Mercurial > repos > iuc > dimet_timecourse_analysis

annotate macros.xml @ 0:d9e56e80a153 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
author iuc
date Fri, 21 Jun 2024 18:45:52 +0000
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d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
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1 <macros>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
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2 <token name="@TOOL_VERSION@">0.2.4</token>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
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3 <token name="@VERSION_SUFFIX@">3</token>
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4 <xml name="requirements">
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5 <requirements>
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6 <requirement type="package" version="@TOOL_VERSION@">dimet</requirement>
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7 </requirements>
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8 </xml>
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9 <xml name="statistical_test_for_multigroup">
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10 <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">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
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11 <option value="KW">Kruskal-Wallis</option>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
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12 </param>
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13 </xml>
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14 <xml name="statistical_test_for_bivariate_analysis">
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15 <param name="stat_test" type="select" value="pearson" display="radio" label="Select statistical to apply" help="Please enter at max 1 statistical test by file">
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16 <option value="pearson">pearson</option>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
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17 <option value="spearman">spearman</option>
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18 </param>
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19 </xml>
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20 <xml name="statistical_test">
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21 <conditional name="statistics">
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22 <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">
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23 <option value="parametric">parametric</option>
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24 <option value="non-parametric-rank" selected="true">non-parametric (rank based)</option>
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25 <option value="non-parametric-distribution">non-parametric (distribution based)</option>
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26 </param>
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27 <when value="parametric">
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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">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
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29 <option value="Tt" selected="true">t-test</option>
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30 </param>
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31 </when>
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32 <when value="non-parametric-rank">
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33 <param name="stat_test" type="select" display="radio" label="Select statistical to apply" help="Please enter at max 1 statistical test by file">
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34 <option value="MW">Mann Whitney</option>
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35 <option value="KW">Kruskal-Wallis</option>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
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36 <option value="ranksum" selected="true">Wilcoxon's rank sum test</option>
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37 <option value="Wcox">Wilcoxon signed-rank test</option>
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38 <option value="BrMu">Brunner-Munzel test</option>
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39 </param>
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40 </when>
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41 <when value="non-parametric-distribution">
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42 <param name="stat_test" type="select" display="radio" label="Select statistical to apply" help="Please enter at max 1 statistical test by file">
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43 <option value="prm-scipy" selected="true">permutations test</option>
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44 <option value="disfit">distribution fitting (of the z-score of the ratios), disfit needs several hundreds of metabolites to be trustful.</option>
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45 </param>
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46 </when>
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47 </conditional>
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48
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49 </xml>
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50 <xml name="citations">
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51 <citations>
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52 <citation type="bibtex">
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53 @software{Galvis_Rodriguez_DIMet,
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54 author = {Galvis Rodriguez, Johanna and Guyon, Joris and Dartigues, Benjamin and Specque, Florian and Daubon, Thomas and Karkar, Slim and Nikolski, Macha},
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55 license = {MIT},
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56 title = {{DIMet}},
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57 url = {https://github.com/cbib/DIMet}
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58 }
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59
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60 </citation>
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61 </citations>
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62
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63 </xml>
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64 <xml name="metadata_file_macros">
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65 <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."/>
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66 </xml>
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67 <xml name="abundance_file_macros">
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68 <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)"/>
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69 </xml>
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70 <xml name="enrichment_file_macros">
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71 <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)"/>
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72 </xml>
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73 <xml name="isotopologue_prop_file_macros">
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74 <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)."/>
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75 </xml>
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76 <xml name="isotopologue_abs_file_macros">
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77 <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)."/>
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78 </xml>
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79 <xml name="input_parameters_pca">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
80 <expand macro="abundance_file_macros"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
81 <param name="me_or_frac_contrib_file" type="data" optional="true" format="tabular" label="Mean enrichment or fraction contribution file"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
82 <expand macro="metadata_file_macros"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
83 </xml>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
84 <xml name="input_parameters_abundance">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
85 <expand macro="abundance_file_macros"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
86 <expand macro="metadata_file_macros"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
87 </xml>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
88 <xml name="input_parameters_enrichment">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
89 <expand macro="enrichment_file_macros"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
90 <expand macro="metadata_file_macros"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
91 </xml>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
92 <xml name="input_parameters_isotopologue">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
93 <expand macro="isotopologue_prop_file_macros"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
