Mercurial > repos > iuc > dimet_pca_analysis
annotate macros.xml @ 3:04c26050d2d0 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 0e7c185547d51ec3fc8ff2d87ac7e2b6d9ae0b0f
author | iuc |
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date | Mon, 04 Mar 2024 19:58:22 +0000 |
parents | c0103ea608fc |
children | 3b9226db8ab6 |
rev | line source |
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04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
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1 <macros> |
3
04c26050d2d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 0e7c185547d51ec3fc8ff2d87ac7e2b6d9ae0b0f
iuc
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2 <token name="@TOOL_VERSION@">0.2.2</token> |
1
a01453baaf5e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 7568e92bfc4560d6e0287e7444455f55c86d135d
iuc
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0
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3 <token name="@VERSION_SUFFIX@">1</token> |
0
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
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4 <token name="@EXECUTABLE@">pca</token> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
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5 <xml name="requirements"> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
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6 <requirements> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
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7 <requirement type="package" version="@TOOL_VERSION@">dimet</requirement> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
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8 </requirements> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
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9 </xml> |
2
c0103ea608fc
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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10 <xml name="statistical_test_for_multigroup"> |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
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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"> |
c0103ea608fc
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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12 <option value="KW">Kruskal-Wallis</option> |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
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13 </param> |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
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14 </xml> |
0
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
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15 <xml name="statistical_test"> |
2
c0103ea608fc
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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16 <conditional name="statistics"> |
c0103ea608fc
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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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"> |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
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18 <option value="parametric">parametric</option> |
c0103ea608fc
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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19 <option value="non-parametric-rank" selected="true">non-parametric (rank based)</option> |
c0103ea608fc
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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20 <option value="non-parametric-distribution">non-parametric (distribution based)</option> |
c0103ea608fc
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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21 </param> |
c0103ea608fc
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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22 <when value="parametric"> |
c0103ea608fc
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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23 <param name="stat_test" type="select" display="radio" label="Select statistical to apply" help="Please enter at max 1 statistical test by file"> |
c0103ea608fc
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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24 <option value="Tt" selected="true">t-test</option> |
c0103ea608fc
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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25 </param> |
c0103ea608fc
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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26 </when> |
c0103ea608fc
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"> |
c0103ea608fc
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"> |
c0103ea608fc
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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29 <option value="MW">Mann Whitney</option> |
c0103ea608fc
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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30 <option value="KW">Kruskal-Wallis</option> |
c0103ea608fc
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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31 <option value="ranksum" selected="true">Wilcoxon's rank sum test</option> |
c0103ea608fc
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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32 <option value="Wcox">Wilcoxon signed-rank test</option> |
c0103ea608fc
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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33 <option value="BrMu">Brunner-Munzel test</option> |
c0103ea608fc
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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34 </param> |
c0103ea608fc
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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35 </when> |
c0103ea608fc
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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36 <when value="non-parametric-distribution"> |
c0103ea608fc
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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37 <param name="stat_test" type="select" display="radio" label="Select statistical to apply" help="Please enter at max 1 statistical test by file"> |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
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38 <option value="prm-scipy" selected="true">permutations test</option> |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
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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> |
c0103ea608fc
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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40 </param> |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
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41 </when> |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
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42 </conditional> |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
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43 |
0
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
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44 </xml> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
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45 <xml name="citations"> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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46 <citations> |
04d213632103
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"> |
04d213632103
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, |
04d213632103
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}, |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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50 license = {MIT}, |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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51 title = {{DIMet}}, |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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52 url = {https://github.com/cbib/DIMet} |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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53 } |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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54 |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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55 </citation> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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56 </citations> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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57 |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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58 </xml> |
04d213632103
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"> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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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."/> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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61 </xml> |
04d213632103
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"> |
04d213632103
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)"/> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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64 </xml> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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65 <xml name="enrichment_file_macros"> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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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)"/> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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67 </xml> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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68 <xml name="isotopologue_prop_file_macros"> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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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)."/> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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70 </xml> |
04d213632103
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"> |
04d213632103
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)."/> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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73 </xml> |
04d213632103
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"> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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75 <expand macro="abundance_file_macros"/> |
04d213632103
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"/> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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77 <expand macro="metadata_file_macros"/> |
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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"/> |
