Mercurial > repos > iuc > dimet_enrichment_plot
annotate macros.xml @ 0:254408bfc5c0 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
author | iuc |
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date | Tue, 10 Oct 2023 11:57:25 +0000 |
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children | 79720105f8c0 |
rev | line source |
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0
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
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1 <macros> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
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changeset
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2 <token name="@TOOL_VERSION@">0.1.4</token> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
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3 <token name="@VERSION_SUFFIX@">0</token> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
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4 <token name="@EXECUTABLE@">pca</token> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
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5 <xml name="factor_repeat"> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
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6 <repeat name="rep_factorName" title="Factor" min="1"> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
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7 <param name="factorName" type="text" value="FactorName" label="Specify a factor name, e.g. effects_drug_x or cancer_markers" |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
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8 help="Only letters, numbers and underscores will be retained in this field"> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
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9 <sanitizer> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
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10 <valid initial="string.letters,string.digits"><add value="_" /></valid> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
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11 </sanitizer> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
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12 </param> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
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13 <repeat name="rep_factorLevel" title="Factor level" min="2" default="2"> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
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14 <param name="factorLevel" type="text" value="FactorLevel" label="Specify a factor level, typical values could be 'tumor', 'normal', 'treated' or 'control'" |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
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15 help="Only letters, numbers and underscores will be retained in this field"> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
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16 <sanitizer> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
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17 <valid initial="string.letters,string.digits"><add value="_" /></valid> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
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18 </sanitizer> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
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19 </param> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
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20 <yield/> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
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21 </repeat> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
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22 </repeat> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
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23 </xml> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
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24 <xml name="requirements"> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
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25 <requirements> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
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26 <requirement type="package" version="@TOOL_VERSION@">dimet</requirement> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
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27 </requirements> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
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28 </xml> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
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29 <xml name="statistical_test"> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
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30 <param name="stat_test" type="select" value="Tt" display="radio" label="Select statistical to apply" help="Please enter at max 1 statistical test by file"> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
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31 <option value="Tt">t-test</option> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
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32 <option value="MW">Mann Whitney</option> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
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33 <option value="KW">Kruskall Wallis</option> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
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34 <option value="ranksum">Wilcoxon's rank sum test</option> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
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35 <option value="Wcox">Wilcoxon signed-rank test</option> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
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36 <option value="BrMu">Brunner-Munzel test</option> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
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changeset
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37 <option value="prm-scipy">permutations test</option> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
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changeset
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38 <option value="disfit">distribution fitting (of the z-score of the ratios), disfit needs several hundreds of metabolites to be trustful.</option> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
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39 </param> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
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40 </xml> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
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41 <xml name="citations"> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
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changeset
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42 <citations> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
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changeset
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43 <citation type="bibtex"> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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44 @software{Galvis_Rodriguez_DIMet, |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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45 author = {Galvis Rodriguez, Johanna and Guyon, Joris and Dartigues, Benjamin and Specque, Florian and Daubon, Thomas and Karkar, Slim and Nikolski, Macha}, |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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46 license = {MIT}, |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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47 title = {{DIMet}}, |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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48 url = {https://github.com/cbib/DIMet} |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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49 } |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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50 |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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51 </citation> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
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52 </citations> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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53 |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
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changeset
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54 </xml> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
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55 <xml name="metadata_file_macros"> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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56 <param name="metadata_path" type="data" format="tabular" label="metadata file" help="The metadata, a unique file with the description of the samples in your measures' files. This is compulsory, see section Metadata File Information."/> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
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57 </xml> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
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58 <xml name="abundance_file_macros"> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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59 <param name="abundance_file" type="data" format="tabular" label="Metabolite abundance file" help="The total abundances file must be organized as a matrix: - The first column must contain Metabolite IDs that are unique (not repeated) within the file. - The rest of the columns correspond to the samples - The rows correspond to the metabolites - The values must be tab separated, with the first row containing the sample/column labels. (see help below for more details)"/> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
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60 </xml> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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61 <xml name="enrichment_file_macros"> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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62 <param name="me_or_frac_contrib_file" type="data" format="tabular" label="Metabolite enrichment file" help="The mean enrichment file must be organized as a matrix: - The first column must contain Metabolite IDs that are unique (not repeated) within the file. - The rest of the columns correspond to the samples. - The rows correspond to the metabolites. - The values must be tab separated, with the first row containing the sample/column labels. (see help below for more details)"/> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
