Mercurial > repos > eschen42 > w4mclassfilter

annotate w4mclassfilter.xml @ 6:38ccf6722d54 draft

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planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
author eschen42
date Mon, 15 Jan 2018 14:06:39 -0500
parents 2cdf7d5982c8
children 582a8a42a93b
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1 <tool id="w4mclassfilter" name="Sample_Subset" version="0.98.6">
0
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2 <description>Filter W4M data by sample class</description>
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3
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4 <requirements>
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5 <!-- <requirement type="package" version="6.2">readline</requirement> -->
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6 <requirement type="package" version="3.4.1">r-base</requirement>
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7 <requirement type="package" version="1.1_4">r-batch</requirement>
6
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8 <requirement type="package" version="0.98.6">w4mclassfilter</requirement>
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9 </requirements>
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10
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11 <stdio>
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12 <exit_code range="1:" level="fatal" />
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13 </stdio>
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14
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15
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16 <command detect_errors="aggressive"><![CDATA[
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17 Rscript $__tool_directory__/w4mclassfilter_wrapper.R
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18 dataMatrix_in '$dataMatrix_in'
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19 sampleMetadata_in '$sampleMetadata_in'
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20 variableMetadata_in '$variableMetadata_in'
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21 sampleclassNames '$sampleclassNames'
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22 inclusive '$inclusive'
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23 wildcards '$wildcards'
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24 classnameColumn '$classnameColumn'
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25 samplenameColumn '$samplenameColumn'
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26 variable_range_filter '$variableRangeFilter'
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27 dataMatrix_out '$dataMatrix_out'
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28 sampleMetadata_out '$sampleMetadata_out'
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29 variableMetadata_out '$variableMetadata_out'
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30 ]]></command>
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31
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32 <inputs>
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33 <param name="dataMatrix_in" label="Data matrix file" type="data" format="tabular" help="variable x sample, decimal: '.', missing: NA, mode: numerical, separator: tab" />
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34 <param name="sampleMetadata_in" label="Sample metadata file" type="data" format="tabular" help="sample x metadata columns, separator: tab" />
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35 <param name="variableMetadata_in" label="Variable metadata file" type="data" format="tabular" help="variable x metadata columns, separator: tab" />
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36 <param name="samplenameColumn" label="Column that names the sample" type="text" value = "sampleMetadata" help="name of the column in the sample metadata file that has the name of the sample - defaults to 'sampleMetadata'" />
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37 <param name="classnameColumn" label="Column that names the sample-class" type="text" value = "class" help="name of the column in sample metadata that has the values to be tested against the 'classes' input parameter - defaults to 'class'" />
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38 <param name="sampleclassNames" label="Names of sample classes" type="text" value = "" help="comma-separated names (or comma-less regular expressions to match names) of sample-classes to filter in or out; defaults to no names">
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39 <sanitizer>
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40 <valid initial="string.letters">
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41 <add preset="string.digits"/>
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42 <add value="&#36;" /> <!-- dollar, dollar-sign -->
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43 <add value="&#40;" /> <!-- left-paren -->
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44 <add value="&#41;" /> <!-- right-paren -->
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45 <add value="&#42;" /> <!-- splat, asterisk -->
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46 <add value="&#43;" /> <!-- plus -->
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47 <add value="&#44;" /> <!-- comma -->
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48 <add value="&#46;" /> <!-- dot, period -->
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49 <add value="&#58;" /> <!-- colon -->
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50 <add value="&#59;" /> <!-- semi, semicolon -->
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51 <add value="&#63;" /> <!-- what, question mark -->
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52 <add value="&#91;" /> <!-- l-squib, left-squre-bracket -->
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53 <add value="&#92;" /> <!-- whack, backslash -->
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54 <add value="&#93;" /> <!-- r-squib, right-squre-bracket -->
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55 <add value="&#94;" /> <!-- hat, caret -->
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56 <add value="&#123;" /> <!-- l-cube, left-curly-bracket -->
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57 <add value="&#124;" /> <!-- pipe -->
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58 <add value="&#125;" /> <!-- r-cube, right-curly-bracket -->
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59 </valid>
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60 </sanitizer>
6
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61 </param>
5
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62
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63 <param name="wildcards" label="Use wild-cards or regular-expressions" type="select" help="wild-cards (the default) - use '*' and '?' to match class names; regular-expressions - use comma-less regular expressions to match class names">
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64 <option value="TRUE" selected="true">wild-cards</option>
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65 <option value="FALSE">regular-expressions</option>
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66 </param>
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67 <param name="inclusive" label="Include named classes" type="select" help="filter-in - include only the named sample classes; filter-out (the default) - exclude only the named sample classes">
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68 <option value="TRUE">filter-in</option>
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69 <option value="FALSE" selected="true">filter-out</option>
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70 </param>
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71
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72 <param name="variableRangeFilter" label="Variable range-filters" type="text" value = "" help="comma-separated filters, each specified as 'variableMetadataColumnName:min:max'; default is no filters. (See help below.)">
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73 <sanitizer>
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74 <valid initial="string.letters">
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75 <add preset="string.digits"/>
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76 <add value="&#44;" /> <!-- comma -->
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77 <add value="&#58;" /> <!-- colon -->
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78 <add value="&#46;" /> <!-- dot, period -->
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79 </valid>
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80 </sanitizer>
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81 </param>
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82
0
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83 </inputs>
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84 <outputs>
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85 <data name="dataMatrix_out" label="${tool.name}_${dataMatrix_in.name}" format="tabular" ></data>
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86 <data name="sampleMetadata_out" label="${tool.name}_${sampleMetadata_in.name}" format="tabular" ></data>
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87 <data name="variableMetadata_out" label="${tool.name}_${variableMetadata_in.name}" format="tabular" ></data>
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88 </outputs>
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89
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90 <tests>
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91 <test>
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92 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
