Mercurial > repos > galaxyp > metaquantome_stat
annotate metaquantome_stat.xml @ 4:d46d64e7964d draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 9204193c3442e427c149b90f15fe3a56fc9802e9"
| author | galaxyp |
|---|---|
| date | Wed, 17 Feb 2021 17:57:12 +0000 |
| parents | 982a442a98dd |
| children | b9d453dca8d3 |
| rev | line source |
|---|---|
|
4
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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020a9ecdc1e1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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2 <description>differential analysis of functional expression and taxonomic abundance</description> |
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020a9ecdc1e1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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3 <macros> |
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020a9ecdc1e1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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4 <import>macros.xml</import> |
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020a9ecdc1e1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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5 </macros> |
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020a9ecdc1e1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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6 <expand macro="requirements" /> |
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020a9ecdc1e1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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7 <command detect_errors="exit_code"><![CDATA[ |
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020a9ecdc1e1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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8 metaquantome stat |
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020a9ecdc1e1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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9 --samps '$samps' |
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020a9ecdc1e1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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10 --mode '$mode_args.mode' |
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020a9ecdc1e1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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11 #if $mode_args.mode == 'f' or $mode_args.mode == 'ft' |
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020a9ecdc1e1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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12 --ontology='$mode_args.ontology_args.ontology' |
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020a9ecdc1e1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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13 #end if |
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020a9ecdc1e1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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14 --file '$file' |
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982a442a98dd
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 74c403057350af3dde81aea154414a0d6a84d2a3"
galaxyp
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15 --control_group '$control_group' |
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0
020a9ecdc1e1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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16 --parametric '$parametric' |
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020a9ecdc1e1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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17 $paired |
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020a9ecdc1e1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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18 --outfile='$outfile' |
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020a9ecdc1e1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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19 ]]></command> |
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020a9ecdc1e1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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20 <inputs> |
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020a9ecdc1e1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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21 <expand macro="SAMPS"/> |
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020a9ecdc1e1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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22 <param argument="--file" type="data" format="tabular" label="metaquantome expanded or filtered file" |
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020a9ecdc1e1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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23 help=""/> |
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020a9ecdc1e1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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24 <conditional name="mode_args"> |
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020a9ecdc1e1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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25 <param argument="--mode" type="select" label="Mode"> |
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020a9ecdc1e1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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26 <option value="f">Functional analysis</option> |
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020a9ecdc1e1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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27 <option value="t">Taxonomic analysis</option> |
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020a9ecdc1e1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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28 <option value="ft">Functional-taxonomic interaction analysis</option> |
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020a9ecdc1e1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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29 </param> |
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020a9ecdc1e1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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30 <when value="f"> |
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020a9ecdc1e1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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31 <expand macro="ONTOLOGY_ARGS"/> |
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020a9ecdc1e1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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32 </when> |
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020a9ecdc1e1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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33 <when value="t"> |
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020a9ecdc1e1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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34 </when> |
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020a9ecdc1e1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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35 <when value="ft"> |
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020a9ecdc1e1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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36 <expand macro="ONTOLOGY_ARGS"/> |
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020a9ecdc1e1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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37 </when> |
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020a9ecdc1e1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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38 </conditional> |
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982a442a98dd
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 74c403057350af3dde81aea154414a0d6a84d2a3"
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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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982a442a98dd
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 74c403057350af3dde81aea154414a0d6a84d2a3"
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40 <validator type="empty_field"/> |
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982a442a98dd
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 74c403057350af3dde81aea154414a0d6a84d2a3"
galaxyp
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41 </param> |
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020a9ecdc1e1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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42 <param argument="--parametric" type="select" label="Statistical test to perform"> |
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020a9ecdc1e1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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43 <option value="False" selected="true">Wilcoxon test (nonparametric)</option> |
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020a9ecdc1e1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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44 <option value="True">standard t-test (parametric)</option> |
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020a9ecdc1e1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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45 </param> |
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020a9ecdc1e1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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46 <param argument="--paired" type="boolean" truevalue="--paired" falsevalue="" checked="false" label="Perform paired tests"/> |
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020a9ecdc1e1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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47 </inputs> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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48 <outputs> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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49 <data format="tabular" name="outfile" label="${tool.name} on ${on_string} stats"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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50 </outputs> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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51 <tests> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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52 <test> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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53 <param name="file" value="ec_ttest.tab" ftype="tabular" /> |
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020a9ecdc1e1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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54 <param name="parametric" value="True" /> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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55 <param name="ontology" value="ec" /> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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56 <param name="mode" value="f" /> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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57 <param name="samps" value="samples_basic.tab" ftype="tabular" /> |
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982a442a98dd
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 74c403057350af3dde81aea154414a0d6a84d2a3"
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58 <param name="control_group" value="s2"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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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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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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66 The *stat* module is the third step in the metaQuantome analysis workflow. The purpose |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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67 of the *stat* module is to perform differential expression analysis between 2 experimental |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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68 conditions. metaQuantome offers paired and unpaired tests, |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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69 as well as parametric and non-parametric options. |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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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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020a9ecdc1e1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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76 ]]></help> |
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020a9ecdc1e1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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changeset
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77 <expand macro="citations" /> |
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020a9ecdc1e1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
galaxyp
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changeset
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78 </tool> |