94 <expand macro="metadata_file_macros"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
95 </xml>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
96 <xml name="input_parameters_metabologram">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
97 <conditional name="data_input">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
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diff changeset
98 <param name="data_input_selector" type="select" label="Abundance, Enrichment or Isotopologues quantification files" help="Select between raw abundance and mean enrichment files">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
99 <option value="abundance" selected="True">abundance</option>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
100 <option value="mean_enrichment">mean_enrichment</option>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
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diff changeset
101 </param>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
102 <when value="abundance">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
103 <expand macro="abundance_file_macros"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
104 <param name="metabolites_list" type="select" optional="false" multiple="true"
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
105 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">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
106 <validator type="length" min="1" message="Please enter at max 2 compartments"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
107 <options from_dataset="abundance_file">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
108 <column name="metabolite_or_isotopologue" index="0"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
109 <column name="value" index="0"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
110 <filter type="unique_value" name="metabolite_or_isotopologue" column="0"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
111 <filter type="remove_value" value="metabolite_or_isotopologue"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
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diff changeset
112 </options>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
113 <sanitizer>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
114 <valid initial="default">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
115 <add preset="string.printable"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
116 <add value="\t"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
117 <remove value="&quot;"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
118 <remove value="&apos;"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
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diff changeset
119 </valid>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
120 </sanitizer>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
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diff changeset
121 </param>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
122 <expand macro="statistical_test"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
123 </when>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
124 <when value="mean_enrichment">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
125 <expand macro="enrichment_file_macros"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
126 <param name="metabolites_list" type="select" optional="false" multiple="true"
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
127 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">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
128 <validator type="length" min="1" message="Please enter at max 2 compartments"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
129 <options from_dataset="me_or_frac_contrib_file">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
130 <column name="metabolite_or_isotopologue" index="0"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
131 <column name="value" index="0"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
132 <filter type="unique_value" name="metabolite_or_isotopologue" column="0"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
133 <filter type="remove_value" value="metabolite_or_isotopologue"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
134 </options>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
135 <sanitizer>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
136 <valid initial="default">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
137 <add preset="string.printable"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
138 <add value="\t"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
139 <remove value="&quot;"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
140 <remove value="&apos;"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
141 </valid>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
142 </sanitizer>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
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diff changeset
143 </param>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
144 <expand macro="statistical_test"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
145 </when>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
146 </conditional>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
147 <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)"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
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148 <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)"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
149 <expand macro="metadata_file_macros"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
150 </xml>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
151 <xml name="input_parameters_bivar_analysis">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
152 <conditional name="data_input">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
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diff changeset
153 <param name="data_input_selector" type="select" label="Abundance, Enrichment or Isotopologues quantification files" help="Select between raw abundance, mean enrichment or isotopologue files">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
154 <option value="abundance" selected="True">abundance</option>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
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diff changeset
155 <option value="mean_enrichment">mean_enrichment</option>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
156 <option value="isotop_prop">isotop_prop</option>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
157 <option value="isotop_abs">isotop_abs</option>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
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diff changeset
158 </param>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
159 <when value="abundance">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
160 <expand macro="abundance_file_macros"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
161
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
162 </when>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
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diff changeset
163 <when value="mean_enrichment">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
164 <expand macro="enrichment_file_macros"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
165 </when>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
166 <when value="isotop_prop">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
167 <expand macro="isotopologue_prop_file_macros"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
168 </when>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
169 <when value="isotop_abs">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
170 <expand macro="isotopologue_abs_file_macros"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
171 </when>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
172 </conditional>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
173 <expand macro="metadata_file_macros"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
174 <expand macro="statistical_test_for_bivariate_analysis"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
175 </xml>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
176 <xml name="input_parameters_diff_analysis">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
177 <conditional name="data_input">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
178 <param name="data_input_selector" type="select" label="Abundance, Enrichment or Isotopologues quantification files" help="Select between raw abundance, mean enrichment or isotopologue files">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
179 <option value="abundance" selected="True">abundance</option>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
180 <option value="mean_enrichment">mean_enrichment</option>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
181 <option value="isotop_prop">isotop_prop</option>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
182 <option value="isotop_abs">isotop_abs</option>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
183 </param>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
