Mercurial > repos > cropgeeks > flapjack
changeset 54:8855844f40a8 draft
Uploaded the latest version of our Flapjack tools for Galaxy.
| author | cropgeeks |
|---|---|
| date | Tue, 14 Nov 2017 06:42:48 -0500 |
| parents | 1de63acd6b12 |
| children | 6777844fd638 |
| files | creatematrix.xml createproject.xml datatypes_conf.xml fj2hdf5.xml flapjack.py hapmap2fj.xml hdf52fj.xml lib/brapi-client.jar lib/flapjack.jar lib/scri-commons.jar mabcstats.xml pedverf1stats.xml transpose.xml |
| diffstat | 12 files changed, 626 insertions(+), 312 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/creatematrix.xml Tue Nov 14 06:42:48 2017 -0500 @@ -0,0 +1,107 @@ +<tool id="flapjack_creatematrix" name="Flapjack Create Similarity Matrix" version="0.0.1"> + <description>Create a similarity matrix from the given Genotype file</description> + <command><![CDATA[ + java + #if $adv_opts.show_advanced + -Xmx$adv_opts.memory + #end if + -cp $__tool_directory__/lib/flapjack.jar jhi.flapjack.io.cmd.CreateMatrix + -g $genotypes + -o $output + #if $map + -m $map + #end if + #if $adv_opts.show_advanced + $adv_opts.allChromosomes + $adv_opts.collapseHets + -M "$adv_opts.missingData" + -S "$adv_opts.hetSep" + $adv_opts.transposed + $adv_opts.decimalEnglish + #end if + #if $create_project + -p $project + #end if + ]]></command> + <inputs> + <param format="fjmap" name="map" type="data" label="Flapjack map file" + help="Flapjack-formatted (tab-delimited text) input file of map data" + optional="true"/> + <param format="fjgenotype" name="genotypes" type="data" label="Flapjack genotype file" + help="Flapjack-formatted (tab-delimited text) input file of genotype data"/> + + <!-- WARNING: Below is the advanced options section shared by all of our tools. If you alter it here you must update the other tools as well.--> + <conditional name="adv_opts"> + <param name="show_advanced" type="boolean" + label="Enable advanced options" + truevalue="show" falsevalue=""> + </param> + <when value="show"> + <param name="allChromosomes" type="boolean" truevalue="-A" falsevalue="" checked="False" + label="Duplicate all markers onto a single 'All Chromosomes' chromosome" + help="Imports the data so that an additional 'All Chromosomes' chromosome is created, containing every marker in the dataset held together."/> + + <param name="collapseHets" type="boolean" truevalue="-C" falsevalue="" checked="True" + label="Don't distinguish between heterozygous alleles" + help="Ignores phase between heterozygous alleles, treating, for example, A/T the same as T/A."/> + + <param name="missingData" type="text" value="-" + label="Missing data string" + help="Alleles with missing data are encoded using this string. Clear the box to use an empty string for missing data instead."/> + + <param name="hetSep" type="text" value="/" + label="Heterozygous allele separator string" + help="Specifies the string used to separator heterozygous alleles (eg 'A/T'). Clear the box to specify no string is used (eg 'AT')"/> + + <param name="transposed" type="boolean" truevalue="-T" falsevalue="" checked="False" + label="Genotype data has been transposed" + help="Flapjack's default format has markers as columns. Select this to specify markers as rows instead."/> + + <param name="decimalEnglish" type="boolean" truevalue="-D" falsevalue="" checked="False" + label="Force English-style decimal marks" + help="Always process input data using '.' as the decimal separator, irrespective of this Galaxy server's locale settings."/> + + <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> + <!-- WARNING: Above is the advanced options section shared by all of our tools. If you alter it here you must update the other tools as well.--> + + <param name="create_project" type="boolean" label="Also create Flapjack project file" + truevalue="true" falsevalue="false" help="Creates an additional Flapjack project file containing the generated similarity matrix."> + </param> + </inputs> + + <outputs> + <data format="tabular" name="output" /> + <data format="flapjack" name="project"> + <filter>create_project</filter> + </data> + </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. + +Flapjack documentation_ + +.. _documentation: http://flapjack.hutton.ac.uk/en/latest/command_line_support.html#creatematrix-exe-jhi-flapjack-io-creatematrix + ]]></help> + + <citations> + <citation type="doi">10.1093/bioinformatics/btq580</citation> + </citations> +</tool> \ No newline at end of file
