Mercurial > repos > iuc > dimet_abundance_plot
annotate macros.xml @ 2:1df18470e3d0 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
author | iuc |
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date | Thu, 15 Feb 2024 12:51:47 +0000 |
parents | 07164270ec13 |
children | 422207876644 |
rev | line source |
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c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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1 <macros> |
2
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
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2 <token name="@TOOL_VERSION@">0.2.1</token> |
1
07164270ec13
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 7568e92bfc4560d6e0287e7444455f55c86d135d
iuc
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3 <token name="@VERSION_SUFFIX@">1</token> |
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c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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4 <token name="@EXECUTABLE@">pca</token> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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5 <xml name="requirements"> |
c9040bdb918c
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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6 <requirements> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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7 <requirement type="package" version="@TOOL_VERSION@">dimet</requirement> |
c9040bdb918c
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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8 </requirements> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
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9 </xml> |
2
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
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10 <xml name="statistical_test_for_multigroup"> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
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11 <param name="stat_test" type="select" value="KW" display="radio" label="Select statistical to apply" help="Please enter at max 1 statistical test by file"> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
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12 <option value="KW">Kruskal-Wallis</option> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
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13 </param> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
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14 </xml> |
0
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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15 <xml name="statistical_test"> |
2
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
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16 <conditional name="statistics"> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
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17 <param name="statistical_test_type" type="select" label="Choose which type of statistical test to perform" help="Choose which type of statistical test to perform"> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
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18 <option value="parametric">parametric</option> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
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19 <option value="non-parametric-rank" selected="true">non-parametric (rank based)</option> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
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20 <option value="non-parametric-distribution">non-parametric (distribution based)</option> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
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21 </param> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
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22 <when value="parametric"> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
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23 <param name="stat_test" type="select" display="radio" label="Select statistical to apply" help="Please enter at max 1 statistical test by file"> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
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24 <option value="Tt" selected="true">t-test</option> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
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changeset
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25 </param> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
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26 </when> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
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27 <when value="non-parametric-rank"> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
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28 <param name="stat_test" type="select" display="radio" label="Select statistical to apply" help="Please enter at max 1 statistical test by file"> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
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29 <option value="MW">Mann Whitney</option> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
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30 <option value="KW">Kruskal-Wallis</option> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
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31 <option value="ranksum" selected="true">Wilcoxon's rank sum test</option> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
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32 <option value="Wcox">Wilcoxon signed-rank test</option> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
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33 <option value="BrMu">Brunner-Munzel test</option> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
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34 </param> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
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35 </when> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
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36 <when value="non-parametric-distribution"> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
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1
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37 <param name="stat_test" type="select" display="radio" label="Select statistical to apply" help="Please enter at max 1 statistical test by file"> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
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38 <option value="prm-scipy" selected="true">permutations test</option> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
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39 <option value="disfit">distribution fitting (of the z-score of the ratios), disfit needs several hundreds of metabolites to be trustful.</option> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
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40 </param> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
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41 </when> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
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42 </conditional> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
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43 |
0
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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44 </xml> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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45 <xml name="citations"> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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46 <citations> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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47 <citation type="bibtex"> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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48 @software{Galvis_Rodriguez_DIMet, |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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49 author = {Galvis Rodriguez, Johanna and Guyon, Joris and Dartigues, Benjamin and Specque, Florian and Daubon, Thomas and Karkar, Slim and Nikolski, Macha}, |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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50 license = {MIT}, |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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51 title = {{DIMet}}, |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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52 url = {https://github.com/cbib/DIMet} |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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53 } |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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54 |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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55 </citation> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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56 </citations> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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57 |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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58 </xml> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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59 <xml name="metadata_file_macros"> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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60 <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."/> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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61 </xml> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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62 <xml name="abundance_file_macros"> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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63 <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)"/> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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64 </xml> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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65 <xml name="enrichment_file_macros"> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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66 <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)"/> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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67 </xml> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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68 <xml name="isotopologue_prop_file_macros"> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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69 <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)."/> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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70 </xml> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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71 <xml name="isotopologue_abs_file_macros"> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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72 <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)."/> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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73 </xml> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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74 <xml name="input_parameters_pca"> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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75 <expand macro="abundance_file_macros"/> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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76 <param name="me_or_frac_contrib_file" type="data" optional="true" format="tabular" label="Mean enrichment or fraction contribution file"/> |
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77 <expand macro="metadata_file_macros"/> |
c9040bdb918c
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78 </xml> |
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79 <xml name="input_parameters_abundance"> |
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80 <expand macro="abundance_file_macros"/> |
c9040bdb918c
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81 <expand macro="metadata_file_macros"/> |
c9040bdb918c
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82 </xml> |
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83 <xml name="input_parameters_enrichment"> |
c9040bdb918c
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84 <expand macro="enrichment_file_macros"/> |
c9040bdb918c
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85 <expand macro="metadata_file_macros"/> |
c9040bdb918c
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86 </xml> |
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87 <xml name="input_parameters_isotopologue"> |
c9040bdb918c
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88 <expand macro="isotopologue_prop_file_macros"/> |
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89 <expand macro="metadata_file_macros"/> |
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90 </xml> |
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91 <xml name="input_parameters_metabologram"> |
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92 <conditional name="data_input"> |
2
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93 <param name="data_input_selector" type="select" label="Abundance, Enrichment or Isotopologues quantification files" help="Select between raw abundance and mean enrichment files"> |
0
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94 <option value="abundance" selected="True">abundance</option> |
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95 <option value="mean_enrichment">mean_enrichment</option> |
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96 </param> |
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97 <when value="abundance"> |
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98 <expand macro="abundance_file_macros"/> |