184 <when value="abundance">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
185 <expand macro="abundance_file_macros"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
186 <expand macro="statistical_test"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
187
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
188 </when>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
189 <when value="mean_enrichment">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
190 <expand macro="enrichment_file_macros"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
191 <expand macro="statistical_test"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
192 </when>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
193 <when value="isotop_prop">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
194 <expand macro="isotopologue_prop_file_macros"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
195 <expand macro="statistical_test"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
196 </when>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
197 <when value="isotop_abs">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
198 <expand macro="isotopologue_abs_file_macros"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
199 <expand macro="statistical_test"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
200 </when>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
201 </conditional>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
202 <expand macro="metadata_file_macros"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
203 </xml>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
204 <xml name="input_parameters_multi_diff_analysis">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
205 <conditional name="data_input">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
206 <param name="data_input_selector" type="select" label="Abundance, Enrichment or Isotopologues quantification files" help="Select between raw abundance, mean enrichment or isotopologue files">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
207 <option value="abundance" selected="True">abundance</option>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
208 <option value="mean_enrichment">mean_enrichment</option>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
209 <option value="isotop_prop">isotop_prop</option>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
210 <option value="isotop_abs">isotop_abs</option>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
211 </param>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
212 <when value="abundance">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
213 <expand macro="abundance_file_macros"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
214 <expand macro="statistical_test_for_multigroup"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
215
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
216 </when>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
217 <when value="mean_enrichment">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
218 <expand macro="enrichment_file_macros"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
219 <expand macro="statistical_test_for_multigroup"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
220 </when>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
221 <when value="isotop_prop">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
222 <expand macro="isotopologue_prop_file_macros"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
223 <expand macro="statistical_test_for_multigroup"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
224 </when>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
225 <when value="isotop_abs">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
226 <expand macro="isotopologue_abs_file_macros"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
227 <expand macro="statistical_test_for_multigroup"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
228 </when>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
229 </conditional>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
230 <expand macro="metadata_file_macros"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
231 </xml>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
232 <xml name="suffix">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
233 <param name="suffix" type="text" optional="false" label="suffix to add to output files" >
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
234 <sanitizer invalid_char="">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
235 <valid initial="string.ascii_letters,string.digits">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
236 <add value="_" />
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
237 </valid>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
238 </sanitizer>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
239 </param>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
240 </xml>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
241 <xml name="conditions">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
242 <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">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
243 <options from_dataset="metadata_path">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
244 <column name="condition" index="1"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
245 <column name="value" index="1"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
246 <filter type="unique_value" name="condition" column="condition"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
247 <filter type="remove_value" value="condition"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
248 </options>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
249 <sanitizer>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
250 <valid initial="default">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
251 <add preset="string.printable"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
252 <add value="\t"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
253 <remove value="&quot;"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
254 <remove value="&apos;"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
255 </valid>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
256 </sanitizer>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
257 </param>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
258 </xml>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
259 <xml name="conditions_multigroup">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
260 <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">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
261 <options from_dataset="metadata_path">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
262 <column name="condition" index="1"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
263 <column name="value" index="1"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
264 <filter type="unique_value" name="condition" column="condition"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
265 <filter type="remove_value" value="condition"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
266 </options>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
267 <sanitizer>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
268 <valid initial="default">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
269 <add preset="string.printable"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
270 <add value="\t"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
271 <remove value="&quot;"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
272 <remove value="&apos;"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
273 </valid>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
274 </sanitizer>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
275 </param>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
276 </xml>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
277 <xml name="timepoint_multigroup">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
278 <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">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
279 <options from_dataset="metadata_path">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
280 <column name="timepoint" index="2"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
281 <column name="value" index="2"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
282 <filter type="unique_value" name="timepoint" column="2"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
283 <filter type="remove_value" value="timepoint"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
284 <filter type="sort_by" name="timepoint" column="1"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
285 </options>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
286 <sanitizer>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
287 <valid initial="default">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
288 <add preset="string.printable"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
289 <add value="\t"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
290 <remove value="&quot;"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
291 <remove value="&apos;"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
292 </valid>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