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93 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
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94 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
6
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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95 <param name="classnameColumn" value="class"/>
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96 <param name="sampleclassNames" value=""/>
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97 <param name="wildcards" value="FALSE"/>
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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98 <param name="samplenameColumn" value="sampleMetadata"/>
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99 <param name="inclusive" value="filter-out"/>
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100 <param name="variableRangeFilter" value="FEATMAX:2e6:,mz:200:,rt::800"/>
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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101 <output name="sampleMetadata_out">
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102 <assert_contents>
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103 <has_text text="HU_028" />
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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104 <has_text text="HU_051" />
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105 <has_text text="HU_060" />
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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106 <has_text text="HU_110" />
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107 <has_text text="HU_149" />
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108 <has_text text="HU_152" />
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109 <has_text text="HU_175" />
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110 <has_text text="HU_178" />
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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111 <has_text text="HU_185" />
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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112 <not_has_text text="HU_204" />
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113 <has_text text="HU_208" />
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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114 <has_text text="HU_017" />
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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115 <has_text text="HU_034" />
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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116 <has_text text="HU_078" />
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117 <has_text text="HU_091" />
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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118 <has_text text="HU_093" />
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119 <has_text text="HU_099" />
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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120 <has_text text="HU_130" />
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121 <has_text text="HU_134" />
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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122 <has_text text="HU_138" />
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123 </assert_contents>
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124 </output>
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125 <output name="variableMetadata_out">
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126 <assert_contents>
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127 <has_text text="HMDB00191" />
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128 <has_text text="HMDB00208" />
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129 <not_has_text text="HMDB00251" />
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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130 <not_has_text text="HMDB00299" />
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131 <not_has_text text="HMDB00512" />
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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132 <not_has_text text="HMDB00518" />
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133 <not_has_text text="HMDB00715" />
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134 <not_has_text text="HMDB00822" />
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135 <has_text text="HMDB01032" />
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136 <has_text text="HMDB01101.1" />
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137 <not_has_text text="HMDB03193" />
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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138 <not_has_text text="HMDB04824" />
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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139 <not_has_text text="HMDB10348" />
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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140 <has_text text="HMDB13189" />
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141 <not_has_text text="HMDB59717" />
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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142 </assert_contents>
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143 </output>
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144 </test>
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145 <test>
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146 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
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147 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
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148 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
0
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149 <param name="classnameColumn" value="gender"/>
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150 <param name="sampleclassNames" value="M"/>
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151 <param name="samplenameColumn" value="sampleMetadata"/>
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152 <param name="inclusive" value="filter-in"/>
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153 <output name="dataMatrix_out">
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154 <assert_contents>
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155 <not_has_text text="HU_028" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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156 <not_has_text text="HU_051" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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157 <not_has_text text="HU_060" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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158 <not_has_text text="HU_110" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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159 <not_has_text text="HU_149" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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160 <not_has_text text="HU_152" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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161 <not_has_text text="HU_175" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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162 <not_has_text text="HU_178" />
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163 <not_has_text text="HU_185" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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164 <not_has_text text="HU_204" />
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165 <not_has_text text="HU_208" />
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166 <has_text text="HU_017" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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167 <has_text text="HU_034" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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168 <has_text text="HU_078" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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169 <has_text text="HU_091" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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170 <has_text text="HU_093" />
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171 <has_text text="HU_099" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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172 <has_text text="HU_130" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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173 <has_text text="HU_134" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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174 <has_text text="HU_138" />
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175 <has_text text="HMDB03193" />
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176 <not_has_text text="HMDB00822" />
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177 <has_text text="HMDB01101" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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178 <has_text text="HMDB01101.1" />
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179 <has_text text="HMDB10348" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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180 <has_text text="HMDB59717" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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181 <has_text text="HMDB13189" />
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182 <has_text text="HMDB00299" />
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183 <has_text text="HMDB00191" />
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184 <has_text text="HMDB00518" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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185 <has_text text="HMDB00715" />