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81 <expand macro="metadata_file_macros"/> |
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82 </xml> |
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83 <xml name="input_parameters_enrichment"> |
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84 <expand macro="enrichment_file_macros"/> |
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85 <expand macro="metadata_file_macros"/> |
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86 </xml> |
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87 <xml name="input_parameters_isotopologue"> |
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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" |
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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"/> |
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105 <filter type="unique_value" name="metabolite_or_isotopologue" column="0"/> |
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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" |
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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> |
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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> |
c0103ea608fc
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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"> |
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159 <expand macro="enrichment_file_macros"/> |
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160 </when> |
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161 <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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162 <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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163 </when> |
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164 <when value="isotop_abs"> |
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165 <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
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166 </when> |
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167 </conditional> |
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168 <expand macro="metadata_file_macros"/> |
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169 </xml> |
0
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170 <xml name="input_parameters_diff_analysis"> |
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171 <conditional name="data_input"> |
2
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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
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173 <option value="abundance" selected="True">abundance</option> |
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174 <option value="mean_enrichment">mean_enrichment</option> |
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175 <option value="isotop_prop">isotop_prop</option> |
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176 <option value="isotop_abs">isotop_abs</option> |
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177 </param> |
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178 <when value="abundance"> |
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179 <expand macro="abundance_file_macros"/> |
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180 <expand macro="statistical_test"/> |
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181 |
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182 </when> |
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183 <when value="mean_enrichment"> |
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184 <expand macro="enrichment_file_macros"/> |
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185 <expand macro="statistical_test"/> |
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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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189 <expand macro="statistical_test"/> |
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190 </when> |
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191 <when value="isotop_abs"> |
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192 <expand macro="isotopologue_abs_file_macros"/> |
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193 <expand macro="statistical_test"/> |
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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> |
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198 <xml name="input_parameters_multi_diff_analysis"> |
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199 <conditional name="data_input"> |
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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"> |
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201 <option value="abundance" selected="True">abundance</option> |
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202 <option value="mean_enrichment">mean_enrichment</option> |
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203 <option value="isotop_prop">isotop_prop</option> |
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204 <option value="isotop_abs">isotop_abs</option> |
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205 </param> |
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206 <when value="abundance"> |
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207 <expand macro="abundance_file_macros"/> |
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208 <expand macro="statistical_test_for_multigroup"/> |
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209 |
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210 </when> |
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211 <when value="mean_enrichment"> |
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212 <expand macro="enrichment_file_macros"/> |
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213 <expand macro="statistical_test_for_multigroup"/> |
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214 </when> |
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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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218 </when> |
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219 <when value="isotop_abs"> |
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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
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221 <expand macro="statistical_test_for_multigroup"/> |
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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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225 </xml> |
0
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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"> |
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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
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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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240 <filter type="unique_value" name="condition" column="condition"/> |
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241 <filter type="remove_value" value="condition"/> |
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242 </options> |
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243 <sanitizer> |
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244 <valid initial="default"> |
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245 <add preset="string.printable"/> |
04d213632103
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"/> |
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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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247 <remove value="""/> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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248 <remove value="'"/> |
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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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249 </valid> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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250 </sanitizer> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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251 </param> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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252 </xml> |
04d213632103
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"> |
04d213632103
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"> |
04d213632103
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"> |
04d213632103
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"/> |
04d213632103
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"/> |
04d213632103
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"/> |
04d213632103
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"/> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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260 </options> |
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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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261 <sanitizer> |
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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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262 <valid initial="default"> |
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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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263 <add preset="string.printable"/> |
04d213632103
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"/> |
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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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265 <remove value="""/> |
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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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266 <remove value="'"/> |
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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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267 </valid> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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268 </sanitizer> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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269 </param> |
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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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270 </xml> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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271 <xml name="timepoint_multigroup"> |
04d213632103
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"> |
