Stability Free Energy</option> | |
43 <option value="DuplexStabilityDisruptEnergy">Duplex Stability Disrupt Energy</option> | |
44 <option value="DNADenaturation">DNA Denaturation</option> | |
45 <option value="PropellorTwist">Propellor Twist</option> | |
46 <option value="BaseStacking">Base Stacking</option> | |
47 <option value="ProteinDeformation">Protein Deformation</option> | |
48 <option value="BendingStiffness">Bending Stiffness</option> | |
49 <option value="ProteinDNATwist">Protein DNA Twist</option> | |
50 <option value="bDNATwist">bDNA Twist</option> | |
51 <option value="APhilicity">APhilicity</option> | |
52 <option value="NucleosomePosition">Nucleosome Position (trinucleotide model)</option> | |
53 <option value="Twist">Twist</option> | |
54 <option value="Tilt">Tilt</option> | |
55 <option value="Roll">Roll</option> | |
56 <option value="Slide">Slide</option> | |
57 <option value="Rise">Rise</option> | |
58 </param> | |
59 | |
60 <param name="N" type="boolean" checked="true" truevalue="-n" falsevalue="" label="Output normalized values" /> | |
61 </inputs> | |
62 <outputs> | |
63 <data format="wig" name="output" label="Calculate ${property.value_label}"> | |
64 <actions> | |
65 <conditional name="refGenomeSource.genomeSource"> | |
66 <when value="indexed"> | |
67 <action type="metadata" name="dbkey"> | |
68 <option type="from_data_table" name="sam_fa_indexes" column="1" offset="0"> | |
69 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/> | |
70 <filter type="param_value" ref="refGenomeSource.index" column="0"/> | |
71 </option> | |
72 </action> | |
73 </when> | |
74 <when value="history"> | |
75 <action type="metadata" name="dbkey"> | |
76 <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" /> | |
77 </action> | |
78 </when> | |
79 </conditional> | |
80 </actions> | |
81 </data> | |
82 </outputs> | |
83 | |
84 <tests> | |
85 <test> | |
86 <param name="genomeSource" value="history"/> | |
87 <param name="ownFile" value="test.fasta"/> | |
88 <param name="property" value="Twist"/> | |
89 <param name="N" value="false"/> | |
90 <output name="output" file="twist.wig"/> | |
91 </test> | |
92 <test> | |
93 <param name="genomeSource" value="history"/> | |
94 <param name="ownFile" value="test.fasta"/> | |
95 <param name="property" value="Twist"/> | |
96 <param name="N" value="true"/> | |
97 <output name="output" file="twist.normalized.wig"/> | |
98 </test> | |
99 </tests> | |
100 | |
101 <help> | |
102 | |
103 This tool will create a new Wig file with genome-wide calculations of sequence-specific DNA properties determined from local n-nucleotide sequences. DNA properties are calculated using AJT_. | |
104 | |
105 .. _AJT: http://www.abeel.be/ajt | |
106 | |
107 ----- | |
108 | |
109 **Example** | |
110 | |
111 To calculate GC-content, choose your genome assembly and select "GC" as the property. This will create a new Wig file in which G and C nucleotides are represented by 1, while A and T nucleotides are represented by -1. If you would like to compute GC-content in 10-bp windows, use the WigMath -> Moving average tool to compute a moving average with 10bp windows. | |
112 | |
113 </help> | |
114 </tool> |