--- a/createproject.xml Tue Aug 29 08:15:12 2017 -0400 +++ b/createproject.xml Tue Nov 14 06:42:48 2017 -0500 @@ -1,50 +1,107 @@ <tool id="flapjack_createproject" name="Flapjack CreateProject" version="0.0.1"> + <description>Create a Flapjack project file from the given input files.</description> + <command><![CDATA[ + java + #if $adv_opts.show_advanced + -Xmx$adv_opts.memory + #end if + -cp $__tool_directory__/lib/flapjack.jar jhi.flapjack.io.cmd.CreateProject + -g $genotypes + -p $output + #if $map + -m $map + #end if + #if $name + -n $name + #end if + #if $qtls + -q $qtls + #end if + #if $traits + -t $traits + #end if + #if $adv_opts.show_advanced + $adv_opts.allChromosomes + $adv_opts.collapseHets + -M "$adv_opts.missingData" + -S "$adv_opts.hetSep" + $adv_opts.transposed + $adv_opts.decimalEnglish + #end if + ]]> + </command> + <inputs> + <param format="fjgenotype" name="genotypes" type="data" label="Flapjack genotype file" + help="Flapjack-formatted (tab-delimited text) input file of genotype data"/> -<!--System.out.println("Usage: createproject <options>\n" - + " where valid options are:\n" - + " -map=<map_file> (optional input file)\n" - + " -genotypes=<genotypes_file> (required input file)\n" - + " -traits=<traits_file> (optional input file)\n" - + " -qtls=<qtl_file> (optional input file)\n" - + " -decimalEnglish (optional input parameter)\n" - + " -project=<project_file> (required output file)\n");--> + <param format="fjmap" name="map" type="data" label="Flapjack map file" + help="Flapjack-formatted (tab-delimited text) input file of map data" + optional="true"/> + + <param format="fjphenotype" name="traits" type="data" label="Flapjack phenotype file" + help="Flapjack-formatted (tab-delimited text) input file of phenotype data" + optional="true"/> + + <param format="fjqtl" name="qtls" type="data" label="Flapjack QTL file" + help="Flapjack-formatted (tab-delimited text) input file of QTL data" + optional="true"/> + + <param format="text" name="name" type="text" label="Optional dataset name" + help="The name for the dataset within Flapjack" + optional="true"/> - <description>Run pedigree verification of F1s (known parents) analysis</description> - <command><![CDATA[ - java -Xmx$memory -cp $__tool_directory__/lib/flapjack.jar jhi.flapjack.io.cmd.CreateProject - -map=$map -genotypes=$genotypes -## -galaxyHTML=$html - -project=$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"/> + <!-- WARNING: Below is the advanced options section shared by all of our tools. If you alter it here you must update the other tools as well.--> + <conditional name="adv_opts"> + <param name="show_advanced" type="boolean" + label="Enable advanced options" + truevalue="show" falsevalue=""> + </param> + <when value="show"> + <param name="allChromosomes" type="boolean" truevalue="-A" falsevalue="" checked="False" + label="Duplicate all markers onto a single 'All Chromosomes' chromosome" + help="Imports the data so that an additional 'All Chromosomes' chromosome is created, containing every marker in the dataset held together."/> + + <param name="collapseHets" type="boolean" truevalue="-C" falsevalue="" checked="True" + label="Don't distinguish between heterozygous alleles" + help="Ignores phase between heterozygous alleles, treating, for example, A/T the same as T/A."/> + + <param name="missingData" type="text" value="-" + label="Missing data string" + help="Alleles with missing data are encoded using this string. Clear the box to use an empty string for missing data instead."