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63 </xml> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
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64 <xml name="isotopologue_prop_file_macros"> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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65 <param name="isotop_prop_file" type="data" format="tabular" label="Isotopologues proportion abundance file" help=" The isotopologue proportions file must be organized as a matrix: - The first column must contain isotopologues IDs that are unique (not repeated) within the file. - The rest of the columns correspond to the samples. - The rows correspond to the isotopologues. - The values must be tab separated, with the first row containing the sample/column labels (see help below for more details)."/> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
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66 </xml> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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67 <xml name="isotopologue_abs_file_macros"> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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68 <param name="isotop_abs_file" type="data" format="tabular" label="Isotopologues absolute abundance file" help="The isotopologue absolute values file must be organized as a matrix: - The first column must contain isotopologues IDs that are unique (not repeated) within the file. - The rest of the columns correspond to the samples. - The rows correspond to the isotopologues. - The values must be tab separated, with the first row containing the sample/column labels (see help below for more details)."/> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
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69 </xml> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
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70 <xml name="input_parameters_pca"> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
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71 <expand macro="abundance_file_macros"/> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
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72 <param name="me_or_frac_contrib_file" type="data" optional="true" format="tabular" label="Mean enrichment or fraction contribution file"/> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
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73 <expand macro="metadata_file_macros"/> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
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74 </xml> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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75 <xml name="input_parameters_abundance"> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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76 <expand macro="abundance_file_macros"/> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
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77 <expand macro="metadata_file_macros"/> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
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78 </xml> |
254408bfc5c0
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79 <xml name="input_parameters_enrichment"> |
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80 <expand macro="enrichment_file_macros"/> |
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81 <expand macro="metadata_file_macros"/> |
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82 </xml> |
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83 <xml name="input_parameters_isotopologue"> |
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84 <expand macro="isotopologue_prop_file_macros"/> |
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85 <expand macro="metadata_file_macros"/> |
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86 </xml> |
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87 <xml name="input_parameters_metabologram"> |
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88 <conditional name="data_input"> |
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89 <param name="data_input_selector" type="select" label="Abundance, Enrichment or Isotopologues count files" help="Select between raw abundance, mean enrichment or isotopologue files"> |
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90 <option value="abundance" selected="True">abundance</option> |
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91 <option value="mean_enrichment">mean_enrichment</option> |
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92 </param> |
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93 <when value="abundance"> |
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94 <expand macro="abundance_file_macros"/> |
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95 <param name="metabolites_list" type="select" optional="false" multiple="true" |
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96 label="Select Metabolite(s) for factor 1 to plot (1 Min.). You have to load a abundance file prior to have access to metabolite list"> |
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97 <validator type="length" min="1" message="Please enter at max 2 compartments"/> |
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98 <options from_dataset="abundance_file"> |
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99 <column name="metabolite_or_isotopologue" index="0"/> |
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100 <column name="value" index="0"/> |
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101 <filter type="unique_value" name="metabolite_or_isotopologue" column="0"/> |
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102 <filter type="remove_value" value="metabolite_or_isotopologue"/> |
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103 </options> |
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104 <sanitizer> |
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105 <valid initial="default"> |
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106 <add preset="string.printable"/> |
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107 <add value="\t"/> |
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108 <remove value="""/> |
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109 <remove value="'"/> |
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110 </valid> |
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111 </sanitizer> |
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112 </param> |
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113 <expand macro="statistical_test"/> |
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114 </when> |
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115 <when value="mean_enrichment"> |
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116 <expand macro="enrichment_file_macros"/> |
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117 <param name="metabolites_list" type="select" optional="false" multiple="true" |
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118 label="Select Metabolite(s) for factor 1 to plot (1 Min.). You have to load a abundance file prior to have access to metabolite list"> |
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119 <validator type="length" min="1" message="Please enter at max 2 compartments"/> |
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120 <options from_dataset="me_or_frac_contrib_file"> |
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121 <column name="metabolite_or_isotopologue" index="0"/> |
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122 <column name="value" index="0"/> |
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123 <filter type="unique_value" name="metabolite_or_isotopologue" column="0"/> |
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124 <filter type="remove_value" value="metabolite_or_isotopologue"/> |
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125 </options> |
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126 <sanitizer> |
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127 <valid initial="default"> |
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128 <add preset="string.printable"/> |
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129 <add value="\t"/> |
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130 <remove value="""/> |
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131 <remove value="'"/> |
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132 </valid> |
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133 </sanitizer> |
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134 </param> |
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135 <expand macro="statistical_test"/> |
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136 </when> |
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137 </conditional> |
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138 <param name="path_kegg_metabolites" type="data" format="tabular" label="Pathways kegg metabolites file" help="A file with the pathways and respective metabolites ID, that must match with those in your metabolomics data. The names of the columns must be the pathways' names, see the minimal data example downloaded from zenodo as explained above. (see help below for more details)"/> |
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139 <param name="path_kegg_transcripts" type="data" format="tabular" label="Pathways kegg transcripts file" help="A file with the pathways and respective gene symbols, which must match with those present in the transcriptomics data. The names of the columns must be the pathways' names, see the minimal data example downloaded from zenodo as explained above. (see help below for more details)"/> |
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140 <expand macro="metadata_file_macros"/> |
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141 </xml> |
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142 <xml name="input_parameters_diff_analysis"> |
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143 <conditional name="data_input"> |
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144 <param name="data_input_selector" type="select" label="Abundance, Enrichment or Isotopologues count files" help="Select between raw abundance and mean enrichment files"> |
