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comparison galaxy-conf/DNAPropertyCalculator.xml @ 9:9266d807ca85

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author timpalpant
date Tue, 06 Mar 2012 21:55:46 -0500
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8:5a3f8b0b80f9 9:9266d807ca85
1 <tool id="DNAPropertyCalculator" name="Calculate sequence-specific DNA properties" version="1.0.0">
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 </tool>