/> + + <param name="hetSep" type="text" value="/" + label="Heterozygous allele separator string" + help="Specifies the string used to separator heterozygous alleles (eg 'A/T'). Clear the box to specify no string is used (eg 'AT')"/> - <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> - <!-- label="${tool.name} on ${on_string}: project.flapjack" --> - <data name="output" format="flapjack" /> - <!--<data name="html" format="html" />--> - </outputs> + <param name="transposed" type="boolean" truevalue="-T" falsevalue="" checked="False" + label="Genotype data has been transposed" + help="Flapjack's default format has markers as columns. Select this to specify markers as rows instead."/> + + <param name="decimalEnglish" type="boolean" truevalue="-D" falsevalue="" checked="False" + label="Force English-style decimal marks" + help="Always process input data using '.' as the decimal separator, irrespective of this Galaxy server's locale settings."/> + + <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> + <!-- WARNING: Above is the advanced options section shared by all of our tools. If you alter it here you must update the other tools as well.--> + </inputs> + + <outputs> + <data name="output" format="flapjack" /> + </outputs> - <stdio> - <exit_code range="1:" /> - </stdio> + <stdio> + <exit_code range="1:" /> + </stdio> - <help><![CDATA[ + <help><![CDATA[ .. class:: infomark **What it does** @@ -54,13 +111,13 @@ This tool creates a Flapjack project file from the supplied tab-delimitted flapjack input files. 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 - - +More information on the CreateProject tool can be found here_ - ]]></help> - <citations> - <citation type="doi">10.1093/bioinformatics/btq580</citation> - </citations> +.. _documentation: http://flapjack.hutton.ac.uk/en/latest/projects_&_data_formats.html +.. _here: http://flapjack.hutton.ac.uk/en/latest/command_line_support.html#createproject-exe-jhi-flapjack-io-createproject + ]]></help> + + <citations> + <citation type="doi">10.1093/bioinformatics/btq580</citation> + </citations> </tool> \ No newline at end of file
--- a/datatypes_conf.xml Tue Aug 29 08:15:12 2017 -0400 +++ b/datatypes_conf.xml Tue Nov 14 06:42:48 2017 -0500 @@ -4,21 +4,21 @@ <datatype_file name="flapjack.py"/> </datatype_files> <registration> - <datatype extension="flapjack" type="galaxy.datatypes.flapjack:FlapjackFormat" display_in_upload="true"> - <display file="jnlp.xml"/> - </datatype> - <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"/> - <datatype extension="fjphenotype" type="galaxy.datatypes.flapjack:FlapjackPhenotypeFormat" mimetype="text/plain" display_in_upload="true"/> - <datatype extension="fjqtl" type="galaxy.datatypes.flapjack:FlapjackQtlFormat" mimetype="text/plain" display_in_upload="true"/> - <datatype extension="fjgraph" type="galaxy.datatypes.flapjack:FlapjackGraphFormat" mimetype="text/plain" display_in_upload="true"/> + <datatype extension="flapjack" type="galaxy.datatypes.flapjack:FlapjackFormat" display_in_upload="true"> + <display file="jnlp.xml"/> + </datatype> + <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"/> + <datatype extension="fjphenotype" type="galaxy.datatypes.flapjack:FlapjackPhenotypeFormat" mimetype="text/plain" display_in_upload="true"/> + <datatype extension="fjqtl" type="galaxy.datatypes.flapjack:FlapjackQtlFormat" mimetype="text/plain" display_in_upload="true"/> + <datatype extension="fjgraph" type="galaxy.datatypes.flapjack:FlapjackGraphFormat" mimetype="text/plain" display_in_upload="true"/> </registration> <sniffers> - <sniffer type="galaxy.datatypes.flapjack:FlapjackFormat"/> - <sniffer type="galaxy.datatypes.flapjack:FlapjackMapFormat"/> - <sniffer type="galaxy.datatypes.flapjack:FlapjackGenotypeFormat"/> - <sniffer type="galaxy.datatypes.flapjack:FlapjackPhenotypeFormat"/> - <sniffer type="galaxy.datatypes.flapjack:FlapjackQtlFormat"/> - <sniffer type="galaxy.datatypes.flapjack:FlapjackGraphFormat"/> + <sniffer type="galaxy.datatypes.flapjack:FlapjackFormat"/> + <sniffer type="galaxy.datatypes.flapjack:FlapjackMapFormat"/> + <sniffer type="galaxy.datatypes.flapjack:FlapjackGenotypeFormat"/> + <sniffer type="galaxy.datatypes.flapjack:FlapjackPhenotypeFormat"/> + <sniffer type="galaxy.datatypes.flapjack:FlapjackQtlFormat"/> + <sniffer type="galaxy.datatypes.flapjack:FlapjackGraphFormat"/> </sniffers> </datatypes>