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186 <has_text text="HMDB01032" />
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187 <has_text text="HMDB00208" />
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188 <has_text text="HMDB04824" />
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189 <has_text text="HMDB00512" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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190 <has_text text="HMDB00251" />
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191 </assert_contents>
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192 </output>
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193 </test>
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194 <test>
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195 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
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196 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
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197 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
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198 <param name="classnameColumn" value="gender"/>
5
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199 <param name="sampleclassNames" value="*"/>
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200 <param name="wildcards" value="TRUE"/>
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201 <param name="samplenameColumn" value="sampleMetadata"/>
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202 <param name="inclusive" value="filter-in"/>
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203 <output name="sampleMetadata_out">
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204 <assert_contents>
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205 <not_has_text text="HU_204" />
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206 <has_text text="HU_028" />
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207 <has_text text="HU_051" />
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208 <has_text text="HU_060" />
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209 <has_text text="HU_110" />
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210 <has_text text="HU_149" />
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211 <has_text text="HU_152" />
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212 <has_text text="HU_175" />
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213 <has_text text="HU_178" />
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214 <has_text text="HU_185" />
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215 <has_text text="HU_208" />
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216 <has_text text="HU_017" />
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217 <has_text text="HU_034" />
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218 <has_text text="HU_078" />
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219 <has_text text="HU_091" />
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220 <has_text text="HU_093" />
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221 <has_text text="HU_099" />
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222 <has_text text="HU_130" />
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223 <has_text text="HU_134" />
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224 <has_text text="HU_138" />
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225 </assert_contents>
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226 </output>
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227 </test>
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228 <test>
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229 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
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230 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
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231 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
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232 <param name="classnameColumn" value="gender"/>
0
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233 <param name="sampleclassNames" value="M"/>
5
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234 <param name="wildcards" value="FALSE"/>
0
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235 <param name="samplenameColumn" value="sampleMetadata"/>
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236 <param name="inclusive" value="filter-in"/>
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237 <output name="sampleMetadata_out">
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238 <assert_contents>
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239 <not_has_text text="HU_028" />
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240 <not_has_text text="HU_051" />
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241 <not_has_text text="HU_060" />
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242 <not_has_text text="HU_110" />
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243 <not_has_text text="HU_149" />
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244 <not_has_text text="HU_152" />
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245 <not_has_text text="HU_175" />
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246 <not_has_text text="HU_178" />
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247 <not_has_text text="HU_185" />
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248 <not_has_text text="HU_204" />
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249 <not_has_text text="HU_208" />
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250 <has_text text="HU_017" />
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251 <has_text text="HU_034" />
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252 <has_text text="HU_078" />
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253 <has_text text="HU_091" />
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254 <has_text text="HU_093" />
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255 <has_text text="HU_099" />
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256 <has_text text="HU_130" />
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257 <has_text text="HU_134" />
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258 <has_text text="HU_138" />
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259 </assert_contents>
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260 </output>
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261 </test>
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262 <test>
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263 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
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264 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
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265 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
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266 <param name="classnameColumn" value="gender"/>
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267 <param name="sampleclassNames" value="M"/>
5
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268 <param name="wildcards" value="FALSE"/>
0
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269 <param name="samplenameColumn" value="sampleMetadata"/>
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270 <param name="inclusive" value="filter-in"/>
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271 <output name="variableMetadata_out">
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272 <assert_contents>
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273 <has_text text="HMDB03193" />
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274 <not_has_text text="HMDB00822" />
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275 <has_text text="HMDB01101" />
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276 <has_text text="HMDB01101.1" />
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277 <has_text text="HMDB10348" />
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278 <has_text text="HMDB59717" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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279 <has_text text="HMDB13189" />
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280 <has_text text="HMDB00299" />
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281 <has_text text="HMDB00191" />
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282 <has_text text="HMDB00518" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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283 <has_text text="HMDB00715" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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284 <has_text text="HMDB01032" />
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285 <has_text text="HMDB00208" />
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286 <has_text text="HMDB04824" />
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287 <has_text text="HMDB00512" />
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288 <has_text text="HMDB00251" />
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289 </assert_contents>
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290 </output>
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291 </test>
4
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292 <test>
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293 <param name="dataMatrix_in" value="input_nofilter_dataMatrix.tsv"/>
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294 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
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295 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
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296 <param name="classnameColumn" value="gender"/>
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297 <param name="sampleclassNames" value="M"/>
