Mercurial > repos > melpetera > intensity_checks
annotate xml_intensity_check.xml @ 8:2e580585782e draft default tip
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit cd7536e93faa5c7ec1164a8e3f12cebfff609d82
| author | workflow4metabolomics |
|---|---|
| date | Wed, 16 Jul 2025 07:21:20 +0000 |
| parents | 00181e66c50f |
| children |
| rev | line source |
|---|---|
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8
2e580585782e
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit cd7536e93faa5c7ec1164a8e3f12cebfff609d82
workflow4metabolomics
parents:
7
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1 <tool id="intens_check" name="Intensity Check" version="@TOOL_VERSION@" profile="22.05"> |
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7
00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
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2 <description>Statistical measures, number of missing values and mean fold change</description> |
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00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
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3 <macros> |
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8
2e580585782e
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit cd7536e93faa5c7ec1164a8e3f12cebfff609d82
workflow4metabolomics
parents:
7
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4 <token name="@TOOL_VERSION@">2.0.1</token> |
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7
00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
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5 </macros> |
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00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
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6 |
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00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
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7 <edam_topics> |
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00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
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8 <edam_topic>topic_3172</edam_topic> |
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00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
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9 </edam_topics> |
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00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
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10 <edam_operations> |
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00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
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11 <edam_operation>operation_2428</edam_operation> |
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00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff
changeset
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12 <edam_operation>operation_2428</edam_operation> |
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00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
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13 </edam_operations> |
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00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
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14 |
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00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
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15 <requirements> |
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00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
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16 <requirement type="package" version="4">r-base</requirement> |
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00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
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17 <requirement type="package" version="2.2.5">r-argparse</requirement> |
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00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
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18 </requirements> |
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00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
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19 |
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00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
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20 <required_files> |
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00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
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21 <include path="wrapper_intensity_check.R"/> |
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00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff
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22 </required_files> |
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00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
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23 |
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00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
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24 <command detect_errors="aggressive"><![CDATA[ |
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00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
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25 Rscript '$__tool_directory__/wrapper_intensity_check.R' |
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00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
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26 --dataMatrix_in '$dataMatrix_in' |
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00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff
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27 --sampleMetadata_in '$sampleMetadata_in' |
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00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
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28 --variableMetadata_in '$variableMetadata_in' |
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00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff
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29 --method '${method_cond.method}' |
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00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
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30 --chosen_stat '${method_cond.chosen_stat}' |
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00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
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31 #if $method_cond.method == "each_class" |
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00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
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32 --class_col '${method_cond.class_col}' |
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00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
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33 --test_fold '${method_cond.test_fold_cond.test_fold}' |
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00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
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34 #if $method_cond.test_fold_cond.test_fold == "Yes" |
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00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
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35 --logarithm '${method_cond.test_fold_cond.logarithm}' |
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00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
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36 #end if |
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00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
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37 #end if |
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00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
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38 #if $method_cond.method == "one_class" |
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00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff
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39 --class_col '${method_cond.class_col}' |
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00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
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40 --class1 '${method_cond.class1}' |
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00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff
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41 --test_fold '${method_cond.test_fold_cond.test_fold}' |
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00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff
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42 #if $method_cond.test_fold_cond.test_fold == "Yes" |
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00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff
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43 --fold_frac '${method_cond.test_fold_cond.fold_frac}' |
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00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff
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44 --logarithm '${method_cond.test_fold_cond.logarithm}' |
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00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
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45 #end if |
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00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
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46 #end if |
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00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