293 </sanitizer>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
294 </param>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
295 </xml>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
296 <xml name="timepoint">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
297 <param name="timepoint" type="select" optional="false" multiple="true" label="Browse timepoint from metadata file (1 min.)">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
298 <options from_dataset="metadata_path">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
299 <column name="timepoint" index="2"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
300 <column name="value" index="2"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
301 <filter type="unique_value" name="timepoint" column="2"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
302 <filter type="remove_value" value="timepoint"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
303 <filter type="sort_by" name="timepoint" column="1"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
304 </options>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
305 <sanitizer>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
306 <valid initial="default">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
307 <add preset="string.printable"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
308 <add value="\t"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
309 <remove value="&quot;"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
310 <remove value="&apos;"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
311 </valid>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
312 </sanitizer>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
313 </param>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
314 </xml>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
315 <xml name="grouping">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
316 <param name="grouping" type="select" optional="false" multiple="true" label="Browse group to compare">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
317 <option value="condition" selected="true">condition</option>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
318 <option value="timepoint" selected="true">timepoint</option>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
319 </param>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
320 </xml>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
321 <xml name="correction_method">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
322 <param name="correction_method" type="select" value="bonferroni" display="radio" label="Select multiple test correction to apply" help="Please enter at max 1 method">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
323 <option value="bonferroni">bonferroni</option>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
324 <option value="holm-sidak">holm-sidak</option>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
325 <option value="holm">holm</option>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
326 <option value="simes-hochberg">simes-hochberg</option>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
327 <option value="hommel">hommel</option>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
328 <option value="fdr_bh">fdr_bh</option>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
329 <option value="fdr_by">fdr_by</option>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
330 <option value="fdr_tsbh">fdr_tsbh</option>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
331 <option value="fdr_tsbky">fdr_tsbky</option>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
332 </param>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
333 </xml>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
334 <xml name="compartments_enrichment">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
335 <param name="compartments" type="select" optional="false" multiple="true"
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
336 label="Browse compartments from metadata file (All needed). You have to load a metadata file prior to have access to compartments">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
337 <options from_dataset="metadata_path">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
338 <column name="compartment" index="4"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
339 <column name="value" index="4"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
340 <filter type="unique_value" name="compartment" column="4"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
341 <filter type="remove_value" value="compartment"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
342 </options>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
343 <sanitizer>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
344 <valid initial="default">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
345 <add preset="string.printable"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
346 <add value="\t"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
347 <remove value="&quot;"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
348 <remove value="&apos;"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
349 </valid>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
350 </sanitizer>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
351 </param>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
352 </xml>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
353 <xml name="compartments_abundance">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
354 <param name="compartments" type="select" optional="false" multiple="true"
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
355 label="Browse compartments from metadata file (All needed). You have to load a metadata file prior to have access to compartments">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
356 <options from_dataset="metadata_path">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
357 <column name="compartment" index="4"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
358 <column name="value" index="4"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
359 <filter type="unique_value" name="compartment" column="4"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
360 <filter type="remove_value" value="compartment"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
361 </options>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
362 <sanitizer>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
363 <valid initial="default">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
364 <add preset="string.printable"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
365 <add value="\t"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
366 <remove value="&quot;"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
367 <remove value="&apos;"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
368 </valid>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
369 </sanitizer>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
370 </param>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
371 </xml>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
372 <xml name="compartments_metabologram">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
373 <param name="compartments" type="select" optional="false" multiple="false"
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
374 label="Browse compartments from metadata file (1 max.). You have to load a metadata file prior to have access to compartments">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
375 <options from_dataset="metadata_path">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
376 <column name="compartment" index="4"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
377 <column name="value" index="4"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
378 <filter type="unique_value" name="compartment" column="4"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
379 <filter type="remove_value" value="compartment"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
380 </options>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
381 <sanitizer>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
382 <valid initial="default">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
383 <add preset="string.printable"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
384 <add value="\t"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
385 <remove value="&quot;"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
386 <remove value="&apos;"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
387 </valid>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
388 </sanitizer>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
389 </param>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
390 </xml>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
391 <xml name="compartments">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
392 <param name="compartments" type="select" optional="false" multiple="true"
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
393 label="Browse compartments from metadata file (1 min.). You have to load a metadata file prior to have access to compartments">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
394 <options from_dataset="metadata_path">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
