Mercurial > repos > blankenberglab > gpca

annotate r-gpca.xml @ 4:ceaa4d404115 draft default tip

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planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit 9ad682131963a72c88a5af1cfc99f90ea9d42a08
author blankenberglab
date Mon, 03 Dec 2018 15:07:32 -0500
parents 8def7dda3bee
children
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ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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1 <tool id="gpca" name="gPCA" version="1.0.0">
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2 <description>Batch Effect Detection via Guided Principal Components Analysis</description>
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
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3 <requirements>
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
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4 <requirement type="package" version="1.0">r-gpca</requirement>
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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5 <requirement type="package" version="1.6.0">r-optparse</requirement>
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
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6 </requirements>
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ceaa4d404115 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit 9ad682131963a72c88a5af1cfc99f90ea9d42a08
blankenberglab
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7 <version_command><![CDATA[Rscript '$__tool_directory__/r-gpca.R' --version]]></version_command>
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ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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8 <command detect_errors="exit_code">
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
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9 <![CDATA[
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10
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
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11 Rscript '$__tool_directory__/r-gpca.R'
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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12 -i '${batch}'
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
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13 -d '${data}'
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
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14 -n '${nperm}'
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15 ${center}
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16 ${scaleY}
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17 #if str($filt):
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
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18 -f '${filt}'
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
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19 #end if
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
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20 #if str($seed):
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
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21 -s '${seed}'
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
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22 #end if
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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23 --npcs '${npcs}'
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
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24 -p '${html_outfile.extra_files_path}'
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
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25 -x '${numbers_outfile}'
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
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26 -o '${html_outfile}';
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
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28 ]]></command>
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
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29
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30 <inputs>
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31 <param type="data" name="data" argument="--data" format="tabular" label="Data input file" />
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
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32 <param type="data" name="batch" argument="--batch" format="tabular" label="Batch input file" />
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
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33 <param type="integer" name="nperm" argument="--nperm" value="1000" help="default=1000" label="Number of permutations to preform"/>
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
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34 <param type="boolean" name="center" argument="--center" checked="false" truevalue="--center" falsevalue="" help="Set to true to prevent gPCA from centering" label="Is the data centered?"/>
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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35 <param type="boolean" name="scaleY" argument="--scaleY" checked="false" truevalue="--scaleY" falsevalue="" help="default=No" label="Should Y be scaled based on number of samples in each batch?"/>
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
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36 <param type="integer" name="filt" optional="true" argument="--filt" min="1" value="" label="How many features to keep?" help="Leave blank for default(NULL)"/>
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
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37 <param type="integer" name="seed" optional="true" argument="--seed" min="1" value="" label="Seed #" help="Leave blank for default(NULL)"/>
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38 <param type="integer" name="npcs" optional="false" argument="--npcs" min="3" value="3" label="Principal Components to calculate" help="Number of principal components to calcualte"/>
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39 </inputs>
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40
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41 <outputs>
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42 <data name="html_outfile" format="html" label="${tool.name} on ${on_string} html"/>
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
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43 <data name="numbers_outfile" format="tabular" label="${tool.name} on ${on_string}: values" />
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44 </outputs>
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45
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46 <tests>
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47 <test>
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48 <param name="batch" ftype="tabular" value="batch_in_1.tabular" />
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49 <param name="data" ftype="tabular" value="data_in_1.tabular" />
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50 <param name="nperm" value="1000" />
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51 <param name="center" value="False" />
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52 <param name="scaleY" value="False" />
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53 <param name="filt" value="" />
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54 <param name="npcs" value="3" />
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55 <param name="seed" value="123456" />
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
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56 <output name="html_outfile" ftype="html" file="html_outfile_1/html_outfile_1.html">
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57 <extra_files type="file" name="gDist_1.png" value="html_outfile_1/gDist_1.png" compare="sim_size"/>
d93629e79f5e planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit 3b791d44853d8928046914cd93112bdcf89d4965
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58 <extra_files type="file" name="guided_1v2_1.png" value="html_outfile_1/guided_1v2_1.png" compare="sim_size"/>
3
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59 <extra_files type="file" name="unguided_1v2_1.png" value="html_outfile_1/unguided_1v2_1.png"
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60 compare="sim_size"/>
1
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61 <extra_files type="file" name="guided_npcs_1.png" value="html_outfile_1/guided_npcs_1.png" compare="sim_size"/>
3
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62 <extra_files type="file" name="unguided_npcs_1.png" value="html_outfile_1/unguided_npcs_1.png"
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63 compare="sim_size"/>
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64 <extra_files type="file" name="guided_var_1.png" value="html_outfile_1/guided_var_1.png" compare="sim_size"/>
3
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65 <extra_files type="file" name="unguided_var_1.png" value="html_outfile_1/unguided_var_1.png"
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66 compare="sim_size"/>