--- a/fj2hdf5.xml Tue Aug 29 08:15:12 2017 -0400 +++ b/fj2hdf5.xml Tue Nov 14 06:42:48 2017 -0500 @@ -1,21 +1,44 @@ <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> + <description>Convert a Flapjack-formatted genotype file into HDF5</description> + <command><![CDATA[ + java + #if $adv_opts.show_advanced + -Xmx$adv_opts.memory + #end if + -cp $__tool_directory__/lib/flapjack.jar jhi.flapjack.io.cmd.FJTabbedToHdf5Converter + -g $genotypes + -h $output + ]]></command> + <inputs> + <param format="fjgenotype" name="genotypes" type="data" label="Flapjack genotype file" + help="Flapjack-formatted (tab-delimited text) input file of genotype data"/> - <help><![CDATA[ + <conditional name="adv_opts"> + <param name="show_advanced" type="boolean" + label="Enable advanced options" + truevalue="show" falsevalue=""> + </param> + <when value="show"> + <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="h5" name="output" /> + </outputs> + + <stdio> + <exit_code range="1:" /> + </stdio> + + <help><![CDATA[ .. class:: infomark **What it does** @@ -26,12 +49,10 @@ 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 - - +.. _documentation: http://flapjack.hutton.ac.uk/en/latest/projects_&_data_formats.html + ]]></help> - ]]></help> - <citations> - <citation type="doi">10.1093/bioinformatics/btq580</citation> - </citations> + <citations> + <citation type="doi">10.1093/bioinformatics/btq580</citation> + </citations> </tool> \ No newline at end of file
--- a/hapmap2fj.xml Tue Aug 29 08:15:12 2017 -0400 +++ b/hapmap2fj.xml Tue Nov 14 06:42:48 2017 -0500 @@ -1,42 +1,51 @@ <tool id="flapjack_hapmap2fj" name="HapMap to Flapjack" version="0.0.1"> + <description>Convert a HapMap-formatted file into a Flapjack-formatted genotype file</description> + <command><![CDATA[ + java + #if $adv_opts.show_advanced + -Xmx$adv_opts.memory + #end if + -cp $__tool_directory__/lib/flapjack.jar jhi.flapjack.io.cmd.HapMapToFJTabbedConverter + -h $hapmap + -s $separator + -m $map + -g $genotypes + ]]></command> + <inputs> + <param format="txt" name="hapmap" type="data" label="Source file" + help="HapMap Formatted File"/> -<!--System.out.println("Usage: hapmap2flapjack <options>\n" - + " where valid options are:\n" - + " -separator=<s or t> (required separator used in input file)\n" - + " -hapmap=<hapmap_file> (required input file)\n" - + " -map=<map_file> (required output file)\n" - + " -genotypes=<genotype_file> (required output file)\n");--> + <param name="separator" type="boolean" label="File is tab-separated" + truevalue="t" falsevalue="s"> + </param> - <description>convert an HapMap formatted file into a Flapjack-formatted genotype file</description> - <command>java -Xmx$memory -cp $__tool_directory__/lib/flapjack.jar jhi.flapjack.io.cmd.HapMapToFJTabbedConverter - -hapmap=$hapmap - -separator=$separator - -map=$map - -genotypes=$genotypes - </command> - <inputs> - <param format="txt" name="hapmap" type="data" label="Source file" - help="HapMap Formatted File"/> - <param name="separator" type="boolean" label="File is tab-separated" - truevalue="t" falsevalue="s"> - </param> - <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="fjmap" name="map" /> - <data format="fjgenotype" name="genotypes" /> - </outputs> - - <stdio> - <exit_code range="1:" /> - </stdio> + <conditional name="adv_opts"> + <param name="show_advanced" type="boolean" + label="Enable advanced options" + truevalue="show" falsevalue=""> + </param> + <when value="show"> + <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> - <help><![CDATA[ + <outputs> + <data format="fjmap" name="map" /> + <data format="fjgenotype" name="genotypes" /> + </outputs> + + <stdio> + <exit_code range="1:" /> + </stdio> + + <help><![CDATA[ .. class:: infomark **What it does** @@ -47,12 +56,10 @@ 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 - - +.. _documentation: https://ics.hutton.ac.uk/wiki/index.php/Flapjack_Help_%2D_Projects_and_Data_Formats + ]]></help> - ]]></help> - <citations> - <citation type="doi">10.1093/bioinformatics/btq580</citation> - </citations> + <citations> + <citation type="doi">10.1093/bioinformatics/btq580</citation> + </citations> </tool> \ No newline at end of file