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99 <param name="metabolites_list" type="select" optional="false" multiple="true" |
2
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100 label="Select Metabolite(s) for condition 1 to plot (1 Min.). You have to load a abundance file prior to have access to metabolite list"> |
0
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101 <validator type="length" min="1" message="Please enter at max 2 compartments"/> |
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102 <options from_dataset="abundance_file"> |
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103 <column name="metabolite_or_isotopologue" index="0"/> |
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104 <column name="value" index="0"/> |
c9040bdb918c
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105 <filter type="unique_value" name="metabolite_or_isotopologue" column="0"/> |
c9040bdb918c
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106 <filter type="remove_value" value="metabolite_or_isotopologue"/> |
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107 </options> |
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108 <sanitizer> |
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109 <valid initial="default"> |
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110 <add preset="string.printable"/> |
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111 <add value="\t"/> |
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112 <remove value="""/> |
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113 <remove value="'"/> |
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114 </valid> |
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115 </sanitizer> |
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116 </param> |
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117 <expand macro="statistical_test"/> |
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118 </when> |
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119 <when value="mean_enrichment"> |
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120 <expand macro="enrichment_file_macros"/> |
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121 <param name="metabolites_list" type="select" optional="false" multiple="true" |
2
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122 label="Select Metabolite(s) for condition 1 to plot (1 Min.). You have to load a abundance file prior to have access to metabolite list"> |
0
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123 <validator type="length" min="1" message="Please enter at max 2 compartments"/> |
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124 <options from_dataset="me_or_frac_contrib_file"> |
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125 <column name="metabolite_or_isotopologue" index="0"/> |
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126 <column name="value" index="0"/> |
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127 <filter type="unique_value" name="metabolite_or_isotopologue" column="0"/> |
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128 <filter type="remove_value" value="metabolite_or_isotopologue"/> |
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129 </options> |
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130 <sanitizer> |
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131 <valid initial="default"> |
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132 <add preset="string.printable"/> |
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133 <add value="\t"/> |
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134 <remove value="""/> |
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135 <remove value="'"/> |
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136 </valid> |
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137 </sanitizer> |
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138 </param> |
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139 <expand macro="statistical_test"/> |
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140 </when> |
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141 </conditional> |
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142 <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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143 <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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144 <expand macro="metadata_file_macros"/> |
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145 </xml> |
2
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146 <xml name="input_parameters_bivar_analysis"> |
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147 <conditional name="data_input"> |
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148 <param name="data_input_selector" type="select" label="Abundance, Enrichment or Isotopologues quantification files" help="Select between raw abundance, mean enrichment or isotopologue files"> |
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149 <option value="abundance" selected="True">abundance</option> |
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150 <option value="mean_enrichment">mean_enrichment</option> |
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151 <option value="isotop_prop">isotop_prop</option> |
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152 <option value="isotop_abs">isotop_abs</option> |
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153 </param> |
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154 <when value="abundance"> |
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155 <expand macro="abundance_file_macros"/> |
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156 |
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157 </when> |
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158 <when value="mean_enrichment"> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
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159 <expand macro="enrichment_file_macros"/> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
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160 </when> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
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161 <when value="isotop_prop"> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
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162 <expand macro="isotopologue_prop_file_macros"/> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
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163 </when> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
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164 <when value="isotop_abs"> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
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165 <expand macro="isotopologue_abs_file_macros"/> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
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166 </when> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
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167 </conditional> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
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168 <expand macro="metadata_file_macros"/> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
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169 </xml> |
0
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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170 <xml name="input_parameters_diff_analysis"> |
c9040bdb918c
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171 <conditional name="data_input"> |
2
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
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172 <param name="data_input_selector" type="select" label="Abundance, Enrichment or Isotopologues quantification files" help="Select between raw abundance, mean enrichment or isotopologue files"> |
0
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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173 <option value="abundance" selected="True">abundance</option> |
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174 <option value="mean_enrichment">mean_enrichment</option> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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175 <option value="isotop_prop">isotop_prop</option> |
c9040bdb918c
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176 <option value="isotop_abs">isotop_abs</option> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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177 </param> |
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178 <when value="abundance"> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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179 <expand macro="abundance_file_macros"/> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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180 <expand macro="statistical_test"/> |
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181 |
c9040bdb918c
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182 </when> |
c9040bdb918c
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183 <when value="mean_enrichment"> |
c9040bdb918c
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184 <expand macro="enrichment_file_macros"/> |
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185 <expand macro="statistical_test"/> |
c9040bdb918c
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186 </when> |
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187 <when value="isotop_prop"> |
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188 <expand macro="isotopologue_prop_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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189 <expand macro="statistical_test"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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190 </when> |
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191 <when value="isotop_abs"> |
c9040bdb918c
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192 <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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193 <expand macro="statistical_test"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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194 </when> |
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195 </conditional> |
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196 <expand macro="metadata_file_macros"/> |
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197 </xml> |
2
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198 <xml name="input_parameters_multi_diff_analysis"> |
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199 <conditional name="data_input"> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
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200 <param name="data_input_selector" type="select" label="Abundance, Enrichment or Isotopologues quantification files" help="Select between raw abundance, mean enrichment or isotopologue files"> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
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201 <option value="abundance" selected="True">abundance</option> |
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202 <option value="mean_enrichment">mean_enrichment</option> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
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203 <option value="isotop_prop">isotop_prop</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
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204 <option value="isotop_abs">isotop_abs</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
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205 </param> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
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206 <when value="abundance"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
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207 <expand macro="abundance_file_macros"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
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208 <expand macro="statistical_test_for_multigroup"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
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209 |
1df18470e3d0
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210 </when> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
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211 <when value="mean_enrichment"> |
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212 <expand macro="enrichment_file_macros"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
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213 <expand macro="statistical_test_for_multigroup"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
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214 </when> |
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iuc
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215 <when value="isotop_prop"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
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216 <expand macro="isotopologue_prop_file_macros"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
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217 <expand macro="statistical_test_for_multigroup"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
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218 </when> |
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219 <when value="isotop_abs"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
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220 <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 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
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221 <expand macro="statistical_test_for_multigroup"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
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222 </when> |
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223 </conditional> |
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224 <expand macro="metadata_file_macros"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