04d213632103
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"> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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274 <column name="timepoint" index="2"/> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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275 <column name="value" index="2"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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276 <filter type="unique_value" name="timepoint" column="2"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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277 <filter type="remove_value" value="timepoint"/> |
04d213632103
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"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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279 </options> |
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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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280 <sanitizer> |
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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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281 <valid initial="default"> |
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282 <add preset="string.printable"/> |
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283 <add value="\t"/> |
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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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284 <remove value="""/> |
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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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285 <remove value="'"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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286 </valid> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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287 </sanitizer> |
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288 </param> |
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289 </xml> |
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290 <xml name="timepoint"> |
2
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
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291 <param name="timepoint" type="select" optional="false" multiple="true" label="Browse timepoint from metadata file (1 min.)"> |
0
04d213632103
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292 <options from_dataset="metadata_path"> |
04d213632103
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293 <column name="timepoint" index="2"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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294 <column name="value" index="2"/> |
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iuc
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295 <filter type="unique_value" name="timepoint" column="2"/> |
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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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296 <filter type="remove_value" value="timepoint"/> |
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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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297 <filter type="sort_by" name="timepoint" column="1"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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298 </options> |
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299 <sanitizer> |
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iuc
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300 <valid initial="default"> |
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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"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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302 <add value="\t"/> |
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iuc
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303 <remove value="""/> |
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304 <remove value="'"/> |
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305 </valid> |
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306 </sanitizer> |
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307 </param> |
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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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308 </xml> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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309 <xml name="grouping"> |
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310 <param name="grouping" type="select" optional="false" multiple="true" label="Browse group to compare"> |
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311 <option value="condition" selected="true">condition</option> |
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312 <option value="timepoint" selected="true">timepoint</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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313 </param> |
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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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314 </xml> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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315 <xml name="correction_method"> |
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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"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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317 <option value="bonferroni">bonferroni</option> |
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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> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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319 <option value="holm">holm</option> |
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iuc
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320 <option value="simes-hochberg">simes-hochberg</option> |
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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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321 <option value="hommel">hommel</option> |
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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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322 <option value="fdr_bh">fdr_bh</option> |
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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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323 <option value="fdr_by">fdr_by</option> |
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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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324 <option value="fdr_tsbh">fdr_tsbh</option> |
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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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325 <option value="fdr_tsbky">fdr_tsbky</option> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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326 </param> |
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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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327 </xml> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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328 <xml name="compartments_enrichment"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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329 <param name="compartments" type="select" optional="false" multiple="true" |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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330 label="Browse compartments from metadata file (All needed). You have to load a metadata file prior to have access to compartments"> |
04d213632103
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"> |
04d213632103
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"/> |
04d213632103
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"/> |
04d213632103
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"/> |
04d213632103
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"/> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
336 </options> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
337 <sanitizer> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
338 <valid initial="default"> |
04d213632103
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"/> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
340 <add value="\t"/> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
341 <remove value="""/> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
342 <remove value="'"/> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
343 </valid> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
344 </sanitizer> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
345 </param> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
346 </xml> |
04d213632103
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"> |
04d213632103
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" |
04d213632103
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"> |
04d213632103
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"> |
04d213632103
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"/> |
04d213632103
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"/> |
04d213632103
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"/> |
04d213632103
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"/> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
355 </options> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
356 <sanitizer> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
357 <valid initial="default"> |
04d213632103
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"/> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
359 <add value="\t"/> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
360 <remove value="""/> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
361 <remove value="'"/> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
362 </valid> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
363 </sanitizer> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
364 </param> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
365 </xml> |
2
c0103ea608fc
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"> |
c0103ea608fc
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" |
c0103ea608fc
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"> |
c0103ea608fc
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"> |
c0103ea608fc
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"/> |
c0103ea608fc
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"/> |
c0103ea608fc
