Mercurial > repos > melpetera > generic_filter

comparison GalFilter/generic_filter.xml @ 2:12cf1eed21f4 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author melpetera
date Tue, 27 Jun 2017 05:57:04 -0400
parents b1fa45bd2b44
children cfd7c4aa5c26
comparison
equal deleted inserted replaced
1:b1fa45bd2b44 2:12cf1eed21f4
1 <tool id="generic_filter" name="Generic_Filter" version="2017.04"> 1 <tool id="generic_filter" name="Generic_Filter" version="2017.06">
2 <description>Removes elements according to numerical or qualitative values</description> 2 <description>Removes elements according to numerical or qualitative values</description>
3 <command interpreter="Rscript"> 3 <requirements>
4 filter_wrap.R 4 <requirement type="package" version="1.1_4">r-batch</requirement>
5 </requirements>
6 <command>
7 Rscript '$__tool_directory__/filter_wrap.R'
5 dataMatrix_in "$dataMatrix_in" 8 dataMatrix_in "$dataMatrix_in"
6 sampleMetadata_in "$sampleMetadata_in" 9 sampleMetadata_in "$sampleMetadata_in"
7 variableMetadata_in "$variableMetadata_in" 10 variableMetadata_in "$variableMetadata_in"
8 11
9 Numeric "${numeric_condition.Factors}" 12 Numeric "${numeric_condition.Factors}"
109 <data name="dataMatrix_out" label="${tool.name}_${dataMatrix_in.name}" format="tabular" ></data> 112 <data name="dataMatrix_out" label="${tool.name}_${dataMatrix_in.name}" format="tabular" ></data>
110 <data name="sampleMetadata_out" label="${tool.name}_${sampleMetadata_in.name}" format="tabular" ></data> 113 <data name="sampleMetadata_out" label="${tool.name}_${sampleMetadata_in.name}" format="tabular" ></data>
111 <data name="variableMetadata_out" label="${tool.name}_${variableMetadata_in.name}" format="tabular" ></data> 114 <data name="variableMetadata_out" label="${tool.name}_${variableMetadata_in.name}" format="tabular" ></data>
112 </outputs> 115 </outputs>
113 116
117 <tests>
118 <test>
119 <param name="dataMatrix_in" value="in_DM1.tabular"/>
120 <param name="sampleMetadata_in" value="in_SM1.tabular"/>
121 <param name="variableMetadata_in" value="in_VM1.tabular"/>
122 <conditional name="numeric_condition">
123 <param name="Factors" value="TRUE"/>
124 <param name="numeric_repeat_0|num_file" value="variable"/>
125 <param name="numeric_repeat_0|parm_col_num" value="rt"/>
126 <param name="numeric_repeat_0|interval_condition|interval" value="lower"/>
127 <param name="numeric_repeat_0|interval_condition|low_value" value="1.2"/>
128 </conditional>
129 <conditional name="qualitative_condition">
130 <param name="Factors" value="TRUE"/>
131 <param name="qualitative_repeat_0|qual_file" value="sample"/>
132 <param name="qualitative_repeat_0|factor_col" value="Time"/>
133 <param name="qualitative_repeat_0|factors_value" value="3"/>
134 </conditional>
135 <output name="dataMatrix_out" file="out_DM1.tabular"/>
136 <output name="sampleMetadata_out" file="out_SM1.tabular"/>
137 <output name="variableMetadata_out" file="out_VM1.tabular"/>
138 </test>
139 </tests>
140
114 <help> 141 <help>
115 142
116 .. class:: infomark 143 .. class:: infomark
117 144
118 **Authors** Marion Landi and Melanie Petera 145 **Authors** Marion Landi and Melanie Petera
252 .. class:: warningmark 279 .. class:: warningmark
253 280
254 Soon see the corresponding "Page" 281 Soon see the corresponding "Page"
255 282
256 </help> 283 </help>
284 <citations>
285 <citation type="doi">10.1093/bioinformatics/btu813</citation>
286 </citations>
257 </tool> 287 </tool>