395 <column name="compartment" index="4"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
396 <column name="value" index="4"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
397 <filter type="unique_value" name="compartment" column="4"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
398 <filter type="remove_value" value="compartment"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
399 </options>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
400 <sanitizer>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
401 <valid initial="default">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
402 <add preset="string.printable"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
403 <add value="\t"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
404 <remove value="&quot;"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
405 <remove value="&apos;"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
406 </valid>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
407 </sanitizer>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
408 </param>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
409 </xml>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
410 <xml name="abundance_metabolites_list">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
411 <param name="metabolites_list" type="select" optional="false" multiple="true"
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
412 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">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
413 <validator type="length" min="1" message="Please enter at max 2 compartments"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
414 <options from_dataset="abundance_file">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
415 <column name="metabolite_or_isotopologue" index="0"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
416 <column name="value" index="0"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
417 <filter type="unique_value" name="metabolite_or_isotopologue" column="0"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
418 <filter type="remove_value" value="metabolite_or_isotopologue"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
419 </options>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
420 <sanitizer>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
421 <valid initial="default">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
422 <add preset="string.printable"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
423 <add value="\t"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
424 <remove value="&quot;"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
425 <remove value="&apos;"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
426 </valid>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
427 </sanitizer>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
428 </param>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
429 </xml>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
430 <xml name="enrichment_metabolites_list">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
431 <param name="metabolites_list" type="select" optional="false" multiple="true"
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
432 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">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
433 <validator type="length" min="1" message="Please enter at min 1 metabolite"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
434 <options from_dataset="me_or_frac_contrib_file">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
435 <column name="ID" index="0"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
436 <column name="value" index="0"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
437 <filter type="unique_value" name="ID" column="0"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
438 <filter type="remove_value" value="ID"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
439 </options>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
440 <sanitizer>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
441 <valid initial="default">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
442 <add preset="string.printable"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
443 <add value="\t"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
444 <remove value="&quot;"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
445 <remove value="&apos;"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
446 </valid>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
447 </sanitizer>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
448 </param>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
449 </xml>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
450 <xml name="isotopologue_metabolites_list">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
451 <param name="metabolites_list" type="select" optional="false" multiple="true"
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
452 label="Select Metabolite(s) to plot (1 Min.). You have to load a abundance file prior to have access to metabolite list">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
453 <validator type="length" min="1" message="Please enter at min 1 metabolite"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
454 <options from_dataset="isotop_prop_file">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
455 <column name="ID" index="0"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
456 <column name="value" index="0"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
457 <filter type="unique_value" name="ID" column="0"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
458 <filter type="remove_value" value="ID"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
459 </options>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
460 <sanitizer>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
461 <valid initial="default">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
462 <add preset="string.printable"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
463 <add value="\t"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
464 <remove value="&quot;"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
465 <remove value="&apos;"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
466 </valid>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
467 </sanitizer>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
468 </param>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
469 </xml>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
470 <xml name="deg_list">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
471 <repeat name="deg_list" title="Deregulated gene set" default="1" min="1">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
472 <param name="input" type="data" format="tabular" label="Deregulated genes set"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
473 <param name="idcol" type="data_column" data_ref="input" label="Column for id" use_header_names="true"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
474 <param name="valuecol" type="data_column" data_ref="input" label="Column for values" use_header_names="true"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
475 <param name="timepoint" type="select" optional="false" multiple="false" label="Browse timepoint from metadata file (1 min.)">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
476 <options from_dataset="metadata_path">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
477 <column name="timepoint" index="2"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
478 <column name="value" index="2"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
479 <filter type="unique_value" name="timepoint" column="2"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
480 <filter type="remove_value" value="timepoint"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
481 <filter type="sort_by" name="timepoint" column="1"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
482 </options>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
483 <sanitizer>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
484 <valid initial="default">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
485 <add preset="string.printable"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
486 <add value="\t"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
487 <remove value="&quot;"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
488 <remove value="&apos;"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
489 </valid>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
490 </sanitizer>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
491 </param>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
492 <repeat name="factor_list" title="Conditions" default="2" min="2" max="2" help="Specify conditions to compare from metadata file (for each comparison, the last specified condition is the reference). You have to load a metadata file prior to have access to condition list">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
493 <param name="condition" label="Condition" type="select" optional="false" multiple="false">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
494 <options from_dataset="metadata_path">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