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225 </xml> |
0
c9040bdb918c
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226 <xml name="suffix"> |
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227 <param name="suffix" type="text" optional="false" label="suffix to add to output files" > |
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228 <sanitizer invalid_char=""> |
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229 <valid initial="string.ascii_letters,string.digits"> |
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230 <add value="_" /> |
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231 </valid> |
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232 </sanitizer> |
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233 </param> |
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234 </xml> |
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235 <xml name="conditions"> |
2
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236 <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 condition list"> |
0
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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237 <options from_dataset="metadata_path"> |
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238 <column name="condition" index="1"/> |
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239 <column name="value" index="1"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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240 <filter type="unique_value" name="condition" column="condition"/> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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241 <filter type="remove_value" value="condition"/> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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242 </options> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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243 <sanitizer> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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244 <valid initial="default"> |
c9040bdb918c
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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245 <add preset="string.printable"/> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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246 <add value="\t"/> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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247 <remove value="""/> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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248 <remove value="'"/> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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249 </valid> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
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250 </sanitizer> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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251 </param> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
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252 </xml> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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253 <xml name="conditions_multigroup"> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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254 <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"> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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255 <options from_dataset="metadata_path"> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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256 <column name="condition" index="1"/> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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257 <column name="value" index="1"/> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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258 <filter type="unique_value" name="condition" column="condition"/> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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259 <filter type="remove_value" value="condition"/> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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260 </options> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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261 <sanitizer> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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262 <valid initial="default"> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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263 <add preset="string.printable"/> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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264 <add value="\t"/> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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265 <remove value="""/> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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266 <remove value="'"/> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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267 </valid> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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268 </sanitizer> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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269 </param> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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270 </xml> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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271 <xml name="timepoint_multigroup"> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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272 <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"> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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273 <options from_dataset="metadata_path"> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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274 <column name="timepoint" index="2"/> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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275 <column name="value" index="2"/> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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276 <filter type="unique_value" name="timepoint" column="2"/> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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277 <filter type="remove_value" value="timepoint"/> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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278 <filter type="sort_by" name="timepoint" column="1"/> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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279 </options> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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280 <sanitizer> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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281 <valid initial="default"> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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282 <add preset="string.printable"/> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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283 <add value="\t"/> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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284 <remove value="""/> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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285 <remove value="'"/> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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286 </valid> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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287 </sanitizer> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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288 </param> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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289 </xml> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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290 <xml name="timepoint"> |
2
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
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1
diff
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291 <param name="timepoint" type="select" optional="false" multiple="true" label="Browse timepoint from metadata file (1 min.)"> |
0
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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292 <options from_dataset="metadata_path"> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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293 <column name="timepoint" index="2"/> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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294 <column name="value" index="2"/> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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295 <filter type="unique_value" name="timepoint" column="2"/> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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296 <filter type="remove_value" value="timepoint"/> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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297 <filter type="sort_by" name="timepoint" column="1"/> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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298 </options> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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299 <sanitizer> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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300 <valid initial="default"> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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301 <add preset="string.printable"/> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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302 <add value="\t"/> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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303 <remove value="""/> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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304 <remove value="'"/> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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305 </valid> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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306 </sanitizer> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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307 </param> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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308 </xml> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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309 <xml name="grouping"> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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310 <param name="grouping" type="select" optional="false" multiple="true" label="Browse group to compare"> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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311 <option value="condition" selected="true">condition</option> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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312 <option value="timepoint" selected="true">timepoint</option> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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313 </param> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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314 </xml> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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315 <xml name="correction_method"> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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316 <param name="correction_method" type="select" value="bonferroni" display="radio" label="Select multiple test correction to apply" help="Please enter at max 1 method"> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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317 <option value="bonferroni">bonferroni</option> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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318 <option value="holm-sidak">holm-sidak</option> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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319 <option value="holm">holm</option> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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320 <option value="simes-hochberg">simes-hochberg</option> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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321 <option value="hommel">hommel</option> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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322 <option value="fdr_bh">fdr_bh</option> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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323 <option value="fdr_by">fdr_by</option> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
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changeset
|
324 <option value="fdr_tsbh">fdr_tsbh</option> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
325 <option value="fdr_tsbky">fdr_tsbky</option> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
326 </param> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
327 </xml> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
328 <xml name="compartments_enrichment"> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
329 <param name="compartments" type="select" optional="false" multiple="true" |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
330 label="Browse compartments from metadata file (All needed). You have to load a metadata file prior to have access to compartments"> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
331 <options from_dataset="metadata_path"> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