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47 --variableMetadata_out '$variableMetadata_out' |
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00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
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48 --graphs_out '$graphs_out' |
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00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
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49 ]]></command> |
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00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
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50 |
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00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
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51 <inputs> |
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00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
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52 <param name="dataMatrix_in" type="data" format="tabular,tsv" label="Data matrix file" |
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00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
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53 help="Main data matrix. Rows are variables (features), columns are samples. The first column must contain variable identifiers, and the first row must contain sample identifiers." /> |
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00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
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54 <param name="sampleMetadata_in" type="data" format="tabular,tsv" label="Sample metadata file" |
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00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
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55 help="Sample metadata table. Each row corresponds to a sample, and columns provide sample annotations (e.g., class, batch, group). The first column must contain sample identifiers matching the data matrix columns." /> |
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00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
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56 <param name="variableMetadata_in" type="data" format="tabular,tsv" label="Variable metadata file" |
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00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
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57 help="Variable metadata table. Each row corresponds to a variable (feature), and columns provide variable annotations (e.g., m/z, retention time). The first column must contain variable identifiers matching the data matrix rows." /> |
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00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
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58 <conditional name="method_cond"> |
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00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
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59 <param name="method" type="select" label="Computation method" |
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00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
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60 help="Choose how to group samples for the calculation of statistics and fold changes. |
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00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
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61 • Without distinction between samples: All samples are treated as a single group. |
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00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
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62 • For each class of samples: Samples are grouped by a class column in the sample metadata. |
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00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
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63 • Between one class and all the remaining samples: Focus on one class versus all others."> |
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00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
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64 <option value="no_class">Without distinction between samples</option> |
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00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
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65 <option value="each_class">For each class of samples</option> |
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00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
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66 <option value="one_class">Between one class and all the remaining samples</option> |
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00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
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67 </param> |
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00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
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68 <when value="no_class"> |
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00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
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69 <param name="chosen_stat" type="select" display="checkboxes" multiple="true" label="Statistics" |
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00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
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70 help="Select one or more statistics to calculate for each variable across all samples. At least one must be selected."> |
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00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
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71 <option value="mean">Mean</option> |
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00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
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72 <option value="sd">Standard deviation</option> |
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00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
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73 <option value="median">Median</option> |
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00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
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74 <option value="quartile">Quartile</option> |
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00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
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75 <option value="decile">Decile</option> |
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00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
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76 <option value="NA">Missing values</option> |
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00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff
changeset
|
77 <validator type="no_options" message="Please choose at least one statistic representation" /> |
|
00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff
changeset
|
78 </param> |
|
00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff
changeset
|
79 </when> |
|
00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff
changeset
|
80 <when value="each_class"> |
|
00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff
changeset
|
81 <param name="class_col" type="data_column" data_ref="sampleMetadata_in" use_header_names="true" |
|
00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff
changeset
|
82 label="Class column" |
|
00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff
changeset
|
83 help="Select the column in the sample metadata file that defines the sample classes (groups) for statistics and fold change calculations." /> |
|
00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff
changeset
|
84 <param name="chosen_stat" type="select" display="checkboxes" multiple="true" label="Statistics" |
|
00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff
changeset
|
85 help="Select one or more statistics to calculate for each variable within each class. Leave blank if you only want to calculate mean fold change."> |
|
00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff
changeset
|
86 <option value="mean">Mean</option> |
|
00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff
changeset
|
87 <option value="sd">Standard deviation</option> |
|
00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff
changeset
|
88 <option value="median">Median</option> |
|
00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff
changeset
|
89 <option value="quartile">Quartile</option> |
|
00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff
changeset
|
90 <option value="decile">Decile</option> |
|
00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff
changeset
|
91 <option value="NA">Missing values</option> |
|
00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff
changeset
|
92 </param> |
|
00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff
changeset
|
93 <conditional name="test_fold_cond"> |
|
00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff
changeset
|
94 <param name="test_fold" type="select" display="radio" label="Calculate the mean fold change" |
|
00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff
changeset
|
95 help="Select 'Yes' to calculate the mean fold change between all pairs of classes."> |
|
00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff
changeset
|
96 <option value="Yes">Yes</option> |
|
00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff
changeset
|
97 <option value="No" selected="true">No</option> |
|
00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff
changeset