0
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67 </output>
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68 <output name="numbers_outfile" ftype="tabular" file="numbers_outfile_1.tabular"/>
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69 </test>
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70 <test>
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71 <param name="batch" ftype="tabular" value="batch_in_multiple_1.tabular" />
d93629e79f5e planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit 3b791d44853d8928046914cd93112bdcf89d4965
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72 <param name="data" ftype="tabular" value="data_in_1.tabular" />
d93629e79f5e planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit 3b791d44853d8928046914cd93112bdcf89d4965
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73 <param name="nperm" value="1000" />
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74 <param name="center" value="False" />
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75 <param name="scaleY" value="False" />
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76 <param name="filt" value="" />
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77 <param name="npcs" value="3" />
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78 <param name="seed" value="123456" />
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79 <output name="html_outfile" ftype="html" file="html_outfile_2/html_outfile_2.html">
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80 <extra_files type="file" name="gDist_1.png" value="html_outfile_2/gDist_1.png" compare="sim_size"/>
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81 <extra_files type="file" name="gDist_2.png" value="html_outfile_2/gDist_2.png" compare="sim_size"/>
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82 <extra_files type="file" name="guided_1v2_1.png" value="html_outfile_2/guided_1v2_1.png" compare="sim_size"/>
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83 <extra_files type="file" name="guided_1v2_2.png" value="html_outfile_2/guided_1v2_2.png" compare="sim_size"/>
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84 <extra_files type="file" name="unguided_1v2_1.png" value="html_outfile_2/unguided_1v2_1.png"
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85 compare="sim_size"/>
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86 <extra_files type="file" name="unguided_1v2_2.png" value="html_outfile_2/unguided_1v2_2.png"
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87 compare="sim_size"/>
1
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88 <extra_files type="file" name="guided_npcs_1.png" value="html_outfile_2/guided_npcs_1.png" compare="sim_size"/>
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89 <extra_files type="file" name="guided_npcs_2.png" value="html_outfile_2/guided_npcs_2.png" compare="sim_size"/>
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90 <extra_files type="file" name="unguided_npcs_1.png" value="html_outfile_2/unguided_npcs_1.png" compare="sim_size"/>
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91 <extra_files type="file" name="unguided_npcs_2.png" value="html_outfile_2/unguided_npcs_2.png" compare="sim_size"/>
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92 <extra_files type="file" name="guided_var_1.png" value="html_outfile_2/guided_var_1.png" compare="sim_size"/>
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93 <extra_files type="file" name="guided_var_2.png" value="html_outfile_2/guided_var_2.png" compare="sim_size"/>
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94 <extra_files type="file" name="unguided_var_1.png" value="html_outfile_2/unguided_var_1.png"
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95 compare="sim_size"/>
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96 <extra_files type="file" name="unguided_var_2.png" value="html_outfile_2/unguided_var_2.png"
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97 compare="sim_size"/>
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98 </output>
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99 <output name="numbers_outfile" ftype="tabular" file="numbers_outfile_2.tabular"/>
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100 </test>
0
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101 </tests>
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102
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103 <help>
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104 <![CDATA[
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105
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106 **What it does**
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107 Utilizes guided principal components analysis for the detection of batch effects in high-throughput data.
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108
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109 Arguments:
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110
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111 batch: a length n vector that indicates batch (group or class) for each observation.
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112
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113 x/data: an nxp matrix of data where n denotes observations and p denotes the numberof features (e.g. probe, gene, SNP, etc.).
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114
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115 filt: (optional) the number of features to retain after applying a variance filter. If NULL, no filter is applied. Filtering can significantly reduce the processing time in the case of very large data sets.
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116
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117 nperm: the number of permutations to perform for the permutation test, default is 1000.
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118
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119 center: (logical) Is your data x centered? If not, then center=FALSE and gPCA.batchdetect will center it for you.
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120
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121 scaleY: (logical) Do you want to scale the Y matrix by the number of samples in each batch? If not, then center=FALSE (default), otherwise, center=TRUE.
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122
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123 seed: the seed number for set.seed(). Default is NULL.
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124
1
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125 npcs: number of principal components to calculate
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126
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127 **Literature**
0
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128 https://cran.r-project.org/web/packages/gPCA/gPCA.pdf
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129
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130 https://cran.r-project.org/web/packages/gPCA/vignettes/gPCA.pdf
1
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131
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132 **Input File Help**
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133 Batch: The batch file must be a tab delimited file. It will be read as a numeric vector, consisting of as many different batches as you like. The test data file batch_in_multiple_1.tabular shows the correct format. The length of batch must conform to the data matrix or an error will occur.
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134
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135 Data: The data file must be a tab delimited file. It will be read in as a matrix. The test data file data_in_1.tabular shows the correct format. If you are receving errors about nonconformed matrices in your matrix you might need to transpose your matrix before using it in the tool.
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136
0
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137 ]]>
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138 </help>
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139
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140 <citations>
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141 <citation type="doi">10.1093/bioinformatics/btt480</citation>
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142 <citation type="bibtex">@unpublished{gpca:2018,
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143 title = "gPCA Galaxy Tool",
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144 author = "Chris Lowe, Daniel Blankenberg",
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145 url = "https://github.com/BlankenbergLab/galaxy-tools-blankenberg/tree/master/tools/r-gpca",
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146 year = "2018 (accessed November 16, 2018)"}
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147 </citation>
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148 </citations>
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
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149 </tool>