5
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298 <param name="wildcards" value="FALSE"/>
4
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299 <param name="samplenameColumn" value="sampleMetadata"/>
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300 <param name="inclusive" value="filter-in"/>
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301 <output name="variableMetadata_out">
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302 <assert_contents>
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303 <has_text text="HMDB03193" />
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304 <not_has_text text="HMDB00822" />
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305 <has_text text="HMDB01101" />
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306 <has_text text="HMDB01101.1" />
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307 <has_text text="HMDB10348" />
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308 <has_text text="HMDB59717" />
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309 <not_has_text text="HMDB13189" />
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310 <has_text text="HMDB00299" />
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311 <has_text text="HMDB00191" />
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312 <has_text text="HMDB00518" />
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313 <has_text text="HMDB00715" />
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314 <has_text text="HMDB01032" />
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315 <has_text text="HMDB00208" />
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316 <has_text text="HMDB04824" />
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317 <has_text text="HMDB00512" />
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318 <has_text text="HMDB00251" />
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319 </assert_contents>
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320 </output>
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321 </test>
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322 <test>
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323 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
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324 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
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325 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
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326 <param name="classnameColumn" value="gender"/>
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327 <param name="sampleclassNames" value="[Mm],[fF]"/>
5
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328 <param name="wildcards" value="FALSE"/>
4
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329 <param name="samplenameColumn" value="sampleMetadata"/>
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330 <param name="inclusive" value="filter-in"/>
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331 <output name="sampleMetadata_out">
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332 <assert_contents>
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333 <has_text text="HU_028" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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334 <has_text text="HU_051" />
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335 <has_text text="HU_060" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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336 <has_text text="HU_110" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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337 <has_text text="HU_149" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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338 <has_text text="HU_152" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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339 <has_text text="HU_175" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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340 <has_text text="HU_178" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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341 <has_text text="HU_185" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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342 <not_has_text text="HU_204" />
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343 <has_text text="HU_208" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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344 <has_text text="HU_017" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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345 <has_text text="HU_034" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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346 <has_text text="HU_078" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
347 <has_text text="HU_091" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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348 <has_text text="HU_093" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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349 <has_text text="HU_099" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
350 <has_text text="HU_130" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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351 <has_text text="HU_134" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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352 <has_text text="HU_138" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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353 </assert_contents>
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354 </output>
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355 </test>
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356 <test>
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357 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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358 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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359 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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360 <param name="classnameColumn" value=""/>
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361 <param name="sampleclassNames" value="M"/>
5
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362 <param name="wildcards" value="FALSE"/>
4
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363 <param name="samplenameColumn" value="sampleMetadata"/>
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364 <param name="inclusive" value="filter-in"/>
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365 <output name="sampleMetadata_out">
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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366 <assert_contents>
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diff changeset
367 <has_text text="HU_028" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
368 <has_text text="HU_051" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
369 <has_text text="HU_060" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
370 <has_text text="HU_110" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
371 <has_text text="HU_149" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
372 <has_text text="HU_152" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
373 <has_text text="HU_175" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
374 <has_text text="HU_178" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
375 <has_text text="HU_185" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
376 <not_has_text text="HU_204" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
377 <has_text text="HU_208" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
378 <has_text text="HU_017" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
379 <has_text text="HU_034" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
380 <has_text text="HU_078" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
381 <has_text text="HU_091" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
382 <has_text text="HU_093" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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383 <has_text text="HU_099" />
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384 <has_text text="HU_130" />
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385 <has_text text="HU_134" />
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386 <has_text text="HU_138" />
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387 </assert_contents>
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388 </output>
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389 </test>
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390 </tests>
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391
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392
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393
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394 <help><![CDATA[
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395
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396
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397 **Author** Arthur Eschenlauer (University of Minnesota, esch0041@umn.edu)
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398
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399 --------------------------------------------------------------------------
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400
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401
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402 **R package**
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403
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404 The *w4mclassfilter* package is available from the Hegeman lab github repository (https://github.com/HegemanLab/w4mclassfilter/releases).