332 <column name="compartment" index="4"/> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
333 <column name="value" index="4"/> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
334 <filter type="unique_value" name="compartment" column="4"/> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
335 <filter type="remove_value" value="compartment"/> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
336 </options> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
337 <sanitizer> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
338 <valid initial="default"> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
339 <add preset="string.printable"/> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
340 <add value="\t"/> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
341 <remove value="""/> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
342 <remove value="'"/> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
343 </valid> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
344 </sanitizer> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
345 </param> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
346 </xml> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
347 <xml name="compartments_abundance"> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
348 <param name="compartments" type="select" optional="false" multiple="true" |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
349 label="Browse compartments from metadata file (All needed). You have to load a metadata file prior to have access to compartments"> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
350 <options from_dataset="metadata_path"> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
351 <column name="compartment" index="4"/> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
352 <column name="value" index="4"/> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
353 <filter type="unique_value" name="compartment" column="4"/> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
354 <filter type="remove_value" value="compartment"/> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
355 </options> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
356 <sanitizer> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
357 <valid initial="default"> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
358 <add preset="string.printable"/> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
359 <add value="\t"/> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
360 <remove value="""/> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
361 <remove value="'"/> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
362 </valid> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
363 </sanitizer> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
364 </param> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
365 </xml> |
2
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
366 <xml name="compartments_metabologram"> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
367 <param name="compartments" type="select" optional="false" multiple="false" |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
368 label="Browse compartments from metadata file (1 max.). You have to load a metadata file prior to have access to compartments"> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
369 <options from_dataset="metadata_path"> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
370 <column name="compartment" index="4"/> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
371 <column name="value" index="4"/> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
372 <filter type="unique_value" name="compartment" column="4"/> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
373 <filter type="remove_value" value="compartment"/> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
374 </options> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
375 <sanitizer> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
376 <valid initial="default"> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
377 <add preset="string.printable"/> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
378 <add value="\t"/> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
379 <remove value="""/> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
380 <remove value="'"/> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
381 </valid> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
382 </sanitizer> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
383 </param> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
384 </xml> |
0
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
385 <xml name="compartments"> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
386 <param name="compartments" type="select" optional="false" multiple="true" |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
387 label="Browse compartments from metadata file (1 min.). You have to load a metadata file prior to have access to compartments"> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
388 <options from_dataset="metadata_path"> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
389 <column name="compartment" index="4"/> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
390 <column name="value" index="4"/> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
391 <filter type="unique_value" name="compartment" column="4"/> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
392 <filter type="remove_value" value="compartment"/> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
393 </options> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
394 <sanitizer> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
395 <valid initial="default"> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
396 <add preset="string.printable"/> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
397 <add value="\t"/> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
398 <remove value="""/> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
399 <remove value="'"/> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
400 </valid> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
401 </sanitizer> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
402 </param> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
403 </xml> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
404 <xml name="abundance_metabolites_list"> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
405 <param name="metabolites_list" type="select" optional="false" multiple="true" |
2
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
406 label="Select Metabolite(s) for condition 1 to plot (1 min). You have to load a abundance file prior to have access to metabolite list"> |
0
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
407 <validator type="length" min="1" message="Please enter at max 2 compartments"/> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
408 <options from_dataset="abundance_file"> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
409 <column name="metabolite_or_isotopologue" index="0"/> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
410 <column name="value" index="0"/> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
411 <filter type="unique_value" name="metabolite_or_isotopologue" column="0"/> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
412 <filter type="remove_value" value="metabolite_or_isotopologue"/> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
413 </options> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
414 <sanitizer> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
415 <valid initial="default"> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
416 <add preset="string.printable"/> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
417 <add value="\t"/> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
418 <remove value="""/> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
419 <remove value="'"/> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
420 </valid> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
421 </sanitizer> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
422 </param> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
423 </xml> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
424 <xml name="enrichment_metabolites_list"> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
425 <param name="metabolites_list" type="select" optional="false" multiple="true" |
2
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
426 label="Select Metabolite(s) for condition 1 to plot (1 Min.). You have to load a abundance file prior to have access to metabolite list"> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
427 <validator type="length" min="1" message="Please enter at min 1 metabolite"/> |
0
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
428 <options from_dataset="me_or_frac_contrib_file"> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
429 <column name="ID" index="0"/> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
430 <column name="value" index="0"/> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
431 <filter type="unique_value" name="ID" column="0"/> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
432 <filter type="remove_value" value="ID"/> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
433 </options> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
434 <sanitizer> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
435 <valid initial="default"> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
436 <add preset="string.printable"/> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
437 <add value="\t"/> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
438 <remove value="""/> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
439 <remove value="'"/> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
440 </valid> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
441 </sanitizer> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
442 </param> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
443 </xml> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
444 <xml name="isotopologue_metabolites_list"> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
445 <param name="metabolites_list" type="select" optional="false" multiple="true" |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
446 label="Select Metabolite(s) to plot (1 Min.). You have to load a abundance file prior to have access to metabolite list"> |
2
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
447 <validator type="length" min="1" message="Please enter at min 1 metabolite"/> |
0
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
448 <options from_dataset="isotop_prop_file"> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
449 <column name="ID" index="0"/> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
450 <column name="value" index="0"/> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
451 <filter type="unique_value" name="ID" column="0"/> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
452 <filter type="remove_value" value="ID"/> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
453 </options> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
454 <sanitizer> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
455 <valid initial="default"> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
456 <add preset="string.printable"/> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
457 <add value="\t"/> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
458 <remove value="""/> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
459 <remove value="'"/> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
460 </valid> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
461 </sanitizer> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
462 </param> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
463 </xml> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
464 <xml name="deg_list"> |
2
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
465 <repeat name="deg_list" title="Deregulated gene set" default="1" min="1"> |
0
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
466 <param name="input" type="data" format="tabular" label="Deregulated genes set"/> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
467 <param name="idcol" type="data_column" data_ref="input" label="Column for id" use_header_names="true"/> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
468 <param name="valuecol" type="data_column" data_ref="input" label="Column for values" use_header_names="true"/> |
2
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
469 <param name="timepoint" type="select" optional="false" multiple="false" label="Browse timepoint from metadata file (1 min.)"> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
470 <options from_dataset="metadata_path"> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
471 <column name="timepoint" index="2"/> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
472 <column name="value" index="2"/> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
473 <filter type="unique_value" name="timepoint" column="2"/> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
474 <filter type="remove_value" value="timepoint"/> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
475 <filter type="sort_by" name="timepoint" column="1"/> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
476 </options> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
477 <sanitizer> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
478 <valid initial="default"> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
479 <add preset="string.printable"/> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
480 <add value="\t"/> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
481 <remove value="""/> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
482 <remove value="'"/> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
483 </valid> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
484 </sanitizer> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
485 </param> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
