Mercurial > repos > timpalpant > java_genomics_toolkit
annotate galaxy-conf/DNAPropertyCalculator.xml @ 15:3e477c7e0e73 draft
Update normalization tools to allow normalizing by chromosome (Z-scorer, scale, etc.) Add new tool to convert any interval file to Bed format. Miscellaneous bug fixes.
| author | timpalpant |
|---|---|
| date | Sat, 09 Jun 2012 16:03:59 -0400 |
| parents | eb53be9a09f4 |
| children |
| rev | line source |
|---|---|
|
15
3e477c7e0e73
Update normalization tools to allow normalizing by chromosome (Z-scorer, scale, etc.) Add new tool to convert any interval file to Bed format. Miscellaneous bug fixes.
timpalpant
parents:
13
diff
changeset
|
1 <tool id="DNAPropertyCalculator" name="Calculate sequence-specific DNA properties" version="2.0.0"> |
| 9 | 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> | |
|
12
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
9
diff
changeset
|
83 |
| 13 | 84 <tests> |
| 85 <test> | |
| 86 <param name="genomeSource" value="history"/> | |
| 87 <param name="ownFile" value="test.fasta"/> | |
|
15
3e477c7e0e73
Update normalization tools to allow normalizing by chromosome (Z-scorer, scale, etc.) Add new tool to convert any interval file to Bed format. Miscellaneous bug fixes.
timpalpant
parents:
13
diff
changeset
|
88 <param name="property" value="Twist"/> |
| 13 | 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"/> | |
|
15
3e477c7e0e73
Update normalization tools to allow normalizing by chromosome (Z-scorer, scale, etc.) Add new tool to convert any interval file to Bed format. Miscellaneous bug fixes.
timpalpant
parents:
13
diff
changeset
|
95 <param name="property" value="Twist"/> |
| 13 | 96 <param name="N" value="true"/> |
| 97 <output name="output" file="twist.normalized.wig"/> | |
| 98 </test> | |
| 99 </tests> | |
| 100 | |
|
12
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
9
diff
changeset
|
101 <help> |
|
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
9
diff
changeset
|
102 |
|
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
9
diff
changeset
|
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_. |
|
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
9
diff
changeset
|
104 |
|
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
9
diff
changeset
|
105 .. _AJT: http://www.abeel.be/ajt |
|
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
9
diff
changeset
|
106 |
|
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
9
diff
changeset
|
107 ----- |
|
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
9
diff
changeset
|
108 |
|
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
9
diff
changeset
|
109 **Example** |
|
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
9
diff
changeset
|
110 |
|
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
9
diff
changeset
|
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. |
|
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
9
diff
changeset
|
112 |
|
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
9
diff
changeset
|
113 </help> |
| 9 | 114 </tool> |