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"/> |
c0103ea608fc
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"/> |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
374 </options> |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
375 <sanitizer> |
c0103ea608fc
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"> |
c0103ea608fc
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"/> |
c0103ea608fc
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"/> |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
379 <remove value="""/> |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
380 <remove value="'"/> |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
381 </valid> |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
382 </sanitizer> |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
383 </param> |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
384 </xml> |
0
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
385 <xml name="compartments"> |
04d213632103
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" |
04d213632103
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"> |
04d213632103
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"> |
04d213632103
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"/> |
04d213632103
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"/> |
04d213632103
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"/> |
04d213632103
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"/> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
393 </options> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
394 <sanitizer> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
395 <valid initial="default"> |
04d213632103
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"/> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
397 <add value="\t"/> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
398 <remove value="""/> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
399 <remove value="'"/> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
400 </valid> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
401 </sanitizer> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
402 </param> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
403 </xml> |
04d213632103
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"> |
04d213632103
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
c0103ea608fc
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
04d213632103
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"/> |
04d213632103
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"> |
04d213632103
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"/> |
04d213632103
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"/> |
04d213632103
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"/> |
04d213632103
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"/> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
413 </options> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
414 <sanitizer> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
415 <valid initial="default"> |
04d213632103
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"/> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
417 <add value="\t"/> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
418 <remove value="""/> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
419 <remove value="'"/> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
420 </valid> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
421 </sanitizer> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
422 </param> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
423 </xml> |
04d213632103
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"> |
04d213632103
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
c0103ea608fc
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"> |
c0103ea608fc
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
04d213632103
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"> |
04d213632103
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"/> |
04d213632103
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"/> |
04d213632103
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"/> |
04d213632103
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"/> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
433 </options> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
434 <sanitizer> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
435 <valid initial="default"> |
04d213632103
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"/> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
437 <add value="\t"/> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
438 <remove value="""/> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
439 <remove value="'"/> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
440 </valid> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
441 </sanitizer> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
442 </param> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
443 </xml> |
04d213632103
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"> |
04d213632103
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" |
04d213632103
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
c0103ea608fc
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
04d213632103
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"> |
04d213632103
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"/> |
04d213632103
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"/> |
04d213632103
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"/> |
04d213632103
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"/> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
453 </options> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
454 <sanitizer> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
455 <valid initial="default"> |
04d213632103
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"/> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
457 <add value="\t"/> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
458 <remove value="""/> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
459 <remove value="'"/> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
460 </valid> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
461 </sanitizer> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
462 </param> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
463 </xml> |
04d213632103
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
c0103ea608fc
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
04d213632103
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"/> |
04d213632103
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"/> |
04d213632103
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
c0103ea608fc
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.)"> |
c0103ea608fc
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"> |
c0103ea608fc
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"/> |
c0103ea608fc
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"/> |
c0103ea608fc
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"/> |
c0103ea608fc
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"/> |
c0103ea608fc
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"/> |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
476 </options> |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
477 <sanitizer> |
c0103ea608fc
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"> |
c0103ea608fc
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"/> |
c0103ea608fc
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"/> |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
481 <remove value="""/> |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
482 <remove value="'"/> |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
483 </valid> |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
484 </sanitizer> |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
485 </param> |
c0103ea608fc
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"> |
c0103ea608fc
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"> |
c0103ea608fc
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"> |
c0103ea608fc
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"/> |
c0103ea608fc
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"/> |
c0103ea608fc
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"/> |
c0103ea608fc
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"/> |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
493 </options> |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
494 <sanitizer> |
c0103ea608fc
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"> |
c0103ea608fc
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"/> |
c0103ea608fc
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"/> |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
498 <remove value="""/> |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
499 <remove value="'"/> |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
500 </valid> |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
501 </sanitizer> |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
502 </param> |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
503 </repeat> |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
504 |
0
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
505 </repeat> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
506 </xml> |
2
c0103ea608fc
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"> |
c0103ea608fc
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"> |
c0103ea608fc
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"> |
c0103ea608fc
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"> |
c0103ea608fc
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"/> |
c0103ea608fc
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"/> |
c0103ea608fc
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"/> |
c0103ea608fc
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"/> |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
515 </options> |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
516 <sanitizer> |
c0103ea608fc
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"> |
c0103ea608fc
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"/> |
c0103ea608fc
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"/> |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
520 <remove value="""/> |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
521 <remove value="'"/> |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
522 </valid> |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
523 </sanitizer> |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
524 </param> |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
525 </repeat> |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
526 </xml> |
c0103ea608fc