486 <repeat name="factor_list" title="Conditions" default="2" min="2" max="2" help="Specify conditions to compare from metadata file (for each comparison, the first specified condition is the reference). You have to load a metadata file prior to have access to condition list"> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
487 <param name="condition" label="Condition" type="select" optional="false" multiple="false"> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
488 <options from_dataset="metadata_path"> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
489 <column name="condition" index="1"/> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
490 <column name="value" index="1"/> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
491 <filter type="unique_value" name="condition" column="condition"/> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
492 <filter type="remove_value" value="condition"/> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
493 </options> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
494 <sanitizer> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
495 <valid initial="default"> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
496 <add preset="string.printable"/> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
497 <add value="\t"/> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
498 <remove value="""/> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
499 <remove value="'"/> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
500 </valid> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
501 </sanitizer> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
502 </param> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
503 </repeat> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
504 |
0
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
505 </repeat> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
506 </xml> |
2
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
507 <xml name="plot_abundance_factor_list"> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
508 <repeat name="plot_abundance_factor_list" title="Conditions" min="1" help="Specify conditions to compare 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 condition list"> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
509 <param name="condition" label="Condition" type="select" optional="false" multiple="false"> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
510 <options from_dataset="metadata_path"> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
511 <column name="condition" index="1"/> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
512 <column name="value" index="1"/> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
513 <filter type="unique_value" name="condition" column="condition"/> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
514 <filter type="remove_value" value="condition"/> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
515 </options> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
516 <sanitizer> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
517 <valid initial="default"> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
518 <add preset="string.printable"/> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
519 <add value="\t"/> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
520 <remove value="""/> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
521 <remove value="'"/> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
522 </valid> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
523 </sanitizer> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
524 </param> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
525 </repeat> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
526 </xml> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
527 <xml name="plot_factor_list"> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
528 <repeat name="plot_factor_list" title="Conditions" min="2" help="Specify conditions to compare 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 condition list"> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
529 <param name="condition" label="Condition" type="select" optional="false" multiple="false"> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
530 <options from_dataset="metadata_path"> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
531 <column name="condition" index="1"/> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
532 <column name="value" index="1"/> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
533 <filter type="unique_value" name="condition" column="condition"/> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
534 <filter type="remove_value" value="condition"/> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
535 </options> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
536 <sanitizer> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
537 <valid initial="default"> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
538 <add preset="string.printable"/> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
539 <add value="\t"/> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
540 <remove value="""/> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
541 <remove value="'"/> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
542 </valid> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
543 </sanitizer> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
544 </param> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
545 </repeat> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
546 </xml> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
547 <xml name="factor_list"> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
548 <repeat name="factor_list" title="Conditions" min="2" max="2" help="Specify conditions to compare from metadata file (for each comparison, the first specified condition is the reference). You have to load a metadata file prior to have access to condition list"> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
549 <param name="condition" label="Condition" type="select" optional="false" multiple="false"> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
550 <options from_dataset="metadata_path"> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
551 <column name="condition" index="1"/> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
552 <column name="value" index="1"/> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
553 <filter type="unique_value" name="condition" column="condition"/> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
554 <filter type="remove_value" value="condition"/> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
555 </options> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
556 <sanitizer> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
557 <valid initial="default"> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
558 <add preset="string.printable"/> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
559 <add value="\t"/> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
560 <remove value="""/> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
561 <remove value="'"/> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
562 </valid> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
563 </sanitizer> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
564 </param> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
565 </repeat> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
566 </xml> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
567 <xml name="palette"> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
568 <param name="palette" type="select" value="pastel" display="radio" label="Select palette colormap to apply to abundance plot." help="For more information see https://seaborn.pydata.org/tutorial/color_palettes.html"> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
569 <option value="pastel" selected="true">pastel</option> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
570 <option value="deep">deep</option> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
571 <option value="muted">muted</option> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
572 <option value="bright">bright</option> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
573 <option value="dark">dark</option> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
574 <option value="colorblind">colorblind</option> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
575 </param> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
576 </xml> |
0
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
577 <token name="@INIT_PCA@"><![CDATA[ |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
578 #import json |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
579 #import re |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
580 |
2
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
581 mkdir -p data && |
0
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
582 |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
583 #if $metadata_path: |
2
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
584 ln -s '$metadata_path' data/metadata.csv && |
0
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
585 #end if |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
586 #if $abundance_file: |
2
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
587 ln -s '$abundance_file' data/abundance.csv && |
0
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
588 #end if |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
589 #if $me_or_frac_contrib_file: |
2
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
590 ln -s '$me_or_frac_contrib_file' data/me_or_frac_contrib.csv && |
0
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
591 #end if |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
592 |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
593 ]]></token> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
594 <token name="@INIT_CONFIG@"><![CDATA[ |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
595 mkdir -p '$__new_file_path__/config' && |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
596 touch '$__new_file_path__/config/config.yaml' && |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
597 ]]></token> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
598 <token name="@REMOVE_CONFIG@"><![CDATA[ |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
599 && rm -r '$__new_file_path__/config' |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
600 ]]></token> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
601 <token name="@INIT_ABUNDANCE_PLOT@"><![CDATA[ |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
602 |
2
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
603 mkdir -p data && |
0
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
604 |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
605 #if $metadata_path: |
2
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
606 ln -s '$metadata_path' data/metadata.csv && |
0
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
607 #end if |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
608 #if $abundance_file: |
2
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
609 ln -s '$abundance_file' data/abundance.csv && |
0
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
610 #end if |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
611 ]]></token> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
612 <token name="@INIT_ENRICHMENT_PLOT@"><![CDATA[ |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
613 |
2
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
614 mkdir -p data && |
0
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
615 |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
616 #if $metadata_path: |
2
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
617 ln -s '$metadata_path' data/metadata.csv && |
0
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
618 #end if |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
619 #if $me_or_frac_contrib_file: |
2
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
620 ln -s '$me_or_frac_contrib_file' data/me_or_frac_contrib.csv && |
0
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
621 #end if |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
622 ]]></token> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
623 <token name="@INIT_ISOTOPOLOGUE_PLOT@"><![CDATA[ |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
624 |
2
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
625 mkdir -p data && |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
626 |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
627 #if $metadata_path: |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
628 ln -s '$metadata_path' data/metadata.csv && |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
629 #end if |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
630 #if $isotop_prop_file: |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
631 ln -s '$isotop_prop_file' data/isotop_prop.csv && |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
632 #end if |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
633 ]]></token> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
634 <token name="@INIT_BI_ANALYSIS@"><![CDATA[ |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
635 |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
636 mkdir -p data && |
0
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
637 |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
638 #if $metadata_path: |
2
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
639 ln -s '$metadata_path' data/metadata.csv && |
0
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
640 #end if |
2
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
641 #set conditions_MDV_comparison = {} |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
642 #silent $conditions_MDV_comparison['isotopologue_proportions']='pearson' |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
643 #set timepoints_MDV_comparison = {} |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
644 #silent $timepoints_MDV_comparison['isotopologue_proportions']='pearson' |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
645 #set conditions_metabolite_time_profiles = {} |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
