Mercurial > repos > cropgeeks > flapjack
changeset 1:87dae67fb9a3 draft
Uploaded
| author | cropgeeks |
|---|---|
| date | Fri, 17 Feb 2017 09:16:30 -0500 |
| parents | 7748147a552f |
| children | 62161f30a69a |
| files | cropgeeks_flapjack/flapjack.xml cropgeeks_flapjack/lib/brapi-client.jar cropgeeks_flapjack/lib/castor-core-1.4.1.jar cropgeeks_flapjack/lib/castor-xml-1.4.1.jar cropgeeks_flapjack/lib/com.fasterxml.jackson.annotations.jar cropgeeks_flapjack/lib/com.fasterxml.jackson.core.jar cropgeeks_flapjack/lib/com.fasterxml.jackson.databind.jar cropgeeks_flapjack/lib/commons-lang3-3.4.jar cropgeeks_flapjack/lib/commons-logging-1.1.1.jar cropgeeks_flapjack/lib/converter-jackson-2.1.0.jar cropgeeks_flapjack/lib/flapjack.jar cropgeeks_flapjack/lib/jcommon-1.0.23.jar cropgeeks_flapjack/lib/jfreechart-1.0.19.jar cropgeeks_flapjack/lib/okhttp-3.4.2.jar cropgeeks_flapjack/lib/okio-1.11.0.jar cropgeeks_flapjack/lib/org.apache.commons.fileupload.jar cropgeeks_flapjack/lib/osxadapter.jar cropgeeks_flapjack/lib/retrofit-2.1.0.jar cropgeeks_flapjack/lib/scri-commons.jar cropgeeks_flapjack/lib/sis-jhdf5-batteries_included.jar cropgeeks_flapjack/lib/sqlite-jdbc-3.7.2.jar cropgeeks_flapjack/lib/xerces-serializer-2.11.0.jar cropgeeks_flapjack/lib/xercesImpl-2.11.0.jar cropgeeks_flapjack/lib/xml-apis.jar flapjack/datatypes_conf.xml flapjack/fj2hdf5.xml flapjack/flapjack.py flapjack/lib/brapi-client.jar flapjack/lib/castor-core-1.4.1.jar flapjack/lib/castor-xml-1.4.1.jar flapjack/lib/com.fasterxml.jackson.annotations.jar flapjack/lib/com.fasterxml.jackson.core.jar flapjack/lib/com.fasterxml.jackson.databind.jar flapjack/lib/commons-lang3-3.4.jar flapjack/lib/commons-logging-1.1.1.jar flapjack/lib/converter-jackson-2.1.0.jar flapjack/lib/flapjack.jar flapjack/lib/jcommon-1.0.23.jar flapjack/lib/jfreechart-1.0.19.jar flapjack/lib/okhttp-3.4.2.jar flapjack/lib/okio-1.11.0.jar flapjack/lib/org.apache.commons.fileupload.jar flapjack/lib/osxadapter.jar flapjack/lib/retrofit-2.1.0.jar flapjack/lib/scri-commons.jar flapjack/lib/sis-jhdf5-batteries_included.jar flapjack/lib/sqlite-jdbc-3.7.2.jar flapjack/lib/xerces-serializer-2.11.0.jar flapjack/lib/xercesImpl-2.11.0.jar flapjack/lib/xml-apis.jar flapjack/mabcstats.xml flapjack/pedverf1stats.xml |
| diffstat | 52 files changed, 281 insertions(+), 37 deletions(-) [+] |
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--- a/cropgeeks_flapjack/flapjack.xml Wed Feb 15 06:01:34 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,37 +0,0 @@ -<tool id="jhi_flapjack" name="Flapjack to HDF5" version="0.0.1"> - <description>convert a Flapjack-formatted genotype file into HDF5</description> - <command>java -Xmx$memory -cp $__tool_directory__/lib/flapjack.jar jhi.flapjack.io.cmd.FJTabbedToHdf5Converter -genotypes=$input_genotypes -hdf5=$output_hdf5</command> - <inputs> - <param format="csv,tabular,txt" name="input_genotypes" type="data" label="Source file" - help="====Flapjack-formatted (tab-delimited text) input file of genotype data"/> - <param name="memory" type="select" label="Memory" - help="How much memory to use; larger files may require more memory"> - <option selected="true" value="64m">64MB</option> - <option value="128m">128MB</option> - <option value="256m">256MB</option> - </param> - </inputs> - <outputs> - <data format="h5" name="output_hdf5" /> - </outputs> - - <help><![CDATA[ -.. class:: infomark - -**What it does** - -Flapjack is a multi-platform application providing interactive visualizations of high-throughput genotype data, -allowing for rapid navigation and comparisons between lines, markers and chromosomes. - -This tool converts a Flapjack-formatted file of genotype data into a corresponding HDF5 file. -See Flapjack's documentation_ for more details on the various Flapjack data formats. - -.. _documentation: https://ics.hutton.ac.uk/wiki/index.php/Flapjack_Help_%2D_Projects_and_Data_Formats - - - - ]]></help> - <citations> - <citation type="doi">10.1093/bioinformatics/btq580</citation> - </citations> -</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/flapjack/datatypes_conf.xml Fri Feb 17 09:16:30 2017 -0500 @@ -0,0 +1,14 @@ +<?xml version="1.0"?