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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 12499da76192d2a61bfd475bc6e21dbe6f23643a"
author galaxyp
date Wed, 16 Jun 2021 19:52:46 +0000
parents c598dfd2c4b4
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c598dfd2c4b4 "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@">
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 metaquantome stat
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9 --samps '$samps'
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10 --mode '$mode_args.mode'
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11 #if $mode_args.mode == 'f' or $mode_args.mode == 'ft'
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12 --ontology='$mode_args.ontology_args.ontology'
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13 #end if
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14 --file '$file'
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15 --control_group '$control_group'
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16 --parametric '$parametric'
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17 $paired
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18 --outfile='$outfile'
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19 ]]></command>
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20 <inputs>
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21 <expand macro="SAMPS"/>
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22 <param argument="--file" type="data" format="tabular" label="metaquantome expanded or filtered file"
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23 help=""/>
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24 <conditional name="mode_args">
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25 <param argument="--mode" type="select" label="Mode">
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26 <option value="f">Functional analysis</option>
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27 <option value="t">Taxonomic analysis</option>
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28 <option value="ft">Functional-taxonomic interaction analysis</option>
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29 </param>
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30 <when value="f">
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31 <expand macro="ONTOLOGY_ARGS"/>
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32 </when>
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33 <when value="t">
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34 </when>
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35 <when value="ft">
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36 <expand macro="ONTOLOGY_ARGS"/>
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37 </when>
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38 </conditional>
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39 <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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40 <validator type="empty_field"/>
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41 </param>
0
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42 <param argument="--parametric" type="select" label="Statistical test to perform">
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43 <option value="False" selected="true">Wilcoxon test (nonparametric)</option>
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44 <option value="True">standard t-test (parametric)</option>
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45 </param>
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46 <param argument="--paired" type="boolean" truevalue="--paired" falsevalue="" checked="false" label="Perform paired tests"/>
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47 </inputs>
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48 <outputs>
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49 <data format="tabular" name="outfile" label="${tool.name} on ${on_string} stats"/>
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50 </outputs>
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51 <tests>
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52 <test>
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53 <param name="file" value="ec_ttest.tab" ftype="tabular" />
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54 <param name="parametric" value="True" />
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55 <param name="ontology" value="ec" />
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56 <param name="mode" value="f" />
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57 <param name="samps" value="samples_basic.tab" ftype="tabular" />
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58 <param name="control_group" value="s2"/>
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59 <output name="outfile" value="ec_ttest_tested.tab" ftype="tabular"/>
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60 </test>
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61 </tests>
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62 <help><![CDATA[
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63 metaQuantome stat
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64 ===================
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65
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66 The *stat* module is the third step in the metaQuantome analysis workflow. The purpose
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67 of the *stat* module is to perform differential expression analysis between 2 experimental
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68 conditions. metaQuantome offers paired and unpaired tests,
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69 as well as parametric and non-parametric options.
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70
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71 Questions, Comments, Problems, Kudos
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72 --------------------------------------
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73
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74 Please file any issues at https://github.com/galaxyproteomics/tools-galaxyp/issues.
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75
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76 ]]></help>
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77 <expand macro="citations" />
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78 </tool>