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"> |
c0103ea608fc
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"> |
c0103ea608fc
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"> |
c0103ea608fc
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"> |
c0103ea608fc
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"/> |
c0103ea608fc
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"/> |
c0103ea608fc
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"/> |
c0103ea608fc
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"/> |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
535 </options> |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
536 <sanitizer> |
c0103ea608fc
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"> |
c0103ea608fc
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"/> |
c0103ea608fc
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"/> |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
540 <remove value="""/> |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
541 <remove value="'"/> |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
542 </valid> |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
543 </sanitizer> |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
544 </param> |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
545 </repeat> |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
546 </xml> |
c0103ea608fc
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"> |
c0103ea608fc
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"> |
c0103ea608fc
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"> |
c0103ea608fc
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"> |
c0103ea608fc
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"/> |
c0103ea608fc
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"/> |
c0103ea608fc
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"/> |
c0103ea608fc
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"/> |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
555 </options> |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
556 <sanitizer> |
c0103ea608fc
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"> |
c0103ea608fc
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"/> |
c0103ea608fc
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"/> |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
560 <remove value="""/> |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
561 <remove value="'"/> |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
562 </valid> |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
563 </sanitizer> |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
564 </param> |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
565 </repeat> |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
566 </xml> |
c0103ea608fc
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"> |
c0103ea608fc
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"> |
c0103ea608fc
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> |
c0103ea608fc
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> |
c0103ea608fc
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> |
c0103ea608fc
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> |
c0103ea608fc
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> |
c0103ea608fc
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> |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
575 </param> |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
576 </xml> |
0
04d213632103
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[ |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
578 #import json |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
579 #import re |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
580 |
2
c0103ea608fc
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
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
582 |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
583 #if $metadata_path: |
2
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
584 ln -s '$metadata_path' data/metadata.csv && |
0
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
585 #end if |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
586 #if $abundance_file: |
2
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
587 ln -s '$abundance_file' data/abundance.csv && |
0
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
588 #end if |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
589 #if $me_or_frac_contrib_file: |
2
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
590 ln -s '$me_or_frac_contrib_file' data/me_or_frac_contrib.csv && |
0
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
591 #end if |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
592 |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
593 ]]></token> |
04d213632103
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[ |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
595 mkdir -p '$__new_file_path__/config' && |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
596 touch '$__new_file_path__/config/config.yaml' && |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
597 ]]></token> |
04d213632103
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[ |
04d213632103
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' |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
600 ]]></token> |
04d213632103
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[ |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
602 |
2
c0103ea608fc
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
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
604 |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
605 #if $metadata_path: |
2
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
606 ln -s '$metadata_path' data/metadata.csv && |
0
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
607 #end if |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
608 #if $abundance_file: |
2
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
609 ln -s '$abundance_file' data/abundance.csv && |
0
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
610 #end if |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
611 ]]></token> |
04d213632103
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[ |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
613 |
2
c0103ea608fc
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
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
615 |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
616 #if $metadata_path: |
2
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
617 ln -s '$metadata_path' data/metadata.csv && |
0
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
618 #end if |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
619 #if $me_or_frac_contrib_file: |
2
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
620 ln -s '$me_or_frac_contrib_file' data/me_or_frac_contrib.csv && |
0
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
621 #end if |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
622 ]]></token> |
04d213632103
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[ |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
624 |
2
c0103ea608fc
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 && |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
626 |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
627 #if $metadata_path: |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
628 ln -s '$metadata_path' data/metadata.csv && |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
629 #end if |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
630 #if $isotop_prop_file: |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
631 ln -s '$isotop_prop_file' data/isotop_prop.csv && |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
632 #end if |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
633 ]]></token> |
c0103ea608fc
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[ |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
635 |
c0103ea608fc
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
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
637 |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
638 #if $metadata_path: |
2
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
639 ln -s '$metadata_path' data/metadata.csv && |
0
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
640 #end if |
2
c0103ea608fc
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 = {} |
c0103ea608fc
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' |
c0103ea608fc
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 = {} |
c0103ea608fc
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' |
c0103ea608fc
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 = {} |
c0103ea608fc
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' |
c0103ea608fc
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' |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
648 |
c0103ea608fc
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 = {} |
c0103ea608fc
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": |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
651 #if $data_input.abundance_file: |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
652 ln -s '$data_input.abundance_file' data/abundance.csv && |
c0103ea608fc
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' |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
654 #end if |
c0103ea608fc
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": |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
656 #if $data_input.me_or_frac_contrib_file: |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
657 ln -s '$data_input.me_or_frac_contrib_file' data/me_or_frac_contrib.csv && |
c0103ea608fc
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' |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
659 #end if |
c0103ea608fc
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": |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
661 #if $data_input.isotop_prop_file: |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
662 ln -s '$data_input.isotop_prop_file' data/isotop_prop.csv && |
c0103ea608fc
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' |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
664 #end if |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
665 #else |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
666 #if $data_input.isotop_abs_file: |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
667 ln -s '$data_input.isotop_abs_file' data/isotop_abs.csv && |
c0103ea608fc
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' |
c0103ea608fc
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
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
670 #end if |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
671 ]]></token> |
04d213632103
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[ |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
673 |
2
c0103ea608fc