--- a/hdf52fj.xml Tue Aug 29 08:15:12 2017 -0400 +++ b/hdf52fj.xml Tue Nov 14 06:42:48 2017 -0500 @@ -1,39 +1,56 @@ <tool id="flapjack_hdf52fj" name="HDF5 to Flapjack" version="0.0.1"> + <description>Convert an HDF5 formatted genotype file into a Flapjack-formatted genotype file</description> + <command><![CDATA[ + java + #if $adv_opts.show_advanced + -Xmx$adv_opts.memory + #end if + -cp $__tool_directory__/lib/flapjack.jar jhi.flapjack.io.cmd.Hdf5ToFJTabbedConverter + -h $hdf5 + -o $genotypes + #if $lines + -l $lines + #end if + #if $markers + -m $markers + #end if + ]]></command> + <inputs> + <param format="h5" name="hdf5" type="data" label="A Flapjack HDF5 genotype file" + help="Flapjack's flavour of HDF5 for storing genotype data."/> + <param format="txt" name="lines" type="data" label="Line file" + help="A list of lines desired in the output. One line name per line on each line of the file." + optional="true"/> + <param format="txt" name="markers" type="data" label="Marker file" + help="A list of markers desired in the output. One line name per marker on each line of the file." + optional="true"/> - <description>convert an HDF5 formatted genotype file into a Flapjack-formatted genotype file</description> - <command>java -Xmx$memory -cp $__tool_directory__/lib/flapjack.jar jhi.flapjack.io.cmd.Hdf5ToFJTabbedConverter - -hdf5=$hdf5 - -lines=$lines - -markers=$markers - -missing_filter=$missing_filter - -heterozygous_filter=$heterozygous_filter - -genotypes=$genotypes - </command> - <inputs> - <param format="h5" name="hdf5" type="data" label="Source file" - help="Flapjack's flavour of HDF5 for storing genotype data."/> - <param format="txt" name="lines" type="data" label="Source file" - help="A list of lines desired in the output. One line name per line on each line of the file."/> - <param format="txt" name="markers" type="data" label="Source file" - help="A list of markers desired in the output. One line name per marker on each line of the file."/> - <param name="missing_filter" type="boolean" label="Filter out missing markers" - truevalue="true" falsevalue="false"> - </param> - <param name="heterozygous_filter" type="boolean" label="Filter out heterozygous markers" - truevalue="true" falsevalue="false"> - </param> - <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="fjgenotype" name="genotypes" /> - </outputs> + <conditional name="adv_opts"> + <param name="show_advanced" type="boolean" + label="Enable advanced options" + truevalue="show" falsevalue=""> + </param> + <when value="show"> + <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> - <help><![CDATA[ + <outputs> + <data format="fjgenotype" name="genotypes" /> + </outputs> + + <stdio> + <exit_code range="1:" /> + </stdio> + + <help><![CDATA[ .. class:: infomark **What it does** @@ -44,12 +61,10 @@ 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 - - +.. _documentation: http://flapjack.hutton.ac.uk/en/latest/projects_&_data_formats.html + ]]></help> - ]]></help> - <citations> - <citation type="doi">10.1093/bioinformatics/btq580</citation> - </citations> + <citations> + <citation type="doi">10.1093/bioinformatics/btq580</citation> + </citations> </tool> \ No newline at end of file