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405
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406 -----------------------------------------------------------------------------------------------------------------------------------------
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407
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408
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409 **Tool updates**
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410
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411 See the **NEWS** section at the bottom of this page
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412
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413 ---------------------------------------------------
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414
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415 ==============================================
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416 Filter Workflow4Metabolomics data matrix files
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417 ==============================================
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418
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419 -----------
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420 Description
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421 -----------
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422
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423 Filter a set of retention-corrected W4M files (dataMatrix, sampleMetadata, variableMetadata) by sample-class
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424
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425 -----------------
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426 Workflow Position
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427 -----------------
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428
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429 - Upstream tool category: Preprocessing
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430 - Downstream tool categories: Normalisation, Statistical Analysis, Quality Control, Filter and Sort
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431
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432 ----------
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433 Motivation
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434 ----------
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435
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436 GC-MS1 and LC-MS1 experiments seek to resolve chemicals as features that have distinct chromatographic behavior and (after ionization) mass-to-charge ratio.
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437 Data for a sample are collected as MS intensities, each of which is associated with a position on a 2D plane with dimensions of m/z ratio and chromatographic retention time.
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438 Ideally, features would be sufficiently reproducible from sample-run to sample-run to identify features that are commmon among samples and those that differ.
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439 However, the chromatographic retention time for a chemical can vary from one run to another.
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440 In the Workflow4Metabolomics (W4M, [Giacomoni *et al.*, 2014, Guitton *et al.* 2017]) "flavor" of Galaxy, the XCMS [Smith *et al.*, 2006] preprocessing tools provide for "retention time correction" to align features among samples, but features may be better aligned if pooled samples and blanks are included.
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441
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442 Multivariate statistical techniques may be used to discover clusters of similar samples, and sometimes it is desirable to apply clustering iteratively to smaller and smaller subsets of samples until observable separation of clusters is no longer significant.
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443 Once feature-alignment has been achieved among samples in GC-MS and LC-MS datasets, however, the presence of pools and blanks may confound identification and separation of clusters.
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444 Multivariate statistical algorithms also may be impacted by missing values or dimensions that have zero variance (Thévenot *et al.*, 2015).
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445
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446 The w4mclassfilter tool provides a way to choose subsets of samples for further analysis.
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447 The tool takes as input the data matrix, sample metadata, and variable metadata Galaxy datasets produced by W4M and produces the same trio of datasets with data only for the selected samples.
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448 The tool uses a "sample-class" column in the sample metadata as the basis for including or eliminating samples for further analysis.
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449 Class-values to be considered are provided by the user as a comma-separated list.
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450 The user also provides an indication whether the list specifies classes to be included in further analysis ("filter-in") or rather to be excluded from it ("filter-out").
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451 Next, missing and negative intensites for features of the remaining samples are imputed to zero.
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452 Finally, samples or features with zero variance are eliminated.
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453
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454 -----------
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455 Input files
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456 -----------
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457
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458 +---------------------------+------------+
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459 | File | Format |
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460 +===========================+============+
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461 | Data matrix | tabular |
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462 +---------------------------+------------+
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463 | Sample metadata | tabular |
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464 +---------------------------+------------+
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465 | Variable metadata | tabular |
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466 +---------------------------+------------+
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467
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468
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469 ----------
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470 Parameters
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471 ----------
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472
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473 Data matrix file
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474 | variable x sample **dataMatrix** (tabular separated values) file of the numeric data matrix, with . as decimal, and NA for missing values; the table must not contain metadata apart from row and column names; the row and column names must be identical to the rownames of the sample and variable metadata, respectively (see below)
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475 |
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476
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477 Sample metadata file
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478 | sample x metadata **sampleMetadata** (tabular separated values) file of the numeric and/or character sample metadata, with . as decimal and NA for missing values
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479 |
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480
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481 Variable metadata file
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482 | variable x metadata **variableMetadata** (tabular separated values) file of the numeric and/or character variable metadata, with . as decimal and NA for missing values
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483 |
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484
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485 Column that names the sample (default = '``sampleMetadata``')
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486 | name of the column in sample metadata that has the name of the sample
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487 |
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488
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489 Column that names the sample-class (default = '``class``')
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490 | name of the column in sample metadata that has the values to be tested against the '``classes``' input parameter
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491 |
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492
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493 Names of sample classes (default = no names)
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494 | comma-separated names of sample classes to include or exclude
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495 |
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496
4
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497 Wild-cards (default = '``wild-cards``')
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498 | '``wild-cards``' - use wild-cards to match names of sample classes (see 'Wild card patterns to match class-names' below)
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499 | '``regular-expressions``' - exclude only the named sample classes (see 'Regular expression patterns to match class-names' below)
0
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500 |
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501
4
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502 Include named classes (default = '``filter-out``')
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503 | '``filter-in``' - include only the named sample classes
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504 | '``filter-out``' - exclude only the named sample classes
0
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505 |
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506
6
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507 Variable-range filters (default = no filters)
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508 | comma-separated names of variable-range filters (see 'Variable-range filters' below)
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509 |
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510
0
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511
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512
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513 ------------
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514 Output files
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515 ------------
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516
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517
2
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518 sampleMetadata
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519 | (tabular separated values) file identical to the **sampleMetadata** file given as an input argument, excepting lacking rows for samples (xC-MS features) that have been filtered out (by the sample-class filter or because of zero variance)
0
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520 |
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521
2
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522 variableMetadata
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523 | (tabular separated values) file identical to the **variableMetadata** file given as an input argument, excepting lacking rows for variables (xC-MS features) that have been filtered out (because of zero variance)
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524 |
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525
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526 dataMatrix
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527 | (tabular separated values) file identical to the **dataMatrix** file given as an input argument, excepting lacking rows for variables (xC-MS features) that have been filtered out (because of zero variance) and columns that have been filtered out (by the sample-class filter or because of zero variance)
0
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528 |
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529
2
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530
4
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531 ---------------------------------------
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532 Wild card patterns to match class-names
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533 ---------------------------------------
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534
5
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535 Beginning with v0.98.2, w4mclassfilter supports use of R "wild card" patterns to select class-names.