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
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
675 |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
676 #if $metadata_path: |
2
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
677 ln -s '$metadata_path' data/metadata.csv && |
0
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
678 #end if |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
679 |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
680 #set $impute_values = {} |
04d213632103
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": |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
682 #if $data_input.abundance_file: |
2
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
683 ln -s '$data_input.abundance_file' data/abundance.csv && |
0
04d213632103
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' |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
685 #end if |
04d213632103
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": |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
687 #if $data_input.me_or_frac_contrib_file: |
2
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
688 ln -s '$data_input.me_or_frac_contrib_file' data/me_or_frac_contrib.csv && |
0
04d213632103
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' |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
690 #end if |
04d213632103
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": |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
692 #if $data_input.isotop_prop_file: |
2
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
693 ln -s '$data_input.isotop_prop_file' data/isotop_prop.csv && |
0
04d213632103
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' |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
695 #end if |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
696 #else |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
697 #if $data_input.isotop_abs_file: |
2
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
698 ln -s '$data_input.isotop_abs_file' data/isotop_abs.csv && |
0
04d213632103
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' |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
700 #end if |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
701 #end if |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
702 ]]></token> |
04d213632103
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[ |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
704 #import json |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
705 #import re |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
706 #import os |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
707 #import csv |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
708 #import subprocess |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
709 |
2
c0103ea608fc
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
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
711 |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
712 #if $path_kegg_metabolites: |
2
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
713 ln -s '$path_kegg_metabolites' data/pathways_kegg_metabolites.csv && |
0
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
714 #end if |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
715 #if $path_kegg_transcripts: |
2
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
716 ln -s '$path_kegg_transcripts' data/pathways_kegg_transcripts.csv && |
0
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
717 #end if |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
718 |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
719 #if $metadata_path: |
2
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
720 ln -s '$metadata_path' data/metadata.csv && |
0
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
721 #end if |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
722 |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
723 #set $impute_values = {} |
04d213632103
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": |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
725 #if $data_input.abundance_file: |
2
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
726 ln -s '$data_input.abundance_file' data/abundance.csv && |
0
04d213632103
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' |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
728 #end if |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
729 #else: |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
730 #if $data_input.me_or_frac_contrib_file: |
2
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
731 ln -s '$data_input.me_or_frac_contrib_file' data/me_or_frac_contrib.csv && |
0
04d213632103
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' |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
733 #end if |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
734 #end if |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
735 |
04d213632103
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) |
04d213632103
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
c0103ea608fc
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
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
739 #end for |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
740 |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
741 |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
742 ]]></token> |
04d213632103
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[ |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
744 |
2
c0103ea608fc
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
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
746 |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
747 #if $metadata_path: |
2
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
748 ln -s '$metadata_path' data/metadata.csv && |
0
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
749 #end if |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
750 |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
751 #set $impute_values = {} |
04d213632103
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": |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
753 #if $data_input.abundance_file: |
2
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
754 ln -s '$data_input.abundance_file' data/abundance.csv && |
0
04d213632103
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' |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
756 #end if |
04d213632103
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": |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
758 #if $data_input.me_or_frac_contrib_file: |
2
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
759 ln -s '$data_input.me_or_frac_contrib_file' data/me_or_frac_contrib.csv && |
0
04d213632103
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' |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
761 #end if |
04d213632103
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": |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
763 #if $data_input.isotop_prop_file: |
2
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
764 ln -s '$data_input.isotop_prop_file' data/isotop_prop.csv && |
0
04d213632103
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' |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
766 #end if |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
767 #else |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
768 #if $data_input.isotop_abs_file: |
2
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
769 ln -s '$data_input.isotop_abs_file' data/isotop_abs.csv && |
0
04d213632103
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' |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
771 #end if |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
772 #end if |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
773 ]]></token> |
04d213632103
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[ |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
775 #import re |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
776 #set $impute_values = {} |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
777 #if $abundance_file: |
04d213632103
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' |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
779 #end if |
04d213632103
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: |
04d213632103
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' |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
782 #end if |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
783 ]]></token> |
04d213632103
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[ |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
785 #import re |
04d213632103
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() |
04d213632103
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": |
04d213632103
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: |
04d213632103
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")) |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
790 #end if |
04d213632103
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": |
04d213632103
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: |
04d213632103
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")) |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
794 #end if |
04d213632103
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": |
04d213632103
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: |
04d213632103
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")) |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
798 #end if |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
799 #else |
04d213632103
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: |
04d213632103
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")) |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
802 #end if |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
803 #end if |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
804 ]]></token> |
04d213632103
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[ |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
806 #import re |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
807 #set $statistical_test = {} |
04d213632103
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": |
04d213632103
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: |
04d213632103
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) |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
811 #end if |
04d213632103
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": |
04d213632103
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: |
04d213632103
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) |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
815 #end if |
04d213632103
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": |
04d213632103
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: |
04d213632103