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145 <option value="abundance" selected="True">abundance</option> |
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146 <option value="mean_enrichment">mean_enrichment</option> |
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147 <option value="isotop_prop">isotop_prop</option> |
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148 <option value="isotop_abs">isotop_abs</option> |
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149 </param> |
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150 <when value="abundance"> |
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151 <expand macro="abundance_file_macros"/> |
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152 <expand macro="statistical_test"/> |
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153 |
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154 </when> |
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155 <when value="mean_enrichment"> |
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156 <expand macro="enrichment_file_macros"/> |
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157 <expand macro="statistical_test"/> |
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158 </when> |
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159 <when value="isotop_prop"> |
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160 <expand macro="isotopologue_prop_file_macros"/> |
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161 <expand macro="statistical_test"/> |
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162 </when> |
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163 <when value="isotop_abs"> |
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164 <expand macro="isotopologue_abs_file_macros"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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165 <expand macro="statistical_test"/> |
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166 </when> |
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167 </conditional> |
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168 <expand macro="metadata_file_macros"/> |
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169 </xml> |
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170 <xml name="suffix"> |
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171 <param name="suffix" type="text" optional="false" label="suffix to add to output files" > |
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172 <sanitizer invalid_char=""> |
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173 <valid initial="string.ascii_letters,string.digits"> |
254408bfc5c0
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174 <add value="_" /> |
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175 </valid> |
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176 </sanitizer> |
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177 </param> |
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178 </xml> |
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179 <xml name="conditions"> |
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180 <param name="conditions" type="select" optional="false" multiple="true" label="Browse conditions from metadata file (1 min. only if two timepoints are set. 2 max.). You have to load a metadata file prior to have access to metabolite list"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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181 <options from_dataset="metadata_path"> |
254408bfc5c0
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182 <column name="condition" index="1"/> |
254408bfc5c0
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183 <column name="value" index="1"/> |
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184 <filter type="unique_value" name="condition" column="condition"/> |
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185 <filter type="remove_value" value="condition"/> |
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186 </options> |
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187 <sanitizer> |
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188 <valid initial="default"> |
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189 <add preset="string.printable"/> |
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190 <add value="\t"/> |
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191 <remove value="""/> |
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192 <remove value="'"/> |
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193 </valid> |
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194 </sanitizer> |
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195 </param> |
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196 </xml> |
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197 <xml name="conditions_multigroup"> |
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198 <param name="conditions" type="select" optional="false" multiple="true" label="Browse conditions from metadata file. (1 min. only if three timepoints are set). You have to load a metadata file prior to have access to conditions"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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199 <options from_dataset="metadata_path"> |
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200 <column name="condition" index="1"/> |
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201 <column name="value" index="1"/> |
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202 <filter type="unique_value" name="condition" column="condition"/> |
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203 <filter type="remove_value" value="condition"/> |
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204 </options> |
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205 <sanitizer> |
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206 <valid initial="default"> |
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207 <add preset="string.printable"/> |
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208 <add value="\t"/> |
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209 <remove value="""/> |
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210 <remove value="'"/> |
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211 </valid> |
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212 </sanitizer> |
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213 </param> |
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214 </xml> |
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215 <xml name="timepoint_multigroup"> |
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216 <param name="timepoint" type="select" optional="true" multiple="true" label="Browse timepoint from metadata file (1 min. only if three conditions are set). You have to load a metadata file prior to have access to conditions"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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217 <options from_dataset="metadata_path"> |
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218 <column name="timepoint" index="2"/> |
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219 <column name="value" index="2"/> |
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220 <filter type="unique_value" name="timepoint" column="2"/> |
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221 <filter type="remove_value" value="timepoint"/> |
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222 <filter type="sort_by" name="timepoint" column="1"/> |
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223 </options> |
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224 <sanitizer> |
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225 <valid initial="default"> |
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226 <add preset="string.printable"/> |
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227 <add value="\t"/> |
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228 <remove value="""/> |
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229 <remove value="'"/> |
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230 </valid> |
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231 </sanitizer> |
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232 </param> |
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233 </xml> |
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234 <xml name="timepoint"> |
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235 <param name="timepoint" type="select" optional="true" multiple="true" label="Browse timepoint from metadata file (1 min. only if two conditions are set.)"> |
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236 <options from_dataset="metadata_path"> |
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237 <column name="timepoint" index="2"/> |
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238 <column name="value" index="2"/> |
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239 <filter type="unique_value" name="timepoint" column="2"/> |
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240 <filter type="remove_value" value="timepoint"/> |
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241 <filter type="sort_by" name="timepoint" column="1"/> |
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242 </options> |
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243 <sanitizer> |
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244 <valid initial="default"> |
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245 <add preset="string.printable"/> |
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246 <add value="\t"/> |
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247 <remove value="""/> |
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248 <remove value="'"/> |
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249 </valid> |
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250 </sanitizer> |
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251 </param> |
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252 </xml> |
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253 <xml name="grouping"> |
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254 <param name="grouping" type="select" optional="false" multiple="true" label="Browse group to compare"> |
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255 <option value="condition" selected="true">condition</option> |
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256 <option value="timepoint" selected="true">timepoint</option> |
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257 </param> |