|
98 </param> |
|
00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff
changeset
|
99 <when value="Yes"> |
|
00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff
changeset
|
100 <param name="logarithm" type="select" label="Logarithm" |
|
00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff
changeset
|
101 help="Choose a logarithmic transformation for the mean fold change values. |
|
00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff
changeset
|
102 • none: No transformation |
|
00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff
changeset
|
103 • log2: Log2 transformation |
|
00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff
changeset
|
104 • log10: Log10 transformation"> |
|
00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff
changeset
|
105 <option value="none" selected='true'>none</option> |
|
00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff
changeset
|
106 <option value="log2">log2</option> |
|
00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff
changeset
|
107 <option value="log10">log10</option> |
|
00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff
changeset
|
108 </param> |
|
00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff
changeset
|
109 </when> |
|
00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff
changeset
|
110 <when value="No"> |
|
00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff
changeset
|
111 </when> |
|
00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff
changeset
|
112 </conditional> |
|
00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff
changeset
|
113 </when> |
|
00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff
changeset
|
114 <when value="one_class"> |
|
00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff
changeset
|
115 <param name="class_col" type="data_column" data_ref="sampleMetadata_in" use_header_names="true" |
|
00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff
changeset
|
116 label="Class column" |
|
00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff
changeset
|
117 help="Select the column in the sample metadata file that defines the sample classes (groups). The selected class will be compared to all other samples." /> |
|
00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff
changeset
|
118 <param name="class1" type="text" label="Selected class" |
|
00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff
changeset
|
119 help="Enter the name of the class to compare against all other samples. This class will be used as numerator or denominator in fold change calculations." /> |
|
00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff
changeset
|
120 <param name="chosen_stat" type="select" display="checkboxes" multiple="true" label="Statistics" |
|
00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff
changeset
|
121 help="Select one or more statistics to calculate for the selected class and the remaining samples. Leave blank if you only want to calculate mean fold change."> |
|
00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff
changeset
|
122 <option value="mean">Mean</option> |
|
00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff
changeset
|
123 <option value="sd">Standard deviation</option> |
|
00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff
changeset
|
124 <option value="median">Median</option> |
|
00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff
changeset
|
125 <option value="quartile">Quartile</option> |
|
00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff
changeset
|
126 <option value="decile">Decile</option> |
|
00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff
changeset
|
127 <option value="NA">Missing values</option> |
|
00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff
changeset
|
128 </param> |
|
00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff
changeset
|
129 <conditional name="test_fold_cond"> |
|
00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff
changeset
|
130 <param name="test_fold" type="select" display="radio" label="Calculate the mean fold change" |
|
00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff
changeset
|
131 help="Select 'Yes' to calculate the mean fold change between the selected class and all other samples."> |
|
00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff
changeset
|
132 <option value="Yes">Yes</option> |
|
00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff
changeset
|
133 <option value="No">No</option> |
|
00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff
changeset
|
134 </param> |
|
00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff
changeset
|
135 <when value="Yes"> |
|
00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff
changeset
|
136 <param name="fold_frac" type="select" label="Where should the class be placed for the mean fold change calculation?" display="radio" |
|
00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff
changeset
|
137 help="Choose whether the selected class should be used as the numerator (Top) or denominator (Bottom) in the fold change calculation."> |
|
00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff
changeset
|
138 <option value="Top">Numerator (Top)</option> |
|
00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff
changeset
|
139 <option value="Bottom">Denominator (Bottom)</option> |
|
00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff
changeset
|
140 </param> |
|
00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff
changeset
|
141 <param name="logarithm" type="select" label="Logarithm" |
|
00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff
changeset
|
142 help="Choose a logarithmic transformation for the mean fold change values. |
|
00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff
changeset
|
143 • none: No transformation |
|
00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff
changeset
|
144 • log2: Log2 transformation |
|
00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff
changeset
|
145 • log10: Log10 transformation"> |
|
00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff
changeset
|
146 <option value="none">none</option> |
|
00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff
changeset
|
147 <option value="log2">log2</option> |
|
00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff
changeset
|
148 <option value="log10">log10</option> |
|
00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff
changeset
|
149 </param> |
|
00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff
changeset
|
150 </when> |
|
00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff
changeset
|
151 <when value="No"> |
|
00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff
changeset
|
152 </when> |
|
00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff
changeset
|
153 </conditional> |
|
00181e66c50f
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff
changeset
|
154 </when> |
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00181e66c50f
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155 </conditional> |
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156 </inputs> |
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157 |
|
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158 <outputs> |
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159 <data name="variableMetadata_out" format="tabular" label="IC_${variableMetadata_in.name}" /> |
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160 <data name="graphs_out" format="pdf" label="IC_Graphs" /> |
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161 </outputs> |
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162 |
|
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163 <tests> |
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164 <test> |
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165 <param name="dataMatrix_in" value="ic_in_dataMatrix.tabular" /> |
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166 <param name="sampleMetadata_in" value="ic_in_sampleMetadata.tabular" /> |
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167 <param name="variableMetadata_in" value="ic_in_variableMetadata.tabular" /> |
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168 <conditional name="method_cond"> |
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169 <param name="method" value="no_class" /> |
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170 <param name="chosen_stat" value="mean,sd,median,quartile,decile,NA" /> |
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171 </conditional> |
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172 <output name="variableMetadata_out" value="ic_out_variableMetadata.tabular" /> |
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173 <output name="graphs_out" value="ic_out_graphs.pdf" /> |
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174 </test> |
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175 <test> |
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176 <param name="dataMatrix_in" value="ic_in_dataMatrix.tabular" /> |
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177 <param name="sampleMetadata_in" value="ic_in_sampleMetadata.tabular" /> |
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178 <param name="variableMetadata_in" value="ic_in_variableMetadata.tabular" /> |
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179 <conditional name="method_cond"> |
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180 <param name="chosen_stat" value="mean,sd,median,quartile,decile,NA" /> |
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181 <param name="method" value="each_class" /> |
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182 <param name="class_col" value="2" /> |
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183 </conditional> |
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184 <output name="variableMetadata_out" value="ic_out_variableMetadata_classes.tabular" /> |