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) |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
819 #end if |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
820 #else |
04d213632103
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: |
04d213632103
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) |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
823 #end if |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
824 #end if |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
825 ]]></token> |
04d213632103
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[ |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
827 #import re |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
828 #set $conds = list() |
04d213632103
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: |
04d213632103
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))) |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
831 #end for |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
832 ]]></token> |
2
c0103ea608fc
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[ |
c0103ea608fc
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() |
c0103ea608fc
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) |
c0103ea608fc
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) |
c0103ea608fc
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))) |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
838 #end for |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
839 ]]></token> |
c0103ea608fc
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[ |
c0103ea608fc
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() |
c0103ea608fc
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) |
c0103ea608fc
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) |
c0103ea608fc
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))) |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
845 #end for |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
846 ]]></token> |
0
04d213632103
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[ |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
848 |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
849 #import re |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
850 #set $timepoints = list() |
04d213632103
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: |
04d213632103
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))) |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
853 #end for |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
854 ]]></token> |
04d213632103
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[ |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
856 #import re |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
857 #set $groups = list() |
04d213632103
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"))) |
04d213632103
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"))) |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
860 |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
861 ]]></token> |
04d213632103
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[ |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
863 #import json |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
864 #import re |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
865 #set $metabolites = {} |
04d213632103
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: |
04d213632103
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() |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
868 #for $met in $metabolites_list: |
2
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
869 #set tmp_met=re.sub('\,', '%%',str($met)) |
c0103ea608fc
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($tmp_met))[0]) |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
871 #set tmp_met_ter=re.sub('%%', '\,',str($tmp_met_bis)) |
c0103ea608fc
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
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
873 #end for |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
874 #end for |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
875 ]]></token> |
04d213632103
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[ |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
877 #set $metabolites = {} |
04d213632103
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: |
04d213632103
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() |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
880 #for $met in $metabolites_list: |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
881 #set tmp_met=re.sub('\,', '--',str($met)) |
04d213632103
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($tmp_met))[0]) |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
883 #set tmp_met_ter=re.sub('--', '\,',str($tmp_met_bis)) |
04d213632103
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))) |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
885 #end for |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
886 #end for |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
887 ]]></token> |
04d213632103
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[ |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
889 #set $comparisons = list() |
04d213632103
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: |
04d213632103
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 |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
892 #set $ctrl="" |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
893 |
04d213632103
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: |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
895 #set $sub_comparisons = list() |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
896 #if str($co) in ["Control", "control","ctrl"]: |
04d213632103
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 |
04d213632103
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) |
04d213632103
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))) |
04d213632103
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))) |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
901 #else: |
04d213632103
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))) |
04d213632103
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))) |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
904 |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
905 #end if |
04d213632103
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) |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
907 #end for |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
908 #end for |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
909 ]]></token> |
04d213632103
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[ |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
911 #import re |
2
c0103ea608fc
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() |
c0103ea608fc
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) |
c0103ea608fc
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) |
c0103ea608fc
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))) |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
916 #end for |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
917 |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
918 ]]></token> |
c0103ea608fc
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[ |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
920 #import re |
c0103ea608fc
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() |
c0103ea608fc
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) |
c0103ea608fc
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) |
c0103ea608fc
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
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
925 #end for |
2
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
926 ]]></token> |
c0103ea608fc
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[ |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
928 #import re |
c0103ea608fc
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() |
c0103ea608fc
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() |
c0103ea608fc
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() |
c0103ea608fc
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) |
c0103ea608fc
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) |
c0103ea608fc
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() |
c0103ea608fc
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) |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
936 #set $sub_comparisons = list() |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
937 #if str($t.condition) not in $conditions: |
c0103ea608fc
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))) |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
939 #end if |
c0103ea608fc
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))) |
c0103ea608fc
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))) |
c0103ea608fc
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) |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
943 #end for |
c0103ea608fc
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))) |
c0103ea608fc
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) |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
946 #end for |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
947 |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
948 |
0
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
949 |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
950 ]]></token> |
04d213632103
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[ |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
952 #import re |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
953 #set $conds = list() |
04d213632103
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: |
04d213632103
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))) |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
956 #end for |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
957 #set $timepoints = list() |
04d213632103
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: |
04d213632103
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))) |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
960 #end for |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
961 |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
962 #set $comparisons = list() |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
963 #if len($conds) > 1: |
04d213632103
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: |
04d213632103
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: |
04d213632103
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 |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
967 #set $ctrl="" |
04d213632103
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() |
04d213632103
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: |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
970 #set $sub_comparisons = list() |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