--- a/mabcstats.xml Tue Aug 29 08:15:12 2017 -0400 +++ b/mabcstats.xml Tue Nov 14 06:42:48 2017 -0500 @@ -1,82 +1,120 @@ <tool id="flapjack_mabcstats" name="Flapjack MABCStats" version="0.0.1"> - - <description>Run marker assisted backcrossing analysis on a dataset</description> + <description>Run marker assisted backcrossing (MABC) analysis on a dataset</description> + <command><![CDATA[ + java + #if $adv_opts.show_advanced + -Xmx$adv_opts.memory + #end if + -cp $__tool_directory__/lib/flapjack.jar jhi.flapjack.io.cmd.GenerateMabcStats + -m $map + -g $genotypes + -q $qtls + -r $parent1 + -d $parent2 + -model $model + -c $coverage + -o $output + #if $adv_opts.show_advanced + $adv_opts.allChromosomes + $adv_opts.collapseHets + -M "$adv_opts.missingData" + -S "$adv_opts.hetSep" + $adv_opts.transposed + $adv_opts.decimalEnglish + #end if + #if $create_project + -p $project + #end if + ]]></command> - <command><![CDATA[ - java - #if $advanced_options.show_advanced - -Xmx$advanced_options.memory - #end if - -cp $__tool_directory__/lib/flapjack.jar jhi.flapjack.io.cmd.GenerateMabcStats - -m $map - -g $genotypes - -q $qtls - -r $parent1 - -d $parent2 - -model $model - -c $coverage - #if $advanced_options.show_advanced - $advanced_options.decimalEnglish - #end if - -o $output - #if $create_project - -p $project - #end if - ]]></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="fjqtl" 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> - <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="fjqtl" 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="float" value="10" label="Maximum coverage of a marker" - help="The maximum length of genome a marker can represent"/> - <conditional name="advanced_options"> - <param name="show_advanced" type="boolean" label="Enable advanced options" - truevalue="show" falsevalue=""> + <param name="coverage" type="float" value="10" label="Maximum coverage of a marker" + help="The maximum length of genome a marker can represent."/> + + <conditional name="adv_opts"> + <param name="show_advanced" type="boolean" + label="Enable advanced options" + truevalue="show" falsevalue=""> + </param> + <when value="show"> + <param name="allChromosomes" type="boolean" truevalue="-A" falsevalue="" checked="False" + label="Duplicate all markers onto a single 'All Chromosomes' chromosome" + help="Imports the data so that an additional 'All Chromosomes' chromosome is created, containing every marker in the dataset held together."/> + + <param name="collapseHets" type="boolean" truevalue="-C" falsevalue="" checked="True" + label="Don't distinguish between heterozygous alleles" + help="Ignores phase between heterozygous alleles, treating, for example, A/T the same as T/A."/> + + <param name="missingData" type="text" value="-" + label="Missing data string" + help="Alleles with missing data are encoded using this string. Clear the box to use an empty string for missing data instead."/> + + <param name="hetSep" type="text" value="/" + label="Heterozygous allele separator string" + help="Specifies the string used to separator heterozygous alleles (eg 'A/T'). Clear the box to specify no string is used (eg 'AT')"/> + + <param name="transposed" type="boolean" truevalue="-T" falsevalue="" checked="False" + label="Genotype data has been transposed" + help="Flapjack's default format has markers as columns. Select this to specify markers as rows instead."/> + + <param name="decimalEnglish" type="boolean" truevalue="-D" falsevalue="" checked="False" + label="Force English-style decimal marks" + help="Always process input data using '.' as the decimal separator, irrespective of this Galaxy server's locale settings."/> + + <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> + + <param name="create_project" type="boolean" label="Also create Flapjack project file" + truevalue="true" falsevalue="false" help="Creates an additional Flapjack project file containing the MABC results."> </param> - <when value="show"> - <param name="decimalEnglish" type="boolean" truevalue="-D" falsevalue="" checked="True" - label="Force English-style decimal marks" - help="Always process input data using '.' as the decimal separator, irrespective of this Galaxy's locale settings"/> - <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> - - <param name="create_project" type="boolean" label="Also create Flapjack project file" - truevalue="true" falsevalue="false" help="Creates an additional Flapjack project file containing the MABC results."