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185 <output name="graphs_out" value="ic_out_graphs_classes.pdf" /> |
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186 </test> |
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187 </tests> |
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188 |
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189 <help><![CDATA[ |
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190 |
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191 .. class:: infomark |
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192 |
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193 **Author:** |
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194 Anthony Fernandes for original code (PFEM - INRA) |
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195 **Maintainer:** Melanie Petera (PFEM - INRAE - MetaboHUB) |
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196 |
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197 --------------------------------------------------- |
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198 |
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199 ==================== |
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200 Intensity Check |
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201 ==================== |
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202 |
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203 ----------- |
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204 Description |
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205 ----------- |
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206 |
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207 This tool performs various metrics: mean fold change calculation, number and proportion of missing values, and mean, sd and decile calculation. |
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208 You can choose to perform these metrics according to sample groups defined in the sample metadata file given as input. |
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209 |
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210 ----------------- |
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211 Workflow position |
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212 ----------------- |
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213 |
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214 .. image:: int_check.png |
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215 :width: 800 |
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216 |
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217 ----------- |
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218 Input files |
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219 ----------- |
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220 |
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221 +----------------------------+------------+ |
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222 | Parameter | Format | |
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223 +============================+============+ |
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224 | 1 : Data matrix file | tabular | |
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225 +----------------------------+------------+ |
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226 | 2 : Sample metadata file | tabular | |
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227 +----------------------------+------------+ |
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228 | 3 : Variable metadata file | tabular | |
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229 +----------------------------+------------+ |
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230 |
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231 ---------- |
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232 |
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233 Parameters |
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234 ---------- |
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235 |
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236 **Computation method** |
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237 - **Without distinction between samples:** calculates chosen statistic(s) for each variable. |
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238 - **For each class of samples:** separates samples between each class (class column to be specified). Chosen statistic(s) and/or mean fold change are calculated for each of them. |
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239 - **Between one class versus all the remaining samples:** If you want to focus only on one class versus all the remaining samples without class distinction. |
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240 |
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241 In the case of two classes: "each class" and "one class" give the same results for statistical measures. We recommend to choose "one class" for mean fold change calculation in order to select the class you want to put as numerator or denominator (see below). |
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242 |
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243 **Statistics** |
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244 Select the statistical measures you want to add in the variable metadata table. If the method is "each class" or "one class", you can choose to leave this section blank if you only want to calculate the mean fold change (see below). |
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245 |
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246 **Class column** (*only if "each class" or "one class"*) |
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247 Select the class column in sample metadata table. |
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248 |
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249 **Selected class** (*only if "one class"*) |
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250 If the method is "one class", specify it. Remaining samples will be named "Other". |
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251 |
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252 **Calculate the mean fold change** (*only if "each class" or "one class"*) |
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253 Choose if you want to calculate the mean fold change. If the method is "each class": mean fold change will be calculated for all combinations of classes. If the method is "one class": it will be calculated between the selected class (see above) and the remaining samples. |
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254 |
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255 **Where should the class be placed for the mean fold change calculation?** (*only if "one class"*) |
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256 If the method is "one class", choose "top" or "bottom" to put the selected class as numerator or denominator (respectively) for the mean fold change calculation. |
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257 |
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258 **Logarithm** (*only if "each class" or "one class"*) |
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259 Choose if you want to transform the mean fold change with a log2 or log10. |
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260 |
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261 ------------ |
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262 Output files |
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263 ------------ |
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264 |
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265 **Variable metadata file** |
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266 Contains the previous columns in variable metadata file and the new ones. |
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267 In the column names for fold, the first class specified is the one used as numerator in the ratio. |
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268 |
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269 **Graphs file** |
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270 Contains barplots with the proportion of NA considering classes and boxplots with the fold values. |
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271 |
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272 --------------------------------------------------- |
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273 |
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274 ---------------------- |
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275 Additional information |
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276 ---------------------- |
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277 |
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278 .. class:: warningmark |
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279 |
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280 For more information about input files, refer to the corresponding "W4M HowTo" page: |
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281 `W4M table format for Galaxy <https://nextcloud.inrae.fr/s/qLkNZRf84QQ5YLY>`_ |
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282 |
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283 ]]></help> |
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284 <citations> |
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285 <citation type="doi">10.1002/cpz1.70095</citation> |
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286 </citations> |
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287 </tool> |