> +<datatypes> + <datatype_files> + <datatype_file name="flapjack.py"/> + </datatype_files> + <registration> + <datatype extension="fjmap" type="galaxy.datatypes.flapjack:FlapjackMapFormat" mimetype="text/plain" display_in_upload="true"/> + <datatype extension="fjgenotype" type="galaxy.datatypes.flapjack:FlapjackGenotypeFormat" mimetype="text/plain" display_in_upload="true"/> + </registration> + <sniffers> + <sniffer type="galaxy.datatypes.flapjack:FlapjackMapFormat"/> + <sniffer type="galaxy.datatypes.flapjack:FlapjackGenotypeFormat"/> + </sniffers> +</datatypes>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/flapjack/fj2hdf5.xml Fri Feb 17 09:16:30 2017 -0500 @@ -0,0 +1,37 @@ +<tool id="flapjack_fj2hdf5" name="Flapjack to HDF5" version="0.0.1"> + <description>convert a Flapjack-formatted genotype file into HDF5</description> + <command>java -Xmx$memory -cp $__tool_directory__/lib/flapjack.jar jhi.flapjack.io.cmd.FJTabbedToHdf5Converter -genotypes=$input_genotypes -hdf5=$output_hdf5</command> + <inputs> + <param format="csv,tabular,txt" name="input_genotypes" type="data" label="Source file" + help="Flapjack-formatted (tab-delimited text) input file of genotype data"/> + <param name="memory" type="select" label="Memory" + help="How much memory to use; larger files may require more memory"> + <option selected="true" value="64m">64MB</option> + <option value="128m">128MB</option> + <option value="256m">256MB</option> + </param> + </inputs> + <outputs> + <data format="h5" name="output_hdf5" /> + </outputs> + + <help><![CDATA[ +.. class:: infomark + +**What it does** + +Flapjack is a multi-platform application providing interactive visualizations of high-throughput genotype data, +allowing for rapid navigation and comparisons between lines, markers and chromosomes. + +This tool converts a Flapjack-formatted file of genotype data into a corresponding HDF5 file. +See Flapjack's documentation_ for more details on the various Flapjack data formats. + +.. _documentation: https://ics.hutton.ac.uk/wiki/index.php/Flapjack_Help_%2D_Projects_and_Data_Formats + + + + ]]></help> + <citations> + <citation type="doi">10.1093/bioinformatics/btq580</citation> + </citations> +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/flapjack/flapjack.py Fri Feb 17 09:16:30 2017 -0500 @@ -0,0 +1,56 @@ +from galaxy.datatypes.data import Text + +class FlapjackMapFormat(Text): + file_ext = "fjmap" + + def sniff( self, filename ): + h = open(filename) + line = h.readline() + if line.rstrip() != "# fjFile = MAP": + h.close() + return False + return True + +class FlapjackGenotypeFormat(Text): + file_ext = "fjgenotype" + + def sniff( self, filename ): + h = open(filename) + line = h.readline() + if line.rstrip() != "# fjFile = GENOTYPE": + h.close() + return False + return True + +class FlapjackPhenotypeFormat(Text): + file_ext = "jfphenotye" + + def sniff( self, filename ): + h = open(filename) + line = h.readline() + if line.rstrip() != "# fjFile = PHENOTYPE": + h.close() + return False + return True + +class FlapjackQtlFormat(Text): + file_ext = "fjqtl" + + def sniff( self, filename ): + h = open(filename) + line = h.readline() + if line.rstrip() != "# fjFile = QTL": + h.close() + return False + return True + +class FlapjackGraphFormat(Text): + file_ext = "fjgraph" + + def sniff( self, filename ): + h = open(filename) + line = h.readline() + if line.rstrip() != "# fjFile = GRAPH": + h.close() + return False + return True \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/flapjack/mabcstats.xml Fri Feb 17 09:16:30 2017 -0500 @@ -0,0 +1,92 @@ +<tool id="flapjack_mabcstats" name="Flapjack MABCStats" version="0.0.1"> + +<!