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258 </xml> |
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259 <xml name="correction_method"> |
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260 <param name="correction_method" type="select" value="bonferroni" display="radio" label="Select multiple test correction to apply" help="Please enter at max 1 method"> |
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261 <option value="bonferroni">bonferroni</option> |
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262 <option value="holm-sidak">holm-sidak</option> |
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263 <option value="holm">holm</option> |
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264 <option value="simes-hochberg">simes-hochberg</option> |
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265 <option value="hommel">hommel</option> |
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266 <option value="fdr_bh">fdr_bh</option> |
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267 <option value="fdr_by">fdr_by</option> |
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268 <option value="fdr_tsbh">fdr_tsbh</option> |
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269 <option value="fdr_tsbky">fdr_tsbky</option> |
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270 </param> |
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271 </xml> |
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272 <xml name="compartments_enrichment"> |
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273 <param name="compartments" type="select" optional="false" multiple="true" |
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274 label="Browse compartments from metadata file (All needed). You have to load a metadata file prior to have access to compartments"> |
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275 <options from_dataset="metadata_path"> |
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276 <column name="compartment" index="4"/> |
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277 <column name="value" index="4"/> |
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278 <filter type="unique_value" name="compartment" column="4"/> |
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279 <filter type="remove_value" value="compartment"/> |
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280 </options> |
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281 <sanitizer> |
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282 <valid initial="default"> |
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283 <add preset="string.printable"/> |
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284 <add value="\t"/> |
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285 <remove value="""/> |
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286 <remove value="'"/> |
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287 </valid> |
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288 </sanitizer> |
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289 </param> |
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290 </xml> |
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291 <xml name="compartments_abundance"> |
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292 <param name="compartments" type="select" optional="false" multiple="true" |
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293 label="Browse compartments from metadata file (All needed). You have to load a metadata file prior to have access to compartments"> |
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294 <options from_dataset="metadata_path"> |
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295 <column name="compartment" index="4"/> |
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296 <column name="value" index="4"/> |
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297 <filter type="unique_value" name="compartment" column="4"/> |
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298 <filter type="remove_value" value="compartment"/> |
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299 </options> |
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300 <sanitizer> |
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301 <valid initial="default"> |
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302 <add preset="string.printable"/> |
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303 <add value="\t"/> |
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304 <remove value="""/> |
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305 <remove value="'"/> |
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306 </valid> |
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307 </sanitizer> |
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308 </param> |
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309 </xml> |
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310 <xml name="compartments"> |
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311 <param name="compartments" type="select" optional="false" multiple="true" |
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312 label="Browse compartments from metadata file (1 min.). You have to load a metadata file prior to have access to compartments"> |
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313 <options from_dataset="metadata_path"> |
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314 <column name="compartment" index="4"/> |
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315 <column name="value" index="4"/> |
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316 <filter type="unique_value" name="compartment" column="4"/> |
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317 <filter type="remove_value" value="compartment"/> |
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318 </options> |
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319 <sanitizer> |
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320 <valid initial="default"> |
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321 <add preset="string.printable"/> |
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322 <add value="\t"/> |
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323 <remove value="""/> |
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324 <remove value="'"/> |
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325 </valid> |
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326 </sanitizer> |
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327 </param> |
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328 </xml> |
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329 <xml name="abundance_metabolites_list"> |
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330 <param name="metabolites_list" type="select" optional="false" multiple="true" |
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331 label="Select Metabolite(s) for factor 1 to plot (1 min). You have to load a abundance file prior to have access to metabolite list"> |
254408bfc5c0
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332 <validator type="length" min="1" message="Please enter at max 2 compartments"/> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
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333 <options from_dataset="abundance_file"> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
334 <column name="metabolite_or_isotopologue" index="0"/> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
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335 <column name="value" index="0"/> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
336 <filter type="unique_value" name="metabolite_or_isotopologue" column="0"/> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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changeset
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337 <filter type="remove_value" value="metabolite_or_isotopologue"/> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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338 </options> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
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changeset
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339 <sanitizer> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
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changeset
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340 <valid initial="default"> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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diff
changeset
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341 <add preset="string.printable"/> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
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342 <add value="\t"/> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
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changeset
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343 <remove value="""/> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
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changeset
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344 <remove value="'"/> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
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345 </valid> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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changeset
|
346 </sanitizer> |
254408bfc5c0
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iuc
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|
347 </param> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
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changeset
|
348 </xml> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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349 <xml name="enrichment_metabolites_list"> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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350 <param name="metabolites_list" type="select" optional="false" multiple="true" |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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changeset
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351 label="Select Metabolite(s) for factor 1 to plot (1 Min.). You have to load a abundance file prior to have access to metabolite list"> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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changeset
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352 <validator type="length" min="1" message="Please enter at max 2 compartments"/> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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changeset