646 #silent $conditions_metabolite_time_profiles['abundances']='pearson' |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
647 #silent $conditions_metabolite_time_profiles['mean_enrichment']='pearson' |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
648 |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
649 #set $impute_values = {} |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
650 #if str( $data_input.data_input_selector ) == "abundance": |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
651 #if $data_input.abundance_file: |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
652 ln -s '$data_input.abundance_file' data/abundance.csv && |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
653 #silent $impute_values['abundances']='min' |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
654 #end if |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
655 #elif str( $data_input.data_input_selector ) == "mean_enrichment": |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
656 #if $data_input.me_or_frac_contrib_file: |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
657 ln -s '$data_input.me_or_frac_contrib_file' data/me_or_frac_contrib.csv && |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
658 #silent $impute_values['mean_enrichment']='min' |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
659 #end if |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
660 #elif str( $data_input.data_input_selector ) == "isotop_prop": |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
661 #if $data_input.isotop_prop_file: |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
662 ln -s '$data_input.isotop_prop_file' data/isotop_prop.csv && |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
663 #silent $impute_values['isotopologue_proportions']='min' |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
664 #end if |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
665 #else |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
666 #if $data_input.isotop_abs_file: |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
667 ln -s '$data_input.isotop_abs_file' data/isotop_abs.csv && |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
668 #silent $impute_values['isotopologues']='min' |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
669 #end if |
0
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
670 #end if |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
671 ]]></token> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
672 <token name="@INIT_DIFF_ANALYSIS@"><![CDATA[ |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
673 |
2
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
674 mkdir -p data && |
0
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
675 |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
676 #if $metadata_path: |
2
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
677 ln -s '$metadata_path' data/metadata.csv && |
0
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
678 #end if |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
679 |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
680 #set $impute_values = {} |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
681 #if str( $data_input.data_input_selector ) == "abundance": |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
682 #if $data_input.abundance_file: |
2
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
683 ln -s '$data_input.abundance_file' data/abundance.csv && |
0
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
684 #silent $impute_values['abundances']='min' |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
685 #end if |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
686 #elif str( $data_input.data_input_selector ) == "mean_enrichment": |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
687 #if $data_input.me_or_frac_contrib_file: |
2
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
688 ln -s '$data_input.me_or_frac_contrib_file' data/me_or_frac_contrib.csv && |
0
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
689 #silent $impute_values['mean_enrichment']='min' |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
690 #end if |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
691 #elif str( $data_input.data_input_selector ) == "isotop_prop": |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
692 #if $data_input.isotop_prop_file: |
2
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
693 ln -s '$data_input.isotop_prop_file' data/isotop_prop.csv && |
0
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
694 #silent $impute_values['isotopologue_proportions']='min' |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
695 #end if |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
696 #else |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
697 #if $data_input.isotop_abs_file: |
2
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
698 ln -s '$data_input.isotop_abs_file' data/isotop_abs.csv && |
0
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
699 #silent $impute_values['isotopologues']='min' |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
700 #end if |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
701 #end if |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
702 ]]></token> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
703 <token name="@INIT_METABOLOGRAM@"><![CDATA[ |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
704 #import json |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
705 #import re |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
706 #import os |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
707 #import csv |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
708 #import subprocess |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
709 |
2
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
710 mkdir -p data && |
0
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
711 |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
712 #if $path_kegg_metabolites: |
2
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
713 ln -s '$path_kegg_metabolites' data/pathways_kegg_metabolites.csv && |
0
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
714 #end if |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
715 #if $path_kegg_transcripts: |
2
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
716 ln -s '$path_kegg_transcripts' data/pathways_kegg_transcripts.csv && |
0
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
717 #end if |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
718 |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
719 #if $metadata_path: |
2
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
720 ln -s '$metadata_path' data/metadata.csv && |
0
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
721 #end if |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
722 |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
723 #set $impute_values = {} |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
724 #if str( $data_input.data_input_selector ) == "abundance": |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
725 #if $data_input.abundance_file: |
2
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
726 ln -s '$data_input.abundance_file' data/abundance.csv && |
0
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
727 #silent $impute_values['abundances']='min' |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
728 #end if |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
729 #else: |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
730 #if $data_input.me_or_frac_contrib_file: |
2
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
731 ln -s '$data_input.me_or_frac_contrib_file' data/me_or_frac_contrib.csv && |
0
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
732 #silent $impute_values['mean_enrichment']='min' |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
733 #end if |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
734 #end if |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
735 |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
736 #for $i, $s in enumerate($deg_list) |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
737 #set $cpt = str($i+1) |
2
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
738 ln -s '${s.input}' data/DEG_comparison'${cpt}'.csv && |
0
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
739 #end for |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
740 |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
741 |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
742 ]]></token> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
743 <token name="@INIT_DIFF_MULTIGROUP_ANALYSIS@"><![CDATA[ |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
744 |
2
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
745 mkdir -p data && |
0
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
746 |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
747 #if $metadata_path: |
2
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
748 ln -s '$metadata_path' data/metadata.csv && |
0
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
749 #end if |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
750 |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
751 #set $impute_values = {} |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
752 #if str( $data_input.data_input_selector ) == "abundance": |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
753 #if $data_input.abundance_file: |
2
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
754 ln -s '$data_input.abundance_file' data/abundance.csv && |
0
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
755 #silent $impute_values['abundances']='min' |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
756 #end if |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
757 #elif str( $data_input.data_input_selector ) == "mean_enrichment": |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
758 #if $data_input.me_or_frac_contrib_file: |
2
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
759 ln -s '$data_input.me_or_frac_contrib_file' data/me_or_frac_contrib.csv && |
0
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
760 #silent $impute_values['mean_enrichment']='min' |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
761 #end if |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
762 #elif str( $data_input.data_input_selector ) == "isotop_prop": |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
763 #if $data_input.isotop_prop_file: |
2
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
764 ln -s '$data_input.isotop_prop_file' data/isotop_prop.csv && |
0
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
765 #silent $impute_values['isotopologue_proportions']='min' |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
766 #end if |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
767 #else |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
768 #if $data_input.isotop_abs_file: |
2
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
769 ln -s '$data_input.isotop_abs_file' data/isotop_abs.csv && |
0
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
770 #silent $impute_values['isotopologues']='min' |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
771 #end if |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
772 #end if |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
773 ]]></token> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
774 <token name="@INIT_IMPUTE_VALUES@"><![CDATA[ |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
775 #import re |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
776 #set $impute_values = {} |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
777 #if $abundance_file: |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
778 #silent $impute_values['abundances']='min' |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
779 #end if |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
780 #if $me_or_frac_contrib_file: |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
781 #silent $impute_values['mean_enrichment']='min' |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
782 #end if |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
783 ]]></token> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
784 <token name="@INIT_DATATYPES@"><![CDATA[ |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
785 #import re |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
786 #set $datatypes_avail = list() |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
787 #if str( $data_input.data_input_selector ) == "abundance": |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
788 #if $data_input.abundance_file: |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
789 $datatypes_avail.append(re.sub('"', '', "abundances")) |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
790 #end if |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
791 #elif str( $data_input.data_input_selector ) == "mean_enrichment": |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
792 #if $data_input.me_or_frac_contrib_file: |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
793 $datatypes_avail.append(re.sub('"', '', "mean_enrichment")) |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
794 #end if |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
795 #elif str( $data_input.data_input_selector ) == "isotop_prop": |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
796 #if $data_input.isotop_prop_file: |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
797 $datatypes_avail.append(re.sub('"', '', "isotopologue_proportions")) |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
798 #end if |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
799 #else |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
800 #if $data_input.isotop_abs_file: |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
801 $datatypes_avail.append(re.sub('"', '', "isotopologues")) |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
802 #end if |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
803 #end if |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
804 ]]></token> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