495 <column name="condition" index="1"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
496 <column name="value" index="1"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
497 <filter type="unique_value" name="condition" column="condition"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
498 <filter type="remove_value" value="condition"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
499 </options>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
500 <sanitizer>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
501 <valid initial="default">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
502 <add preset="string.printable"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
503 <add value="\t"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
504 <remove value="&quot;"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
505 <remove value="&apos;"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
506 </valid>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
507 </sanitizer>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
508 </param>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
509 </repeat>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
510
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
511 </repeat>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
512 </xml>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
513 <xml name="plot_abundance_factor_list">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
514 <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">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
515 <param name="condition" label="Condition" type="select" optional="false" multiple="false">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
516 <options from_dataset="metadata_path">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
517 <column name="condition" index="1"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
518 <column name="value" index="1"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
519 <filter type="unique_value" name="condition" column="condition"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
520 <filter type="remove_value" value="condition"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
521 </options>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
522 <sanitizer>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
523 <valid initial="default">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
524 <add preset="string.printable"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
525 <add value="\t"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
526 <remove value="&quot;"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
527 <remove value="&apos;"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
528 </valid>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
529 </sanitizer>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
530 </param>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
531 </repeat>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
532 </xml>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
533 <xml name="plot_factor_list">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
534 <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">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
535 <param name="condition" label="Condition" type="select" optional="false" multiple="false">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
536 <options from_dataset="metadata_path">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
537 <column name="condition" index="1"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
538 <column name="value" index="1"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
539 <filter type="unique_value" name="condition" column="condition"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
540 <filter type="remove_value" value="condition"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
541 </options>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
542 <sanitizer>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
543 <valid initial="default">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
544 <add preset="string.printable"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
545 <add value="\t"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
546 <remove value="&quot;"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
547 <remove value="&apos;"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
548 </valid>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
549 </sanitizer>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
550 </param>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
551 </repeat>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
552 </xml>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
553 <xml name="factor_list">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
554 <repeat name="factor_list" title="Conditions" min="2" max="2" help="Specify conditions to be taken into account from metadata file (for each comparison, the last specified condition is the reference). You have to load a metadata file prior to have access to condition list">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
555 <param name="condition" label="Condition" type="select" optional="false" multiple="false">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
556 <options from_dataset="metadata_path">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
557 <column name="condition" index="1"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
558 <column name="value" index="1"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
559 <filter type="unique_value" name="condition" column="condition"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
560 <filter type="remove_value" value="condition"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
561 </options>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
562 <sanitizer>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
563 <valid initial="default">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
564 <add preset="string.printable"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
565 <add value="\t"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
566 <remove value="&quot;"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
567 <remove value="&apos;"/>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
568 </valid>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
569 </sanitizer>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
570 </param>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
571 </repeat>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
572 </xml>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
573 <xml name="palette">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
574 <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">
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
575 <option value="pastel" selected="true">pastel</option>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
576 <option value="deep">deep</option>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
577 <option value="muted">muted</option>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
578 <option value="bright">bright</option>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
579 <option value="dark">dark</option>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
580 <option value="colorblind">colorblind</option>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
581 </param>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
582 </xml>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
583 <token name="@INIT_PCA@"><![CDATA[
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
584 #import json
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
585 #import re
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
586
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
587 mkdir -p data &&
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
588
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
589 #if $metadata_path:
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
590 ln -s '$metadata_path' data/metadata.csv &&
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
591 #end if
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
592 #if $abundance_file:
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
593 ln -s '$abundance_file' data/abundance.csv &&
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
594 #end if
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
595 #if $me_or_frac_contrib_file:
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
596 ln -s '$me_or_frac_contrib_file' data/me_or_frac_contrib.csv &&
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
597 #end if
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
598
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
599 ]]></token>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
600 <token name="@INIT_CONFIG@"><![CDATA[
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
601 mkdir -p 'config' &&
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
602 touch 'config/config.yaml' &&
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
603 ]]></token>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
604 <token name="@REMOVE_CONFIG@"><![CDATA[
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
605 && rm -r 'config'