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353 <options from_dataset="me_or_frac_contrib_file"> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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changeset
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354 <column name="ID" index="0"/> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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changeset
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355 <column name="value" index="0"/> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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changeset
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356 <filter type="unique_value" name="ID" column="0"/> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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changeset
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357 <filter type="remove_value" value="ID"/> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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358 </options> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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changeset
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359 <sanitizer> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
360 <valid initial="default"> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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changeset
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361 <add preset="string.printable"/> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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changeset
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362 <add value="\t"/> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
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changeset
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363 <remove value="""/> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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changeset
|
364 <remove value="'"/> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
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changeset
|
365 </valid> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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|
366 </sanitizer> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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changeset
|
367 </param> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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|
368 </xml> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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369 <xml name="isotopologue_metabolites_list"> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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370 <param name="metabolites_list" type="select" optional="false" multiple="true" |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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changeset
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371 label="Select Metabolite(s) to plot (1 Min.). You have to load a abundance file prior to have access to metabolite list"> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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372 <validator type="length" min="1" message="Please enter at max 2 compartments"/> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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373 <options from_dataset="isotop_prop_file"> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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374 <column name="ID" index="0"/> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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changeset
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375 <column name="value" index="0"/> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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376 <filter type="unique_value" name="ID" column="0"/> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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377 <filter type="remove_value" value="ID"/> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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378 </options> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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changeset
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379 <sanitizer> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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changeset
|
380 <valid initial="default"> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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changeset
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381 <add preset="string.printable"/> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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changeset
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382 <add value="\t"/> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
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changeset
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383 <remove value="""/> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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changeset
|
384 <remove value="'"/> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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385 </valid> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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|
386 </sanitizer> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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|
387 </param> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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388 </xml> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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389 <xml name="deg_list"> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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390 <repeat name="deg_list" title="Deregulated gene set"> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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391 <param name="input" type="data" format="tabular" label="Deregulated genes set"/> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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392 <param name="idcol" type="data_column" data_ref="input" label="Column for id" use_header_names="true"/> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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393 <param name="valuecol" type="data_column" data_ref="input" label="Column for values" use_header_names="true"/> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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394 </repeat> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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395 </xml> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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396 <token name="@INIT_PCA@"><![CDATA[ |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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397 #import json |
254408bfc5c0
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iuc
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398 #import re |
254408bfc5c0
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iuc
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|
399 |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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400 mkdir -p data/raw && |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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401 mkdir -p data/processed && |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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changeset
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402 |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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403 #if $metadata_path: |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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404 ln -s '$metadata_path' data/raw/metadata.csv && |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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changeset
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405 #end if |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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406 #if $abundance_file: |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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407 ln -s '$abundance_file' data/raw/abundance.csv && |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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changeset
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408 #end if |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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changeset
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409 #if $me_or_frac_contrib_file: |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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changeset
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410 ln -s '$me_or_frac_contrib_file' data/raw/me_or_frac_contrib.csv && |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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411 #end if |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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changeset
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412 |
254408bfc5c0
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iuc
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413 ]]></token> |
254408bfc5c0
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iuc
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changeset
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414 <token name="@INIT_CONFIG@"><![CDATA[ |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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changeset
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415 mkdir -p '$__new_file_path__/config' && |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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416 touch '$__new_file_path__/config/config.yaml' && |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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changeset
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417 ]]></token> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
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changeset