4
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536
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537 - use '``?``' to match a single character
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538 - use '``*``' to match zero or more characters
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539 - the entire pattern must match the sample name
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540
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541 For example
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542
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543 - '``??.samp*``' matches '``my.sample``' but not '``my.own.sample``'
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544 - '``*.sample``' matches '``my.sample``' and '``my.own.sample``'
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545 - '``*.sampl``' matches neither '``my.sample``' nor '``my.own.sample``'
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546
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547 ------------------------------------------------
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548 Regular expression patterns to match class-names
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549 ------------------------------------------------
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550
5
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551 Beginning with v0.98.2, w4mclassfilter supports use of R "regular expression" patterns to select class-names.
4
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552
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553 R uses POSIX 1003.2 standard regular expressions, which allow precise pattern-matching and are exhaustively defined at:
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554 http://pubs.opengroup.org/onlinepubs/9699919799/basedefs/V1_chap09.html
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555
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556 However, only a few basic building blocks of regular expressions need to be mastered for most cases:
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557
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558 - '``^``' matches the beginning of a class-name
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559 - '``$``' matches the end of a class-name
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560 - '``.``' outside of square brackets matches a single character
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561 - '``*``' matches character specified immediately before zero or more times
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562 - square brackets specify a set of characters to be matched.
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563
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564 Within square brackets
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565
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566 - '``^``' as the first character specifies that the list of characters are those that should **not** be matched.
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567 - '``-``' is used to specify ranges of characters
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568
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569 Caveat: The tool wrapper uses the comma ('``,``') to split a list of sample-class names, so **commas may not be used within regular expressions for this tool**
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570
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571 First Example: Consider a field of class-names consisting of '``marq3,marq6,marq9,marq12,front3,front6,front9,front12``'
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572
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573 - The regular expression '``^front[0-9][0-9]*$``' will match the same sample-classes as '``front3,front6,front9,front12``'
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574 - The regular expression '``^[a-z][a-z]3$``' will match the same sample-classes as '``front3,marq3``'
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575 - The regular expression '``^[a-z][a-z]12$``' will match the same sample-classes as '``front12,marq12``'
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576 - The regular expression '``^[a-z][a-z][0-9]$``' will match the same sample-classes as '``front3,front6,front9,marq3,marq6,marq9``'
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577
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578 Second Example: Consider these regular expression patterns as possible matches to a sample-class name '``AB0123``':
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579
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580 - '``^[A-Z][A-Z][0-9][0-9]*$``' - MATCHES '``**^AB0123$**``'
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581 - '``^[A-Z][A-Z]*[0-9][0-9]*$``' - MATCHES '``**^AB0123$**``'
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582 - '``^[A-Z][0-9]*``' - MATCHES '``**^A** B0123$``' - first character is a letter, '``*``' can specify zero characters, and end of line did not need to be matched.
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583 - '``^[A-Z][A-Z][0-9]``' - MATCHES '``**^AB0** 123$``' - first two characters are letters aind the third is a digit.
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584 - '``^[A-Z][A-Z]*[0-9][0-9]$``' - NO MATCH - the name does not end with the pattern '``[A-Z][0-9][0-9]$``', i.e., it ends with four digits, not two.
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585 - '``^[A-Z][0-9]*$``' - NO MATCH - the pattern specifies that second character and all those that follow, if present, must be digits.