805 <token name="@INIT_STAT_TEST@"><![CDATA[ |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
806 #import re |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
807 #set $statistical_test = {} |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
808 #if str( $data_input.data_input_selector ) == "abundance": |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
809 #if $data_input.abundance_file: |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
810 #silent $statistical_test['abundances']=str($data_input.stat_test) |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
811 #end if |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
812 #elif str( $data_input.data_input_selector ) == "mean_enrichment": |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
813 #if $data_input.me_or_frac_contrib_file: |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
814 #silent $statistical_test['mean_enrichment']=str($data_input.stat_test) |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
815 #end if |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
816 #elif str( $data_input.data_input_selector ) == "isotop_prop": |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
817 #if $data_input.isotop_prop_file: |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
818 #silent $statistical_test['isotopologue_proportions']=str($data_input.stat_test) |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
819 #end if |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
820 #else |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
821 #if $data_input.isotop_abs_file: |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
822 #silent $statistical_test['isotopologues']=str($data_input.stat_test) |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
823 #end if |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
824 #end if |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
825 ]]></token> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
826 <token name="@INIT_CONDITIONS@"><![CDATA[ |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
827 #import re |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
828 #set $conds = list() |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
829 #for $co in $conditions: |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
830 $conds.append(re.sub('"', '', str($co))) |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
831 #end for |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
832 ]]></token> |
2
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
833 <token name="@INIT_PLOT_CONDITIONS@"><![CDATA[ |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
834 #set $conditions = list() |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
835 #for $i, $s in enumerate($plot_factor_list) |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
836 #set $cpt = str($i+1) |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
837 $conditions.append(re.sub('"', '', str($s.condition))) |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
838 #end for |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
839 ]]></token> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
840 <token name="@INIT_ABUNDANCE_PLOT_CONDITIONS@"><![CDATA[ |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
841 #set $conditions = list() |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
842 #for $i, $s in enumerate($plot_abundance_factor_list) |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
843 #set $cpt = str($i+1) |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
844 $conditions.append(re.sub('"', '', str($s.condition))) |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
845 #end for |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
846 ]]></token> |
0
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
847 <token name="@INIT_TIMEPOINTS@"><![CDATA[ |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
848 |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
849 #import re |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
850 #set $timepoints = list() |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
851 #for $tp in $timepoint: |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
852 $timepoints.append(re.sub('"', '', str($tp))) |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
853 #end for |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
854 ]]></token> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
855 <token name="@INIT_GROUPS@"><![CDATA[ |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
856 #import re |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
857 #set $groups = list() |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
858 $groups.append(re.sub('"', '', str("condition"))) |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
859 $groups.append(re.sub('"', '', str("timepoint"))) |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
860 |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
861 ]]></token> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
862 <token name="@INIT_ENRICHMENT_METABOLITES@"><![CDATA[ |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
863 #import json |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
864 #import re |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
865 #set $metabolites = {} |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
866 #for $cp in $compartments: |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
867 #silent $metabolites[re.sub('"', '', str($cp))]=list() |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
868 #for $met in $metabolites_list: |
2
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
869 #set tmp_met=re.sub('\,', '%%',str($met)) |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
870 #set tmp_met_bis=str(re.split('_m', str($tmp_met))[0]) |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
871 #set tmp_met_ter=re.sub('%%', '\,',str($tmp_met_bis)) |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
872 $metabolites[re.sub('"', '', str($cp))].append(re.sub('"', '\'', str(tmp_met_ter))) |
0
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
873 #end for |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
874 #end for |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
875 ]]></token> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
876 <token name="@INIT_ISOTOPOLOGUE_METABOLITES@"><![CDATA[ |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
877 #set $metabolites = {} |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
878 #for $cp in $compartments: |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
879 #silent $metabolites[re.sub('"', '', str($cp))]=list() |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
880 #for $met in $metabolites_list: |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
881 #set tmp_met=re.sub('\,', '--',str($met)) |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
882 #set tmp_met_bis=str(re.split('_m', str($tmp_met))[0]) |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
883 #set tmp_met_ter=re.sub('--', '\,',str($tmp_met_bis)) |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
884 $metabolites[re.sub('"', '', str($cp))].append(re.sub('"', '\'', str(tmp_met_ter))) |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
885 #end for |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
886 #end for |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
887 ]]></token> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
888 <token name="@INIT_MULTIGROUP_COMPARISONS@"><![CDATA[ |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
889 #set $comparisons = list() |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
890 #for $tp in $timepoint: |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
891 #set $ctrl_found=False |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
892 #set $ctrl="" |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
893 |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
894 #for $co in $conditions: |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
895 #set $sub_comparisons = list() |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
896 #if str($co) in ["Control", "control","ctrl"]: |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
897 #set $ctrl_found=True |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
898 #set $ctrl=str($co) |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
899 $sub_comparisons.append(re.sub('"', '', str($co))) |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
900 $sub_comparisons.append(re.sub('"', '', str($tp))) |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
901 #else: |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
902 $sub_comparisons.append(re.sub('"', '', str($co))) |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
903 $sub_comparisons.append(re.sub('"', '', str($tp))) |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
904 |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
905 #end if |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
906 $comparisons.append($sub_comparisons) |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
907 #end for |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
908 #end for |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
909 ]]></token> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
910 <token name="@INIT_CONDITIONS_TIMECOURSE@"><![CDATA[ |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
911 #import re |
2
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
912 #set $conditions = list() |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
913 #for $i, $s in enumerate($factor_list) |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
914 #set $cpt = str($i+1) |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
915 $conditions.append(re.sub('"', '', str($s.condition))) |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
916 #end for |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
917 |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
918 ]]></token> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
919 <token name="@INIT_BIVAR_COMPARISONS@"><![CDATA[ |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
920 #import re |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
921 #set $conditions = list() |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
922 #for $i, $s in enumerate($plot_factor_list) |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
923 #set $cpt = str($i+1) |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
924 $conditions.append(re.sub('"', '', str($s.condition))) |
0
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
925 #end for |
2
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
926 ]]></token> |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
927 <token name="@INIT_COMPARISONS_METABOLOGRAM@"><![CDATA[ |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
928 #import re |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
929 #set $conditions = list() |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
930 #set $timepoints = list() |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
931 #set $comparisons = list() |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
932 #for $i, $s in enumerate($deg_list) |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
933 #set $cpt = str($i+1) |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
934 #set $comparisons_bis = list() |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
935 #for $j, $t in enumerate($s.factor_list) |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
936 #set $sub_comparisons = list() |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
937 #if str($t.condition) not in $conditions: |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
938 $conditions.append(re.sub('"', '', str($t.condition))) |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
939 #end if |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
940 $sub_comparisons.append(re.sub('"', '', str($t.condition))) |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
941 $sub_comparisons.append(re.sub('"', '', str($s.timepoint))) |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
942 $comparisons_bis.append($sub_comparisons) |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
943 #end for |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
944 $timepoints.append(re.sub('"', '', str($s.timepoint))) |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
945 $comparisons.append($comparisons_bis) |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
946 #end for |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
947 |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
948 |
0
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
949 |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
950 ]]></token> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
951 <token name="@INIT_COMPARISONS@"><![CDATA[ |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
952 #import re |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
953 #set $conds = list() |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
954 #for $co in $conditions: |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
955 $conds.append(re.sub('"', '', str($co))) |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
956 #end for |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
957 #set $timepoints = list() |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
958 #for $tp in $timepoint: |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
959 $timepoints.append(re.sub('"', '', str($tp))) |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
960 #end for |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
961 |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
962 #set $comparisons = list() |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
963 #if len($conds) > 1: |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
964 #if len($timepoints) > 0: |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
965 #for $tp in $timepoint: |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
966 #set $ctrl_found=False |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