|
418 <token name="@REMOVE_CONFIG@"><![CDATA[ |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
419 && rm -r '$__new_file_path__/config' |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
420 ]]></token> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
421 <token name="@INIT_ABUNDANCE_PLOT@"><![CDATA[ |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
422 |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
423 mkdir -p data/raw && |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
424 mkdir -p data/processed && |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
425 |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
426 #if $metadata_path: |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
427 ln -s '$metadata_path' data/raw/metadata.csv && |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
428 #end if |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
429 #if $abundance_file: |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
430 ln -s '$abundance_file' data/raw/abundance.csv && |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
431 #end if |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
432 ]]></token> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
433 <token name="@INIT_ENRICHMENT_PLOT@"><![CDATA[ |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
434 |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
435 mkdir -p data/raw && |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
436 mkdir -p data/processed && |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
437 |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
438 #if $metadata_path: |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
439 ln -s '$metadata_path' data/raw/metadata.csv && |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
440 #end if |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
441 #if $me_or_frac_contrib_file: |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
442 ln -s '$me_or_frac_contrib_file' data/raw/me_or_frac_contrib.csv && |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
443 #end if |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
444 ]]></token> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
445 <token name="@INIT_ISOTOPOLOGUE_PLOT@"><![CDATA[ |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
446 |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
447 mkdir -p data/raw && |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
448 mkdir -p data/processed && |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
449 |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
450 #if $metadata_path: |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
451 ln -s '$metadata_path' data/raw/metadata.csv && |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
452 #end if |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
453 #if $isotop_prop_file: |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
454 ln -s '$isotop_prop_file' data/raw/isotop_prop.csv && |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
455 #end if |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
456 ]]></token> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
457 <token name="@INIT_DIFF_ANALYSIS@"><![CDATA[ |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
458 |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
459 mkdir -p data/raw && |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
460 mkdir -p data/processed && |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
461 |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
462 #if $metadata_path: |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
463 ln -s '$metadata_path' data/raw/metadata.csv && |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
464 #end if |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
465 |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
466 #set $impute_values = {} |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
467 #if str( $data_input.data_input_selector ) == "abundance": |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
468 #if $data_input.abundance_file: |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
469 ln -s '$data_input.abundance_file' data/raw/abundance.csv && |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
470 #silent $impute_values['abundances']='min' |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
471 #end if |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
472 #elif str( $data_input.data_input_selector ) == "mean_enrichment": |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
473 #if $data_input.me_or_frac_contrib_file: |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
474 ln -s '$data_input.me_or_frac_contrib_file' data/raw/me_or_frac_contrib.csv && |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
475 #silent $impute_values['mean_enrichment']='min' |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
476 #end if |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
477 #elif str( $data_input.data_input_selector ) == "isotop_prop": |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
478 #if $data_input.isotop_prop_file: |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
479 ln -s '$data_input.isotop_prop_file' data/raw/isotop_prop.csv && |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
480 #silent $impute_values['isotopologue_proportions']='min' |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
481 #end if |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
482 #else |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
483 #if $data_input.isotop_abs_file: |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
484 ln -s '$data_input.isotop_abs_file' data/raw/isotop_abs.csv && |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
485 #silent $impute_values['isotopologues']='min' |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
486 #end if |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
487 #end if |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
488 ]]></token> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
489 <token name="@INIT_METABOLOGRAM@"><![CDATA[ |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
490 #import json |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
491 #import re |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
492 #import os |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
493 #import csv |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
494 #import subprocess |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
495 |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
496 mkdir -p data/raw && |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
497 mkdir -p data/processed && |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
498 mkdir -p data/integration_files && |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
499 |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
500 #if $path_kegg_metabolites: |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
501 ln -s '$path_kegg_metabolites' data/integration_files/pathways_kegg_metabolites.csv && |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
502 #end if |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
503 #if $path_kegg_transcripts: |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
504 ln -s '$path_kegg_transcripts' data/integration_files/pathways_kegg_transcripts.csv && |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
505 #end if |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
506 |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
507 #if $metadata_path: |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
508 ln -s '$metadata_path' data/raw/metadata.csv && |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
509 #end if |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
510 |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
511 #set $impute_values = {} |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
512 #if str( $data_input.data_input_selector ) == "abundance": |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
513 #if $data_input.abundance_file: |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
514 ln -s '$data_input.abundance_file' data/raw/abundance.csv && |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
515 #silent $impute_values['abundances']='min' |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
516 #end if |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
517 #else: |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
518 #if $data_input.me_or_frac_contrib_file: |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
519 ln -s '$data_input.me_or_frac_contrib_file' data/raw/me_or_frac_contrib.csv && |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
520 #silent $impute_values['mean_enrichment']='min' |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
521 #end if |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
522 #end if |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
523 |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
524 #for $i, $s in enumerate($deg_list) |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
525 #set $cpt = str($i+1) |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
526 ln -s '${s.input}' data/integration_files/DEG_comparison'${cpt}'.csv && |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
527 #end for |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
528 |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
529 |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
530 ]]></token> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
531 <token name="@INIT_DIFF_MULTIGROUP_ANALYSIS@"><![CDATA[ |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
532 |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
533 mkdir -p data/raw && |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
534 mkdir -p data/processed && |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
535 |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
536 #if $metadata_path: |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
537 ln -s '$metadata_path' data/raw/metadata.csv && |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
538 #end if |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
539 |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
540 #set $impute_values = {} |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
541 #if str( $data_input.data_input_selector ) == "abundance": |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
542 #if $data_input.abundance_file: |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