--System.out.println("Usage: mabcstats <options>\n" + + " where valid options are:\n" + + " -map=<map_file> (required input file)\n" + + " -genotypes=<genotypes_file> (required input file)\n" + + " -qtls=<qtl_file> (required input file)\n" + + " -parent1=<index_of_line> (required parameter, first line is index 1)\n" + + " -parent2=<index_of_line> (required parameter, first line is index 1)\n" + + " -model=weighted|unweighted (required parameter)\n" + + " -coverage=<coverage_value> (optional floating point parameter)\n" + + " -decimalEnglish (optional parameter)\n" + + " -output=<output_file> (required output file)");--> + + <description>Run marker assisted backcrossing analysis on a dataset</description> + <command>java -Xmx$memory -cp $__tool_directory__/lib/flapjack.jar jhi.flapjack.io.cmd.GenerateMabcStats -map=$map -genotypes=$genotypes -qtls=$qtls -parent1=$parent1 -parent2=$parent2 -model=$model -coverage=$coverage $decimalEnglish -output=$output</command> + <inputs> + <param format="fjmap" name="map" type="data" label="Flapjack map file" + help="Flapjack-formatted (tab-delimited text) input file of map data"/> + <param format="fjgenotype" name="genotypes" type="data" label="Flapjack genotype file" + help="Flapjack-formatted (tab-delimited text) input file of genotype data"/> + <param format="bam" name="qtls" type="data" label="Flapjack QTL file" + help="Flapjack-formatted (tab-delimited text) input file of QTL data"/> + <param name="parent1" type="integer" value="1" label="Index of recurrent parent" + help="The index of the recurrent parent in the genotype file"/> + <param name="parent2" type="integer" value="2" label="Index of donor parent" + help="The index of the donor parent in the genotype file"/> + <param name="model" type="select" label="Model" + help="The model to use for calculating statistics"> + <option selected="true" value="weighted">Weighted</option> + <option value="unweighted">Unweighted</option> + </param> + <param name="coverage" type="integer" value="10" label="Maximum coverage of a marker" + help="The maximum length of genome a marker can represent"/> + <!--<param name="decimalEnglish" type="boolean" truevalue="-decimalEnglish" falsevalue="" checked="True" + label="Use English-style decimal marks" + help="Process input data using '.' as the decimal separator (as opposed to ',')"/> + <param name="memory" type="select" label="Memory" + help="How much memory to use; larger files may require more memory"> + <option selected="true" value="64m">64MB</option> + <option value="128m">128MB</option> + <option value="256m">256MB</option> + </param>--> + + + <conditional name="advanced_options"> + <param name="show_advanced" type="boolean" label="Show advanced options" + truevalue="show" falsevalue=""> + </param> + <when value="show"> + <param name="decimalEnglish" type="boolean" truevalue="-decimalEnglish" falsevalue="" checked="True" + label="Use English-style decimal marks" + help="Process input data using '.' as the decimal separator (as opposed to ',')"/> + <param name="memory" type="select" label="Memory" + help="How much memory to use; larger files may require more memory"> + <option selected="true" value="64m">64MB</option> + <option value="128m">128MB</option> + <option value="256m">256MB</option> + </param> + </when> + </conditional> + + + </inputs> + <outputs> + <data format="tabular" name="output" /> + </outputs> + + <stdio> + <exit_code range="1:" /> + </stdio> + + <help><![CDATA[ +.. class:: infomark + +**What it does** + +Flapjack is a multi-platform application providing interactive visualizations of high-throughput genotype data, +allowing for rapid navigation and comparisons between lines, markers and chromosomes. + +This tool converts a Flapjack-formatted file of genotype data into a corresponding HDF5 file. +See Flapjack's documentation_ for more details on the various Flapjack data formats. + +.. _documentation: https://ics.hutton.ac.uk/wiki/index.php/Flapjack_Help_%2D_Projects_and_Data_Formats + + + + ]]></help> + <citations> + <citation type="doi">10.1093/bioinformatics/btq580</citation> + </citations> +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/flapjack/pedverf1stats.xml Fri Feb 17 09:16:30 2017 -0500 @@ -0,0 +1,82 @@ +<tool id="flapjack_pedverstats" name="Flapjack PedVerStats" version="0.0.1"> + +<!