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
606 ]]></token>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
607 <token name="@INIT_ABUNDANCE_PLOT@"><![CDATA[
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
608
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
609 mkdir -p data &&
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
610 #if $metadata_path:
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
611 ln -s '$metadata_path' data/metadata.csv &&
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
612 #end if
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
613 #if $abundance_file:
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
614 ln -s '$abundance_file' data/abundance.csv &&
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
615 #end if
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
616 #set $axisx = "condition"
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
617 #if str( $output_options.bar_color ) == "condition":
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
618 #set $axisx = "timepoint"
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
619 #end if
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
620
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
621 ]]></token>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
622 <token name="@INIT_ENRICHMENT_PLOT@"><![CDATA[
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
623
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
624 mkdir -p data &&
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
625
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
626 #if $metadata_path:
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
627 ln -s '$metadata_path' data/metadata.csv &&
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
628 #end if
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
629 #if $me_or_frac_contrib_file:
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
630 ln -s '$me_or_frac_contrib_file' data/me_or_frac_contrib.csv &&
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
631 #end if
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
632 ]]></token>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
633 <token name="@INIT_ISOTOPOLOGUE_PLOT@"><![CDATA[
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
634
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
635 mkdir -p data &&
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
636
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
637 #if $metadata_path:
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
638 ln -s '$metadata_path' data/metadata.csv &&
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
639 #end if
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
640 #if $isotop_prop_file:
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
641 ln -s '$isotop_prop_file' data/isotop_prop.csv &&
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
642 #end if
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
643 ]]></token>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
644 <token name="@INIT_BI_ANALYSIS@"><![CDATA[
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
645
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
646 mkdir -p data &&
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
647
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
648 #if $metadata_path:
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
649 ln -s '$metadata_path' data/metadata.csv &&
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
650 #end if
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
651
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
652
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
653 #set conditions_MDV_comparison = {}
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
654 #set timepoints_MDV_comparison = {}
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
655 #set conditions_metabolite_time_profiles = {}
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
656
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
657 #if str( $stat_test ) == "pearson":
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
658 #silent $conditions_MDV_comparison['isotopologue_proportions']='pearson'
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
659 #silent $timepoints_MDV_comparison['isotopologue_proportions']='pearson'
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
660 #silent $conditions_metabolite_time_profiles['abundances']='pearson'
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
661 #silent $conditions_metabolite_time_profiles['mean_enrichment']='pearson'
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
662 #else
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
663 #silent $conditions_MDV_comparison['isotopologue_proportions']='spearman'
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
664 #silent $timepoints_MDV_comparison['isotopologue_proportions']='spearman'
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
665 #silent $conditions_metabolite_time_profiles['abundances']='spearman'
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
666 #silent $conditions_metabolite_time_profiles['mean_enrichment']='spearman'
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
667 #end if
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
668 #set $impute_values = {}
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
669 #if str( $data_input.data_input_selector ) == "abundance":
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
670 #if $data_input.abundance_file:
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
671 ln -s '$data_input.abundance_file' data/abundance.csv &&
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
672 #silent $impute_values['abundances']='min'
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
673 #end if
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
674 #elif str( $data_input.data_input_selector ) == "mean_enrichment":
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
675 #if $data_input.me_or_frac_contrib_file:
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
676 ln -s '$data_input.me_or_frac_contrib_file' data/me_or_frac_contrib.csv &&
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
677 #silent $impute_values['mean_enrichment']='min'
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
678 #end if
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
679 #elif str( $data_input.data_input_selector ) == "isotop_prop":
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
680 #if $data_input.isotop_prop_file:
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
681 ln -s '$data_input.isotop_prop_file' data/isotop_prop.csv &&
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
682 #silent $impute_values['isotopologue_proportions']='min'
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
683 #end if
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
684 #else
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
685 #if $data_input.isotop_abs_file:
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
686 ln -s '$data_input.isotop_abs_file' data/isotop_abs.csv &&
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
687 #silent $impute_values['isotopologues']='min'
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
688 #end if
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
689 #end if
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
690 ]]></token>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
691 <token name="@INIT_DIFF_ANALYSIS@"><![CDATA[
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
692
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
693 mkdir -p data &&
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
694
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
695 #if $metadata_path:
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
696 ln -s '$metadata_path' data/metadata.csv &&
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
697 #end if
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
698
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
699 #set $impute_values = {}
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
700 #if str( $data_input.data_input_selector ) == "abundance":
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
701 #if $data_input.abundance_file:
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
702 ln -s '$data_input.abundance_file' data/abundance.csv &&
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
703 #silent $impute_values['abundances']='min'
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
704 #end if
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
705 #elif str( $data_input.data_input_selector ) == "mean_enrichment":
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
706 #if $data_input.me_or_frac_contrib_file:
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
707 ln -s '$data_input.me_or_frac_contrib_file' data/me_or_frac_contrib.csv &&
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
708 #silent $impute_values['mean_enrichment']='min'
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
709 #end if
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
710 #elif str( $data_input.data_input_selector ) == "isotop_prop":
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
711 #if $data_input.isotop_prop_file:
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