543 ln -s '$data_input.abundance_file' data/raw/abundance.csv && |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
544 #silent $impute_values['abundances']='min' |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
545 #end if |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
546 #elif str( $data_input.data_input_selector ) == "mean_enrichment": |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
547 #if $data_input.me_or_frac_contrib_file: |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
548 ln -s '$data_input.me_or_frac_contrib_file' data/raw/me_or_frac_contrib.csv && |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
549 #silent $impute_values['mean_enrichment']='min' |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
550 #end if |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
551 #elif str( $data_input.data_input_selector ) == "isotop_prop": |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
552 #if $data_input.isotop_prop_file: |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
553 ln -s '$data_input.isotop_prop_file' data/raw/isotop_prop.csv && |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
554 #silent $impute_values['isotopologue_proportions']='min' |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
555 #end if |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
556 #else |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
557 #if $data_input.isotop_abs_file: |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
558 ln -s '$data_input.isotop_abs_file' data/raw/isotop_abs.csv && |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
559 #silent $impute_values['isotopologues']='min' |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
560 #end if |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
561 #end if |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
562 ]]></token> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
563 <token name="@INIT_IMPUTE_VALUES@"><![CDATA[ |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
564 #import re |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
565 #set $impute_values = {} |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
566 #if $abundance_file: |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
567 #silent $impute_values['abundances']='min' |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
568 #end if |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
569 #if $me_or_frac_contrib_file: |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
570 #silent $impute_values['mean_enrichment']='min' |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
571 #end if |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
572 ]]></token> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
573 <token name="@INIT_DATATYPES@"><![CDATA[ |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
574 #import re |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
575 #set $datatypes_avail = list() |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
576 #if str( $data_input.data_input_selector ) == "abundance": |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
577 #if $data_input.abundance_file: |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
578 $datatypes_avail.append(re.sub('"', '', "abundances")) |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
579 #end if |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
580 #elif str( $data_input.data_input_selector ) == "mean_enrichment": |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
581 #if $data_input.me_or_frac_contrib_file: |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
582 $datatypes_avail.append(re.sub('"', '', "mean_enrichment")) |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
583 #end if |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
584 #elif str( $data_input.data_input_selector ) == "isotop_prop": |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
585 #if $data_input.isotop_prop_file: |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
586 $datatypes_avail.append(re.sub('"', '', "isotopologue_proportions")) |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
587 #end if |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
588 #else |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
589 #if $data_input.isotop_abs_file: |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
590 $datatypes_avail.append(re.sub('"', '', "isotopologues")) |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
591 #end if |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
592 #end if |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
593 ]]></token> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
594 <token name="@INIT_STAT_TEST@"><![CDATA[ |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
595 #import re |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
596 #set $statistical_test = {} |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
597 #if str( $data_input.data_input_selector ) == "abundance": |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
598 #if $data_input.abundance_file: |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
599 #silent $statistical_test['abundances']=str($data_input.stat_test) |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
600 #end if |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
601 #elif str( $data_input.data_input_selector ) == "mean_enrichment": |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
602 #if $data_input.me_or_frac_contrib_file: |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
603 #silent $statistical_test['mean_enrichment']=str($data_input.stat_test) |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
604 #end if |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
605 #elif str( $data_input.data_input_selector ) == "isotop_prop": |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
606 #if $data_input.isotop_prop_file: |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
607 #silent $statistical_test['isotopologue_proportions']=str($data_input.stat_test) |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
608 #end if |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
609 #else |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
610 #if $data_input.isotop_abs_file: |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
611 #silent $statistical_test['isotopologues']=str($data_input.stat_test) |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
612 #end if |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
613 #end if |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
614 ]]></token> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
615 <token name="@INIT_CONDITIONS@"><![CDATA[ |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
616 #import re |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
617 #set $conds = list() |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
618 #for $co in $conditions: |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
619 $conds.append(re.sub('"', '', str($co))) |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
620 #end for |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
621 ]]></token> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
622 <token name="@INIT_TIMEPOINTS@"><![CDATA[ |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
623 |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
624 #import re |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
625 #set $timepoints = list() |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
626 #for $tp in $timepoint: |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
627 $timepoints.append(re.sub('"', '', str($tp))) |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
628 #end for |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
629 ]]></token> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
630 <token name="@INIT_GROUPS@"><![CDATA[ |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
631 #import re |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
632 #set $groups = list() |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
633 $groups.append(re.sub('"', '', str("condition"))) |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
634 $groups.append(re.sub('"', '', str("timepoint"))) |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
635 |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
636 ]]></token> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
637 <token name="@INIT_ENRICHMENT_METABOLITES@"><![CDATA[ |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
638 #import json |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
639 #import re |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
640 #set $metabolites = {} |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
641 #for $cp in $compartments: |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
642 #silent $metabolites[re.sub('"', '', str($cp))]=list() |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
643 #for $met in $metabolites_list: |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
644 $metabolites[re.sub('"', '', str($cp))].append(re.sub('"', '\'', str($met))) |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
645 #end for |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
646 #end for |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
647 ]]></token> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
648 <token name="@INIT_ISOTOPOLOGUE_METABOLITES@"><![CDATA[ |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
649 #set $metabolites = {} |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
650 #for $cp in $compartments: |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
651 #silent $metabolites[re.sub('"', '', str($cp))]=list() |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
652 #for $met in $metabolites_list: |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
653 #set tmp_met=re.sub('\,', '--',str($met)) |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
654 #set tmp_met_bis=str(re.split('_m', str($tmp_met))[0]) |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
655 #set tmp_met_ter=re.sub('--', '\,',str($tmp_met_bis)) |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
656 $metabolites[re.sub('"', '', str($cp))].append(re.sub('"', '\'', str(tmp_met_ter))) |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
657 #end for |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
658 #end for |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
659 ]]></token> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
660 <token name="@INIT_MULTIGROUP_COMPARISONS@"><![CDATA[ |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
661 #set $comparisons = list() |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
