Mercurial > repos > galaxyp > metaquantome_stat

annotate metaquantome_stat.xml @ 6:b9d453dca8d3 draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit ec66b5b0627e7cf15b6e67e90d82ba8e0743b761
author galaxyp
date Mon, 18 Mar 2024 12:34:50 +0000
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d46d64e7964d "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 9204193c3442e427c149b90f15fe3a56fc9802e9"
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1 <tool id="metaquantome_stat" name="metaQuantome: stat" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
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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>
6
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6 <expand macro="xrefs"/>
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7 <expand macro="requirements" />
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8 <command detect_errors="exit_code"><![CDATA[
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9 metaquantome stat
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10 --samps '$samps'
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11 --mode '$mode_args.mode'
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12 #if $mode_args.mode == 'f' or $mode_args.mode == 'ft'
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13 --ontology='$mode_args.ontology_args.ontology'
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14 #end if
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15 --file '$file'
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16 --control_group '$control_group'
0
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17 --parametric '$parametric'
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18 $paired
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19 --outfile='$outfile'
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20 ]]></command>
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21 <inputs>
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22 <expand macro="SAMPS"/>
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23 <param argument="--file" type="data" format="tabular" label="metaquantome expanded or filtered file"
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24 help=""/>
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25 <conditional name="mode_args">
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26 <param argument="--mode" type="select" label="Mode">
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27 <option value="f">Functional analysis</option>
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28 <option value="t">Taxonomic analysis</option>
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29 <option value="ft">Functional-taxonomic interaction analysis</option>
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30 </param>
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31 <when value="f">
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32 <expand macro="ONTOLOGY_ARGS"/>
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33 </when>
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34 <when value="t">
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35 </when>
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36 <when value="ft">
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37 <expand macro="ONTOLOGY_ARGS"/>
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38 </when>
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39 </conditional>
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40 <param argument="--control_group" type="text" label="Name of the control sample group of control (used as denominator for fold change evaluation).">
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41 <validator type="empty_field"/>
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42 </param>
0
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43 <param argument="--parametric" type="select" label="Statistical test to perform">
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44 <option value="False" selected="true">Wilcoxon test (nonparametric)</option>
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45 <option value="True">standard t-test (parametric)</option>
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46 </param>
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47 <param argument="--paired" type="boolean" truevalue="--paired" falsevalue="" checked="false" label="Perform paired tests"/>
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48 </inputs>
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49 <outputs>
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50 <data format="tabular" name="outfile" label="${tool.name} on ${on_string} stats"/>
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51 </outputs>
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52 <tests>
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53 <test>
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54 <param name="file" value="ec_ttest.tab" ftype="tabular" />
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55 <param name="parametric" value="True" />
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56 <param name="ontology" value="ec" />
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57 <param name="mode" value="f" />
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58 <param name="samps" value="samples_basic.tab" ftype="tabular" />
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59 <param name="control_group" value="s2"/>
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60 <output name="outfile" value="ec_ttest_tested.tab" ftype="tabular"/>
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61 </test>
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62 </tests>
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63 <help><![CDATA[
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64 metaQuantome stat
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65 ===================
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66
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67 The *stat* module is the third step in the metaQuantome analysis workflow. The purpose
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68 of the *stat* module is to perform differential expression analysis between 2 experimental
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69 conditions. metaQuantome offers paired and unpaired tests,
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70 as well as parametric and non-parametric options.
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71
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72 Questions, Comments, Problems, Kudos
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73 --------------------------------------
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74
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75 Please file any issues at https://github.com/galaxyproteomics/tools-galaxyp/issues.
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76
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77 ]]></help>
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78 <expand macro="citations" />
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79 </tool>