Mercurial > repos > timpalpant > java_genomics_toolkit

annotate galaxy-conf/DNAPropertyCalculator.xml @ 25:b43c420a6135 draft default tip

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Incorporate fix: https://github.com/timpalpant/java-genomics-toolkit/commit/9a6c61b7c6b8d85a1cd3f595eed657a537b85dc9
author timpalpant
date Sat, 09 Feb 2019 14:02:24 -0500
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20
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1 <tool id="DNAPropertyCalculator" name="Calculate sequence-specific DNA properties" version="2.0.0">
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2 <description>for a genome</description>
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3 <command interpreter="bash">galaxyToolRunner.sh dna.DNAPropertyCalculator -i
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4 #if $refGenomeSource.genomeSource == "history":
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5 $refGenomeSource.ownFile
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6 #else
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7 ${refGenomeSource.index.fields.path}
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8 #end if
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9 $N -p $property -o $output
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10 </command>
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11 <inputs>
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12 <conditional name="refGenomeSource">
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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">
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14 <option value="indexed">Use a built-in index</option>
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15 <option value="history">Use one from the history</option>
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16 </param>
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17 <when value="indexed">
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18 <param name="index" type="select" label="Select a reference genome" help="if your genome of interest is not listed - contact Galaxy team">
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19 <options from_data_table="sam_fa_indexes">
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20 <filter type="sort_by" column="1" />
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21 <validator type="no_options" message="No indexes are available" />
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22 </options>
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23 </param>
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24 </when>
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25 <when value="history">
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26 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" />
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27 </when> <!-- history -->
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28 </conditional> <!-- refGenomeSource -->
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29
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30 <param name="property" type="select" label="Property to calculate">
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31 <option value="ATG-density">ATG</option>
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32 <option value="G-content">G</option>
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33 <option value="C-content">C</option>
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34 <option value="T-content">T</option>
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35 <option value="A-content">A</option>
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36 <option value="GC-content">GC</option>
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37 <option value="AT-content">AT</option>
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38 <option value="Pyrimidine-content">Pyrimidine</option>
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39 <option value="Purine-content">Purine</option>
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40 <option value="Bendability">Bendability</option>
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41 <option value="zDNA">zDNA</option>
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42 <option value="DuplexStabilityFreeEnergy">Duplex Stability Free Energy</option>
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43 <option value="DuplexStabilityDisruptEnergy">Duplex Stability Disrupt Energy</option>
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44 <option value="DNADenaturation">DNA Denaturation</option>
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45 <option value="PropellorTwist">Propellor Twist</option>
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46 <option value="BaseStacking">Base Stacking</option>
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47 <option value="ProteinDeformation">Protein Deformation</option>
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48 <option value="BendingStiffness">Bending Stiffness</option>
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49 <option value="ProteinDNATwist">Protein DNA Twist</option>
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50 <option value="bDNATwist">bDNA Twist</option>
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51 <option value="APhilicity">APhilicity</option>
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52 <option value="NucleosomePosition">Nucleosome Position (trinucleotide model)</option>
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53 <option value="Twist">Twist</option>
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54 <option value="Tilt">Tilt</option>
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55 <option value="Roll">Roll</option>
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56 <option value="Slide">Slide</option>
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57 <option value="Rise">Rise</option>
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58 </param>
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59
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60 <param name="N" type="boolean" checked="true" truevalue="-n" falsevalue="" label="Output normalized values" />
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61 </inputs>
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62 <outputs>
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63 <data format="wig" name="output" label="Calculate ${property.value_label}">
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64 <actions>
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65 <conditional name="refGenomeSource.genomeSource">
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66 <when value="indexed">
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67 <action type="metadata" name="dbkey">
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68 <option type="from_data_table" name="sam_fa_indexes" column="1" offset="0">
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69 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
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70 <filter type="param_value" ref="refGenomeSource.index" column="0"/>
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71 </option>
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72 </action>
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73 </when>
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74 <when value="history">
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75 <action type="metadata" name="dbkey">
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76 <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
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77 </action>
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78 </when>
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79 </conditional>
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80 </actions>
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81 </data>
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82 </outputs>
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83
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84 <tests>
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85 <test>
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86 <param name="genomeSource" value="history"/>
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87 <param name="ownFile" value="test.fasta"/>
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88 <param name="property" value="Twist"/>
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89 <param name="N" value="false"/>
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90 <output name="output" file="twist.wig"/>
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91 </test>
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92 <test>
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93 <param name="genomeSource" value="history"/>
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94 <param name="ownFile" value="test.fasta"/>
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95 <param name="property" value="Twist"/>
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96 <param name="N" value="true"/>
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97 <output name="output" file="twist.normalized.wig"/>
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98 </test>
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99 </tests>
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100
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101 <help>
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102
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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_.
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104
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105 .. _AJT: http://www.abeel.be/ajt
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106
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107 -----
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108
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109 **Example**
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110
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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.
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112
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113 </help>
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114 </tool>