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586
6
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587 ----------------------
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588 Variable-range filters
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589 ----------------------
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590
6
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591 An array of range-specification strings may be supplied in the `variableRangeFilter`
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592 argument. If supplied, only features having numerical values in the specified column
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593 of `variableMetadata` that fall within the specified ranges will be retained
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594 in the output. Each range is a string of three colon-separated values (e.g., "mz:200:800") in the
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595 following order:
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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596
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597 - the **name of a column of `variableMetadata`** which must have numerical data (e.g., "mz");
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598 - the **minimum allowed value** in that column for the feature to be retained (e.g., 200);
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599 - the **maximum allowed value** (e.g., 800).
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600
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601 Note for the range specification strings:
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602
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603 - **If the "maximum" is less than the "minimum", then the range is exclusive** (e.g., "mz:800:200" means retain only features whose mz is NOT in the range 200-800)
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604 - **If the name supplied in the first field is 'FEATMAX',** then the string is defining the minimum (and possibly, though less useful, maximum) intensity for each feature in the dataMatrix. For example, "FEATMAX:1e6:" would specify that any feature would be excluded if no sample had an intensity for that feature greater than 1000000.
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605
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606 - Note, however, that when the "maximum" is greater than the "minimum" for the FEATMAX range specification, then the specification is ignored.
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607
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608 -----------------------------------------------------------------------------
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609
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610 ----------------
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611 WORKING EXAMPLES
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612 ----------------
2
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613
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614 .. class:: infomark
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615
6
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616 -----------
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617 Input Files
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618 -----------
2
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619
6
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620 +------------------------------------------------------------------------------------------------------------------------+
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621 | Input File URL |
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622 +========================================================================================================================+
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623 | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/test-data/input_dataMatrix.tsv |
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624 +------------------------------------------------------------------------------------------------------------------------+
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625 | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/test-data/input_sampleMetadata.tsv |
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626 +------------------------------------------------------------------------------------------------------------------------+
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627 | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/test-data/input_variableMetadata.tsv |
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628 +------------------------------------------------------------------------------------------------------------------------+
2
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629
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630 .. class:: infomark
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631
6
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632 -------------------------------
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633 Running Without Range-Filtering
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634 -------------------------------
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diff changeset
635
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636 This example retains only samples whose 'gender' attribute is 'M'.
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637
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638 **Input parameters**
0
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639
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640 +------------------------------------+-----------------+
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641 | Input Parameter | Value |
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642 +====================================+=================+
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643 | Names of sample classes | M |
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644 +------------------------------------+-----------------+
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645 | Include named classes | filter-in |
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646 +------------------------------------+-----------------+
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647 | Column that names the sample-class | gender |
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648 +------------------------------------+-----------------+
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649 | Column that names the sample | sampleMetadata |
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650 +------------------------------------+-----------------+
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651
6
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652 **Expected outputs**
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653
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654 +-------------------+---------------------------------------------------------------------------------------------------------------------------+
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655 | Expected Output | Download from URL |
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656 +===================+===========================================================================================================================+
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657 | Data matrix | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/test-data/expected_dataMatrix.tsv |
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658 +-------------------+---------------------------------------------------------------------------------------------------------------------------+
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659 | Sample metadata | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/test-data/expected_sampleMetadata.tsv |
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660 +-------------------+---------------------------------------------------------------------------------------------------------------------------+
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661 | Variable metadata | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/test-data/expected_variableMetadata.tsv |
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662 +-------------------+---------------------------------------------------------------------------------------------------------------------------+
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663
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664 .. class:: infomark
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665
6
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666 ----------------------------
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667 Running With Range-Filtering
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668 ----------------------------
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669
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670 This example retains only features whose mz is greater than 200, whose rt is less than 800, and whose maximum intensity across all samples is 2,000,000.
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671 This example retains all samples (except those having zero variance for all feature), although it would be possible to filter on samples as well.