> - </param> - </inputs> + </inputs> - <outputs> - <data format="tabular" name="output" /> - <data format="flapjack" name="project"> - <filter>create_project</filter> - </data> - - </outputs> + <outputs> + <data format="tabular" name="output" /> + <data format="flapjack" name="project"> + <filter>create_project</filter> + </data> + </outputs> - <stdio> - <exit_code range="1:" /> - </stdio> + <stdio> + <exit_code range="1:" /> + </stdio> - <help><![CDATA[ + <help><![CDATA[ .. class:: infomark **What it does** @@ -84,13 +122,12 @@ 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. +Flapjack documentation_ -.. _documentation: https://ics.hutton.ac.uk/wiki/index.php/Flapjack_Help_%2D_Projects_and_Data_Formats +.. _documentation: http://flapjack.hutton.ac.uk/en/latest/command_line_support.html#mabcstats-exe-jhi-flapjack-io-generatemabcstats + ]]></help> - ]]></help> - <citations> - <citation type="doi">10.1093/bioinformatics/btq580</citation> - </citations> + <citations> + <citation type="doi">10.1093/bioinformatics/btq580</citation> + </citations> </tool> \ No newline at end of file
--- a/pedverf1stats.xml Tue Aug 29 08:15:12 2017 -0400 +++ b/pedverf1stats.xml Tue Nov 14 06:42:48 2017 -0500 @@ -1,66 +1,112 @@ <tool id="flapjack_pedverstats" name="Flapjack PedVerStats" version="0.0.1"> + <description>Run pedigree verification of F1s (known parents) analysis</description> + <command><![CDATA[ + java + #if $adv_opts.show_advanced + -Xmx$adv_opts.memory + #end if + -cp $__tool_directory__/lib/flapjack.jar jhi.flapjack.io.cmd.GeneratePedVerF1sStats + -m $map + -g $genotypes + -f $parent1 + -s $parent2 + -o $output + #if $simulate_f1.simulate_f1_selector == False + -e $simulate_f1.expectedF1 + #end if + #if $adv_opts.show_advanced + $adv_opts.allChromosomes + $adv_opts.collapseHets + -M "$adv_opts.missingData" + -S "$adv_opts.hetSep" + $adv_opts.transposed + $adv_opts.decimalEnglish + #end if + #if $create_project + -p $project + #end if + ]]></command> + <inputs> + <param format="fjmap" name="map" type="data" label="Flapjack map file" + help="Flapjack-formatted (tab-delimited text) input file of map data"/> -<!--System.out.println("Usage: pedverf1sstats <options>\n" - + " where valid options are:\n" - + " -map=<map_file> (required input file)\n" - + " -genotypes=<genotypes_file> (required input file)\n" - + " -parent1=<index_of_line> (required parameter, first line is index 1)\n" - + " -parent2=<index_of_line> (required parameter, first line is index 1)\n" - + " -expectedf1=<index_of_line> (optional parameter, first line is index 1)\n" - + " -decimalEnglish (optional parameter)\n" - + " -output=<output_file> (required output file)\n");--> + <param format="fjgenotype" name="genotypes" type="data" label="Flapjack genotype file" + help="Flapjack-formatted (tab-delimited text) input file of genotype data"/> + + <param name="parent1" type="integer" value="1" label="Index of parent 1" + help="The index of the first parent in the genotype file"/> + + <param name="parent2" type="integer" value="2" label="Index of parent 2" + help="The index of the second parent in the genotype file"/> + + <conditional name="simulate_f1"> + <param name="simulate_f1_selector" type="boolean" label="Simulate expected F1 (or use F1 from file)" + truevalue="" falsevalue="show" checked="true"> + </param> + <when value="show"> + <param argument="-expectedF1" type="integer" value="3" label="Index of expected F1" + help="The index of the donor parent in the genotype file"/> + </when> + </conditional> - <description>Run pedigree verification of F1s (known parents) analysis</description> - <command><![CDATA[ - java -Xmx$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="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 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> + <!