967 #set $ctrl="" |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
968 #set $comparisons_bis = list() |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
969 #for $co in $conditions: |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
970 #set $sub_comparisons = list() |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
971 #if str($co) in ["'Control'", "'control'", "'ctrl'"]: |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
972 #set $ctrl_found=True |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
973 #set $ctrl=str($co) |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
974 #else: |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
975 $sub_comparisons.append(re.sub('"', '', str($co))) |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
976 $sub_comparisons.append(re.sub('"', '', str($tp))) |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
977 |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
978 #end if |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
979 $comparisons_bis.append($sub_comparisons) |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
980 #end for |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
981 |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
982 #if $ctrl_found: |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
983 $sub_comparisons.append(str($ctrl)) |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
984 $sub_comparisons.append(str($tp)) |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
985 $comparisons_bis.append($sub_comparisons) |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
986 #end if |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
987 |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
988 $comparisons.append($comparisons_bis) |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
989 #end for |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
990 #else |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
991 #for $co in $conditions: |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
992 $comparisons.append(re.sub('"', '', str($co))) |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
993 #end for |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
994 #end if |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
995 |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
996 #else |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
997 #if len($conds) > 0: |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
998 #if len($timepoints) > 1: |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
999 #for $co in $conditions: |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
1000 #set $comparisons_bis = list() |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
1001 #for $tp in $timepoint: |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
1002 #set $sub_comparisons = list() |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
1003 $sub_comparisons.append(re.sub('"', '', str($co))) |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
1004 $sub_comparisons.append(re.sub('"', '', str($tp))) |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
1005 $comparisons_bis.append($sub_comparisons) |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
1006 #end for |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
1007 $comparisons.append($comparisons_bis) |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
1008 #end for |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
1009 #end if |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
1010 #else |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
1011 #for $tp in $timepoint: |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
1012 $comparisons.append(re.sub('"', '', str($tp))) |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
1013 #end for |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
1014 #end if |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
1015 #end if |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
1016 ]]></token> |
2
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1017 <token name="@INIT_DIFF_ANALYSIS_COMPARISONS@"><![CDATA[ |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1018 #import re |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1019 #set $conditions = list() |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1020 #for $i, $s in enumerate($factor_list) |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1021 #set $cpt = str($i+1) |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1022 $conditions.append(re.sub('"', '', str($s.condition))) |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1023 #end for |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1024 |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1025 #set $timepoints = list() |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1026 #for $tp in $timepoint: |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1027 $timepoints.append(re.sub('"', '', str($tp))) |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1028 #end for |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1029 |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1030 #set $comparisons = list() |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1031 #if len($conditions) > 1: |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1032 #if len($timepoints) > 0: |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1033 #for $tp in $timepoint: |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1034 #set $ctrl_found=False |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1035 #set $ctrl="" |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1036 #set $comparisons_bis = list() |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1037 |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1038 #for $co in $conditions: |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1039 #set $sub_comparisons = list() |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1040 #if str($co) in ["'Control'", "'control'", "'ctrl'"]: |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1041 #set $ctrl_found=True |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1042 #set $ctrl=str($co) |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1043 #else: |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1044 $sub_comparisons.append(re.sub('"', '', str($co))) |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1045 $sub_comparisons.append(re.sub('"', '', str($tp))) |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1046 |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1047 #end if |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1048 $comparisons_bis.append($sub_comparisons) |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1049 #end for |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1050 |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1051 #if $ctrl_found: |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1052 $sub_comparisons.append(str($ctrl)) |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1053 $sub_comparisons.append(str($tp)) |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1054 $comparisons_bis.append($sub_comparisons) |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1055 #end if |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1056 |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1057 $comparisons.append($comparisons_bis) |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1058 #end for |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1059 #else |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1060 #for $co in $conditions: |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1061 $comparisons.append(re.sub('"', '', str($co))) |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1062 #end for |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1063 #end if |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1064 |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1065 #else |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1066 #if len($conditions) > 0: |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1067 #if len($timepoints) > 1: |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
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parents:
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1068 #for $co in $conditions: |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
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parents:
1
diff
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1069 #set $comparisons_bis = list() |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
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1070 #for $tp in $timepoint: |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
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1071 #set $sub_comparisons = list() |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
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1072 $sub_comparisons.append(re.sub('"', '', str($co))) |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
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1073 $sub_comparisons.append(re.sub('"', '', str($tp))) |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
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diff
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|
1074 $comparisons_bis.append($sub_comparisons) |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
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diff
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1075 #end for |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
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1076 $comparisons.append($comparisons_bis) |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
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1077 #end for |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
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1078 #end if |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
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1079 #else |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
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1080 #for $tp in $timepoint: |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
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1081 $comparisons.append(re.sub('"', '', str($tp))) |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
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1082 #end for |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1083 #end if |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
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1084 #end if |
1df18470e3d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
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1085 ]]></token> |
0
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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parents:
diff
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|
1086 <token name="@INIT_TRANSCRIPTS@"><![CDATA[ |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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1087 #import re |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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1088 #import os |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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1089 #import subprocess |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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1090 #set $transcripts = list() |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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1091 |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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1092 #for $i, $s in enumerate($deg_list) |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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1093 #set $cpt = str($i+1) |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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1094 $transcripts.append(re.sub('"', '', "DEG_comparison"+str($i+1))) |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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1095 #set $deg_one_values = os.fsdecode(subprocess.check_output('head -n1 ' + str($s.input) + '| cut -f' + str($s.valuecol), shell=True)) |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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1096 #set $deg_one_id = os.fsdecode(subprocess.check_output('head -n1 ' + str($s.input) + '| cut -f' + str($s.idcol), shell=True)) |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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1097 #end for |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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1098 ]]></token> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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1099 <token name="@INIT_PATHWAYS@"><![CDATA[ |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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1100 #set $pathways = {} |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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1101 #if $path_kegg_metabolites: |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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1102 #silent $pathways['metabolites']='pathways_kegg_metabolites' |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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parents:
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1103 #end if |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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1104 #if $path_kegg_transcripts: |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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1105 #silent $pathways['transcripts']='pathways_kegg_transcripts' |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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1106 #end if |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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1107 ]]></token> |
c9040bdb918c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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1108 </macros> |