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672
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673 **Input parameters**
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674
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675 +------------------------------------+-------------------------------+
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676 | Input Parameter | Value |
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677 +====================================+===============================+
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678 | Names of sample classes | (Leave this field empty.) |
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679 +------------------------------------+-------------------------------+
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680 | Include named classes | filter-out |
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681 +------------------------------------+-------------------------------+
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682 | Column that names the sample-class | class |
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683 +------------------------------------+-------------------------------+
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684 | Column that names the sample | sampleMetadata |
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685 +------------------------------------+-------------------------------+
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686 | Variable range-filters | FEATMAX:2e6:,mz:200:,rt::800 |
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687 +------------------------------------+-------------------------------+
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688
2
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diff changeset
689 **Expected outputs**
23c6d271def9 planemo upload
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690
6
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diff changeset
691 +-------------------+------------------------------------------------------------------------------------------------------------------------------+
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
692 | Expected Output | Download from URL |
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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693 +===================+==============================================================================================================================+
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
694 | Data matrix | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/test-data/rangefilter_dataMatrix.tsv |
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
695 +-------------------+------------------------------------------------------------------------------------------------------------------------------+
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
696 | Sample metadata | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/test-data/rangefilter_sampleMetadata.tsv |
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
697 +-------------------+------------------------------------------------------------------------------------------------------------------------------+
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
698 | Variable metadata | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/test-data/rangefilter_variableMetadata.tsv |
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
699 +-------------------+------------------------------------------------------------------------------------------------------------------------------+
0
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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diff changeset
700
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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diff changeset
701 -----------------------------------------------------------------------------
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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diff changeset
702
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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diff changeset
703 ----
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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diff changeset
704 NEWS
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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diff changeset
705 ----
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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diff changeset
706
6
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
707 Changes in version 0.98.6
5
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64
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diff changeset
708 =========================
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64
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diff changeset
709
6
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
710 New features
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
711
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
712 * Added support for filtering out features whose attributes fall outside specified ranges.
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
713 For more detail, see "Variable-range filters" above.
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
714
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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parents: 5
diff changeset
715 Internal modifications
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
716
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
717 * Now uses w4mclassfilter R package v0.98.6.
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
718 * Now sorts sample names and feature names in output files because some statistical tools expect the same order in `dataMatrix` row and column names as in the corresponding metadata files.
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
719
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
720 Changes in version 0.98.3
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
721 =========================
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
722
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
723 Internal modifications
5
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64
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diff changeset
724
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64
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diff changeset
725 * Improved input handling.
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64
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diff changeset
726 * Now uses w4mclassfilter R package v0.98.3, although that version has no functional implications for this tool.
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64
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diff changeset
727 * Improved reference-list.
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64
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diff changeset
728
6
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
729 Changes in version 0.98.2
4
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
730 =========================
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
731
6
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
732 New features
4
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
733
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
734 * Added support for R-flavored regular expression pattern-matching when selecting names of sample-classes.
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
735 * Empty classes argument or zero-length class_column result in no samples filtered out.
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
736
6
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
737 Internal modifications
4
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
738
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
739 * Support and tests for new features.
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
740
6
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
741 Changes in version 0.98.1
0
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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diff changeset
742 =========================
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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diff changeset
743
3
191a720488ce planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit dacc1bae8e60340a431907fe8a8b490357e1bfc0
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diff changeset
744 First release - Wrap the w4mclassfilter R package that implements filtering of W4M data matrix, variable metadata, and sample metadata by class of sample.
0
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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diff changeset
745
6
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
746 New features
0
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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diff changeset
747
6
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
748 * *dataMatrix* *is* modified by the tool, so it *does* appear as an output file
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
749 * *sampleMetadata* *is* modified by the tool, so it *does* appear as an output file
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
750 * *variableMetadata* *is* modified by the tool, so it *does* appear as an output file
0
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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diff changeset
751
6
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
752 Internal modifications
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
753
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
754 * N/A
3
191a720488ce planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit dacc1bae8e60340a431907fe8a8b490357e1bfc0
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diff changeset
755
5
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64
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diff changeset
756 ]]></help>
0
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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diff changeset
757 <citations>
5
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64
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diff changeset
758 <!-- Giacomoni_2014 W4M 2.5 -->
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64
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diff changeset
759 <citation type="doi">10.1093/bioinformatics/btu813</citation>
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64
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diff changeset
760 <!-- Guitton_2017 W4M 3.0 -->
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64
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diff changeset
761 <citation type="doi">10.1016/j.biocel.2017.07.002</citation>
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64
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diff changeset
762 <!-- Smith_2006 XCMS -->
3
191a720488ce planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit dacc1bae8e60340a431907fe8a8b490357e1bfc0
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diff changeset
763 <citation type="doi">10.1021/ac051437y</citation>
5
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64
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diff changeset
764 <!-- Th_venot_2015 Urinary metabolome statistics -->
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64
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diff changeset
765 <citation type="doi">10.1021/acs.jproteome.5b00354</citation>
0
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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diff changeset
766 </citations>
3
191a720488ce planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit dacc1bae8e60340a431907fe8a8b490357e1bfc0
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diff changeset
767 <!--
191a720488ce planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit dacc1bae8e60340a431907fe8a8b490357e1bfc0
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diff changeset
768 vim:noet:sw=4:ts=4
191a720488ce planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit dacc1bae8e60340a431907fe8a8b490357e1bfc0
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769 --> </tool>