-- WARNING: Below is the advanced options section shared by all of our tools. If you alter it here you must update the other tools as well.--> + <conditional name="adv_opts"> + <param name="show_advanced" type="boolean" + label="Enable advanced options" + truevalue="show" falsevalue=""> + </param> + <when value="show"> + <param name="allChromosomes" type="boolean" truevalue="-A" falsevalue="" checked="False" + label="Duplicate all markers onto a single 'All Chromosomes' chromosome" + help="Imports the data so that an additional 'All Chromosomes' chromosome is created, containing every marker in the dataset held together."/> + + <param name="collapseHets" type="boolean" truevalue="-C" falsevalue="" checked="True" + label="Don't distinguish between heterozygous alleles" + help="Ignores phase between heterozygous alleles, treating, for example, A/T the same as T/A."/> + + <param name="missingData" type="text" value="-" + label="Missing data string" + help="Alleles with missing data are encoded using this string. Clear the box to use an empty string for missing data instead."/> + + <param name="hetSep" type="text" value="/" + label="Heterozygous allele separator string" + help="Specifies the string used to separator heterozygous alleles (eg 'A/T'). Clear the box to specify no string is used (eg 'AT')"/> + + <param name="transposed" type="boolean" truevalue="-T" falsevalue="" checked="False" + label="Genotype data has been transposed" + help="Flapjack's default format has markers as columns. Select this to specify markers as rows instead."/> + + <param name="decimalEnglish" type="boolean" truevalue="-D" falsevalue="" checked="False" + label="Force English-style decimal marks" + help="Always process input data using '.' as the decimal separator, irrespective of this Galaxy server's locale settings."/> + + <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> + <!-- WARNING: Above is the advanced options section shared by all of our tools. If you alter it here you must update the other tools as well.--> + <param name="create_project" type="boolean" label="Also create Flapjack project file" + truevalue="true" falsevalue="false" help="Creates an additional Flapjack project file containing the pedigree verification of F1s (known parents) results."> </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> + </inputs> - <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> + <outputs> + <data format="tabular" name="output" /> + <data format="flapjack" name="project"> + <filter>create_project</filter> + </data> + </outputs> - <stdio> - <exit_code range="1:" /> - </stdio> + <stdio> + <exit_code range="1:" /> + </stdio> - <help><![CDATA[ + <help><![CDATA[ .. class:: infomark **What it does** @@ -68,15 +114,12 @@ 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. +Flapjack documentation_ -.. _documentation: https://ics.hutton.ac.uk/wiki/index.php/Flapjack_Help_%2D_Projects_and_Data_Formats - +.. _documentation: http://flapjack.hutton.ac.uk/en/latest/command_line_support.html#pedverf1stats-exe-jhi-flapjack-io-generatepedverf1sstats + ]]></help> - - ]]></help> - <citations> - <citation type="doi">10.1093/bioinformatics/btq580</citation> - </citations> + <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/transpose.xml Tue Nov 14 06:42:48 2017 -0500 @@ -0,0 +1,27 @@ +<tool id="flapjack_transpose" name="Transpose" version="0.0.1"> + <description>Transpose a file's contents</description> + <command><![CDATA[ + java + -cp $__tool_directory__/lib/flapjack.jar jhi.flapjack.io.cmd.Transpose + $input + $output + ]]></command> + <inputs> + <param format="tabular" name="input" type="data" label="Source file"/> + </inputs> + <outputs> + <data format="tabular" name="output" /> + </outputs> + + <stdio> + <exit_code range="1:" /> + </stdio> + + <help><![CDATA[ +.. class:: infomark + +**What it does** +This tool transposes data files. + ]]></help> + +</tool> \ No newline at end of file