662 #for $tp in $timepoint: |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
663 #set $ctrl_found=False |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
664 #set $ctrl="" |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
665 |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
666 #for $co in $conditions: |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
667 #set $sub_comparisons = list() |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
668 #if str($co) in ["Control", "control","ctrl"]: |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
669 #set $ctrl_found=True |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
670 #set $ctrl=str($co) |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
671 $sub_comparisons.append(re.sub('"', '', str($co))) |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
672 $sub_comparisons.append(re.sub('"', '', str($tp))) |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
673 #else: |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
674 $sub_comparisons.append(re.sub('"', '', str($co))) |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
675 $sub_comparisons.append(re.sub('"', '', str($tp))) |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
676 |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
677 #end if |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
678 $comparisons.append($sub_comparisons) |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
679 #end for |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
680 #end for |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
681 ]]></token> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
682 <token name="@INIT_CONDITIONS_TIMECOURSE@"><![CDATA[ |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
683 #import re |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
684 #set $conds = list() |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
685 #for $co in $conditions: |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
686 $conds.append(re.sub('"', '', str($co))) |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
687 #end for |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
688 |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
689 ]]></token> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
690 <token name="@INIT_COMPARISONS@"><![CDATA[ |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
691 #import re |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
692 #set $conds = list() |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
693 #for $co in $conditions: |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
694 $conds.append(re.sub('"', '', str($co))) |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
695 #end for |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
696 #set $timepoints = list() |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
697 #for $tp in $timepoint: |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
698 $timepoints.append(re.sub('"', '', str($tp))) |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
699 #end for |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
700 |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
701 #set $comparisons = list() |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
702 #if len($conds) > 1: |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
703 #if len($timepoints) > 0: |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
704 #for $tp in $timepoint: |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
705 #set $ctrl_found=False |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
706 #set $ctrl="" |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
707 #set $comparisons_bis = list() |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
708 #for $co in $conditions: |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
709 #set $sub_comparisons = list() |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
710 #if str($co) in ["'Control'", "'control'", "'ctrl'"]: |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
711 #set $ctrl_found=True |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
712 #set $ctrl=str($co) |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
713 #else: |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
714 $sub_comparisons.append(re.sub('"', '', str($co))) |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
715 $sub_comparisons.append(re.sub('"', '', str($tp))) |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
716 |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
717 #end if |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
718 $comparisons_bis.append($sub_comparisons) |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
719 #end for |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
720 |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
721 #if $ctrl_found: |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
722 $sub_comparisons.append(str($ctrl)) |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
723 $sub_comparisons.append(str($tp)) |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
724 $comparisons_bis.append($sub_comparisons) |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
725 #end if |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
726 |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
727 $comparisons.append($comparisons_bis) |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
728 #end for |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
729 #else |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
730 #for $co in $conditions: |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
731 $comparisons.append(re.sub('"', '', str($co))) |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
732 #end for |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
733 #end if |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
734 |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
735 #else |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
736 #if len($conds) > 0: |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
737 #if len($timepoints) > 1: |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
738 #for $co in $conditions: |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
739 #set $comparisons_bis = list() |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
740 #for $tp in $timepoint: |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
741 #set $sub_comparisons = list() |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
742 $sub_comparisons.append(re.sub('"', '', str($co))) |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
743 $sub_comparisons.append(re.sub('"', '', str($tp))) |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
744 $comparisons_bis.append($sub_comparisons) |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
745 #end for |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
746 $comparisons.append($comparisons_bis) |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
747 #end for |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
748 #end if |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
749 #else |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
750 #for $tp in $timepoint: |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
751 $comparisons.append(re.sub('"', '', str($tp))) |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
752 #end for |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
753 #end if |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
754 #end if |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
755 ]]></token> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
756 <token name="@INIT_TRANSCRIPTS@"><![CDATA[ |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
757 #import re |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
758 #import os |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
759 #import subprocess |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
760 #set $transcripts = list() |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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761 |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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762 #for $i, $s in enumerate($deg_list) |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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763 #set $cpt = str($i+1) |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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764 $transcripts.append(re.sub('"', '', "DEG_comparison"+str($i+1))) |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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765 #set $deg_one_values = os.fsdecode(subprocess.check_output('head -n1 ' + str($s.input) + '| cut -f' + str($s.valuecol), shell=True)) |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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766 #set $deg_one_id = os.fsdecode(subprocess.check_output('head -n1 ' + str($s.input) + '| cut -f' + str($s.idcol), shell=True)) |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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767 #end for |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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768 ]]></token> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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769 <token name="@INIT_PATHWAYS@"><![CDATA[ |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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770 #set $pathways = {} |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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771 #if $path_kegg_metabolites: |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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772 #silent $pathways['metabolites']='pathways_kegg_metabolites' |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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773 #end if |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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774 #if $path_kegg_transcripts: |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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775 #silent $pathways['transcripts']='pathways_kegg_transcripts' |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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776 #end if |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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777 ]]></token> |
254408bfc5c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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778 </macros> |