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author galaxyp
date Fri, 08 Feb 2019 10:36:53 -0500
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1 <tool id="metaquantome_stat" name="metaQuantome: stat" version="@VERSION@.0">
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2 <description>differential analysis of functional expression and taxonomic abundance</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <command detect_errors="exit_code"><![CDATA[
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8 @MAKE_SAMPS_TSV@
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9 metaquantome stat
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10 --samps samp_file.tab
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11 --mode '$mode'
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12 --ontology '$ontology'
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13 --file '$file'
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14 --parametric '$parametric'
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15 $paired
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16 --outfile='$outfile'
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17 ]]></command>
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18 <inputs>
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19 <expand macro="SAMPS"/>
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20 <param argument="--file" type="data" format="tabular" label="metaquantome expanded or filtered file"
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21 help=""/>
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22 <param argument="--mode" type="select" label="Mode">
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23 <option value="f">Functional analysis</option>
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24 <option value="t">Taxonomic analysis</option>
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25 <option value="ft">Functional-taxonomic interaction analysis</option>
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26 </param>
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27 <param name="ontology" type="select" label="Ontology">
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28 <option value="go">Gene Ontology (GO) terms</option>
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29 <option value="ec">Enzyme Commission (EC) numbers</option>
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30 <option value="cog">COG (column named 'cog')</option>
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31 </param>
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32 <param argument="--parametric" type="select" label="Statistical test to perform">
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33 <option value="False" selected="true">Wilcoxon test (nonparametric)</option>
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34 <option value="True">standard t-test (parametric)</option>
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35 </param>
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36 <param argument="--paired" type="boolean" truevalue="--paired" falsevalue="" checked="false" label="Perform paired tests"/>
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37 <expand macro="output_samples_choice"/>
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38 </inputs>
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39 <outputs>
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40 <data format="tabular" name="outfile" label="${tool.name} on ${on_string} stats"/>
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41 <expand macro="output_samples"/>
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42 </outputs>
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43 <tests>
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44 <test>
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45 <param name="file" value="ec_ttest.tab" ftype="tabular" />
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46 <param name="parametric" value="True" />
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47 <param name="ontology" value="ec" />
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48 <param name="mode" value="f" />
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49 <output name="outfile" value="ec_ttest_tested.tab" ftype="tabular"/>
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50 <param name="samps_src" value="build" />
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51 <repeat name="samps">
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52 <param name="group_name" value="s1"/>
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53 <param name="col_names" value="int1,int2,int3"/>
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54 </repeat>
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55 <repeat name="samps">
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56 <param name="group_name" value="s2"/>
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57 <param name="col_names" value="int4,int5,int6"/>
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58 </repeat>
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59 </test>
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60 </tests>
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61 <help><![CDATA[
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62 metaQuantome stat
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63 ===================
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64
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65 The *stat* module is the third step in the metaQuantome analysis workflow. The purpose
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66 of the *stat* module is to perform differential expression analysis between 2 experimental
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67 conditions. metaQuantome offers paired and unpaired tests,
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68 as well as parametric and non-parametric options.
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69
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70 Questions, Comments, Problems, Kudos
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71 --------------------------------------
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72
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73 Please file any issues at https://github.com/galaxyproteomics/tools-galaxyp/issues.
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74
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75 ]]></help>
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76 <expand macro="citations" />
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77 </tool>