--System.out.println("Usage: pedverf1sstats <options>\n" + + " where valid options are:\n" + + " -map=<map_file> (required input file)\n" + + " -genotypes=<genotypes_file> (required input file)\n" + + " -parent1=<index_of_line> (required parameter, first line is index 1)\n" + + " -parent2=<index_of_line> (required parameter, first line is index 1)\n" + + " -expectedf1=<index_of_line> (optional parameter, first line is index 1)\n" + + " -decimalEnglish (optional parameter)\n" + + " -output=<output_file> (required output file)\n");--> + + <description>Run pedigree verification of F1s (known parents) analysis</description> + <command><![CDATA[ + java -Xmx$memory -cp $__tool_directory__/lib/flapjack.jar jhi.flapjack.io.cmd.GeneratePedVerF1sStats + -map=$map -genotypes=$genotypes -parent1=$parent1 -parent2=$parent2 + #if $simulate_f1.simulate_f1_selector == "file": + -expectedf1=$simulate_f1.expectedF1 + #end if + $decimalEnglish -output=$output + ]]> + </command> + <inputs> + <param format="csv,tabular,txt" name="map" type="data" label="Flapjack map file" + help="Flapjack-formatted (tab-delimited text) input file of map data"/> + <param format="csv,tabular,txt" name="genotypes" type="data" label="Flapjack genotype file" + help="Flapjack-formatted (tab-delimited text) input file of genotype data"/> + <param name="parent1" type="integer" value="1" label="Index of parent 1" + help="The index of the first parent in the genotype file"/> + <param name="parent2" type="integer" value="2" label="Index of parent 2" + help="The index of the second parent in the genotype file"/> + + <conditional name="simulate_f1"> + <param name="simulate_f1_selector" type="select" label="Simulate expected F1 (or use F1 from file)"> + <option value="simulate" selected="True">Simulate</option> + <option value="file">Select from file</option> + </param> + <when value="file"> + <param argument="-expectedF1" type="integer" value="3" label="Index of expected F1" + help="The index of the donor parent in the genotype file"/> + </when> + </conditional> + + <param argument="decimalEnglish" type="boolean" truevalue="-decimalEnglish" falsevalue="" checked="True" + label="Read input data using decimal English" + help="Build the index using a perfect hash rather than a dense hash. This will require less memory + (especially during quantification), but will take longer to construct "/> + <param name="memory" type="select" label="Memory" + help="How much memory to use; larger files may require more memory"> + <option selected="true" value="64m">64MB</option> + <option value="128m">128MB</option> + <option value="256m">256MB</option> + </param> + </inputs> + <outputs> + <data format="tabular" name="output" /> + </outputs> + + <stdio> + <exit_code range="1:" /> + </stdio> + + <help><![CDATA[ +.. class:: infomark + +**What it does** + +Flapjack is a multi-platform application providing interactive visualizations of high-throughput genotype data, +allowing for rapid navigation and comparisons between lines, markers and chromosomes. + +This tool converts a Flapjack-formatted file of genotype data into a corresponding HDF5 file. +See Flapjack's documentation_ for more details on the various Flapjack data formats. + +.. _documentation: https://ics.hutton.ac.uk/wiki/index.php/Flapjack_Help_%2D_Projects_and_Data_Formats + + + + ]]></help> + <citations> + <citation type="doi">10.1093/bioinformatics/btq580</citation> + </citations> +</tool> \ No newline at end of file