971 #if str($co) in ["'Control'", "'control'", "'ctrl'"]: |
04d213632103
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 |
04d213632103
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) |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
974 #else: |
04d213632103
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))) |
04d213632103
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))) |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
977 |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
978 #end if |
04d213632103
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) |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
980 #end for |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
981 |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
982 #if $ctrl_found: |
04d213632103
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)) |
04d213632103
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)) |
04d213632103
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) |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
986 #end if |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
987 |
04d213632103
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) |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
989 #end for |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
990 #else |
04d213632103
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: |
04d213632103
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))) |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
993 #end for |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
994 #end if |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
995 |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
996 #else |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
997 #if len($conds) > 0: |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
998 #if len($timepoints) > 1: |
04d213632103
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: |
04d213632103
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() |
04d213632103
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: |
04d213632103
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() |
04d213632103
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))) |
04d213632103
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))) |
04d213632103
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) |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
1006 #end for |
04d213632103
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) |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
1008 #end for |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
1009 #end if |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
1010 #else |
04d213632103
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: |
04d213632103
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))) |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
1013 #end for |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
1014 #end if |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
1015 #end if |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
1016 ]]></token> |
2
c0103ea608fc
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[ |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1018 #import re |
c0103ea608fc
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() |
c0103ea608fc
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) |
c0103ea608fc
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) |
c0103ea608fc
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))) |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1023 #end for |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1024 |
c0103ea608fc
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() |
c0103ea608fc
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: |
c0103ea608fc
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))) |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1028 #end for |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1029 |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1030 #set $comparisons = list() |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1031 #if len($conditions) > 1: |
c0103ea608fc
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: |
c0103ea608fc
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: |
c0103ea608fc
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 |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1035 #set $ctrl="" |
c0103ea608fc
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() |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1037 |
c0103ea608fc
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: |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1039 #set $sub_comparisons = list() |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1040 #if str($co) in ["'Control'", "'control'", "'ctrl'"]: |
c0103ea608fc
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 |
c0103ea608fc
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) |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1043 #else: |
c0103ea608fc
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))) |
c0103ea608fc
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))) |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1046 |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1047 #end if |
c0103ea608fc
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) |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1049 #end for |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1050 |
c0103ea608fc
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: |
c0103ea608fc
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)) |
c0103ea608fc
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)) |
c0103ea608fc
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) |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1055 #end if |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1056 |
c0103ea608fc
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) |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1058 #end for |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1059 #else |
c0103ea608fc
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: |
c0103ea608fc
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))) |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1062 #end for |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1063 #end if |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1064 |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1065 #else |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1066 #if len($conditions) > 0: |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1067 #if len($timepoints) > 1: |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1068 #for $co in $conditions: |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1069 #set $comparisons_bis = list() |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1070 #for $tp in $timepoint: |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1071 #set $sub_comparisons = list() |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1072 $sub_comparisons.append(re.sub('"', '', str($co))) |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1073 $sub_comparisons.append(re.sub('"', '', str($tp))) |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1074 $comparisons_bis.append($sub_comparisons) |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1075 #end for |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1076 $comparisons.append($comparisons_bis) |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1077 #end for |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1078 #end if |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1079 #else |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1080 #for $tp in $timepoint: |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1081 $comparisons.append(re.sub('"', '', str($tp))) |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1082 #end for |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1083 #end if |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1084 #end if |
c0103ea608fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents:
1
diff
changeset
|
1085 ]]></token> |
0
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
1086 <token name="@INIT_TRANSCRIPTS@"><![CDATA[ |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
1087 #import re |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
1088 #import os |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff
changeset
|
1089 #import subprocess |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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1090 #set $transcripts = list() |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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1091 |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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1092 #for $i, $s in enumerate($deg_list) |
04d213632103
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) |
04d213632103
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))) |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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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)) |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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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)) |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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1097 #end for |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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1098 ]]></token> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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1099 <token name="@INIT_PATHWAYS@"><![CDATA[ |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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1100 #set $pathways = {} |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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1101 #if $path_kegg_metabolites: |
04d213632103
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' |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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1103 #end if |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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1104 #if $path_kegg_transcripts: |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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1105 #silent $pathways['transcripts']='pathways_kegg_transcripts' |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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1106 #end if |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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1107 ]]></token> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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1108 </macros> |