712 ln -s '$data_input.isotop_prop_file' data/isotop_prop.csv &&
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
713 #silent $impute_values['isotopologue_proportions']='min'
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
714 #end if
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
715 #else
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
716 #if $data_input.isotop_abs_file:
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
717 ln -s '$data_input.isotop_abs_file' data/isotop_abs.csv &&
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
718 #silent $impute_values['isotopologues']='min'
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
719 #end if
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
720 #end if
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
721 ]]></token>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
722 <token name="@INIT_METABOLOGRAM@"><![CDATA[
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
723 #import json
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
724 #import re
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
725 #import os
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
726 #import csv
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
727 #import subprocess
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
728
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
729 mkdir -p data &&
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
730
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
731 #if $path_kegg_metabolites:
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
732 ln -s '$path_kegg_metabolites' data/pathways_kegg_metabolites.csv &&
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
733 #end if
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
734 #if $path_kegg_transcripts:
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
735 ln -s '$path_kegg_transcripts' data/pathways_kegg_transcripts.csv &&
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
736 #end if
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
737
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
738 #if $metadata_path:
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
739 ln -s '$metadata_path' data/metadata.csv &&
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
740 #end if
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
741
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
742 #set $impute_values = {}
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
743 #if str( $data_input.data_input_selector ) == "abundance":
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
744 #if $data_input.abundance_file:
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
745 ln -s '$data_input.abundance_file' data/abundance.csv &&
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
746 #silent $impute_values['abundances']='min'
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
747 #end if
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
748 #else:
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
749 #if $data_input.me_or_frac_contrib_file:
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
750 ln -s '$data_input.me_or_frac_contrib_file' data/me_or_frac_contrib.csv &&
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
751 #silent $impute_values['mean_enrichment']='min'
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
752 #end if
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
753 #end if
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
754
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
755 #for $i, $s in enumerate($deg_list)
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
756 #set $cpt = str($i+1)
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
757 ln -s '${s.input}' data/DEG_comparison'${cpt}'.csv &&
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
758 #end for
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
759
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
760
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
761 ]]></token>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
762 <token name="@INIT_DIFF_MULTIGROUP_ANALYSIS@"><![CDATA[
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
763
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
764 mkdir -p data &&
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
765
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
766 #if $metadata_path:
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
767 ln -s '$metadata_path' data/metadata.csv &&
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
768 #end if
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
769
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
770 #set $impute_values = {}
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
771 #if str( $data_input.data_input_selector ) == "abundance":
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
772 #if $data_input.abundance_file:
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
773 ln -s '$data_input.abundance_file' data/abundance.csv &&
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
774 #silent $impute_values['abundances']='min'
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
775 #end if
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
776 #elif str( $data_input.data_input_selector ) == "mean_enrichment":
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
777 #if $data_input.me_or_frac_contrib_file:
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
778 ln -s '$data_input.me_or_frac_contrib_file' data/me_or_frac_contrib.csv &&
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
779 #silent $impute_values['mean_enrichment']='min'
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
780 #end if
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
781 #elif str( $data_input.data_input_selector ) == "isotop_prop":
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
782 #if $data_input.isotop_prop_file:
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
783 ln -s '$data_input.isotop_prop_file' data/isotop_prop.csv &&
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
784 #silent $impute_values['isotopologue_proportions']='min'
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
785 #end if
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
786 #else
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
787 #if $data_input.isotop_abs_file:
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
788 ln -s '$data_input.isotop_abs_file' data/isotop_abs.csv &&
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
789 #silent $impute_values['isotopologues']='min'
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
790 #end if
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
791 #end if
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
792 ]]></token>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
793 <token name="@INIT_IMPUTE_VALUES@"><![CDATA[
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
794 #import re
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
795 #set $impute_values = {}
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
796 #if $abundance_file:
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
797 #silent $impute_values['abundances']='min'
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
798 #end if
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
799 #if $me_or_frac_contrib_file:
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
800 #silent $impute_values['mean_enrichment']='min'
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
801 #end if
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
802 ]]></token>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
803 <token name="@INIT_DATATYPES@"><![CDATA[
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
804 #import re
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
805 #set $datatypes_avail = list()
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
806 #if str( $data_input.data_input_selector ) == "abundance":
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
807 #if $data_input.abundance_file:
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
808 $datatypes_avail.append(re.sub('"', '', "abundances"))
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
809 #end if
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
810 #elif str( $data_input.data_input_selector ) == "mean_enrichment":
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
811 #if $data_input.me_or_frac_contrib_file:
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
812 $datatypes_avail.append(re.sub('"', '', "mean_enrichment"))
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
813 #end if
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
814 #elif str( $data_input.data_input_selector ) == "isotop_prop":
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
815 #if $data_input.isotop_prop_file:
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
816 $datatypes_avail.append(re.sub('"', '', "isotopologue_proportions"))
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
817 #end if
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
818 #else
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
819 #if $data_input.isotop_abs_file:
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
820 $datatypes_avail.append(re.sub('"', '', "isotopologues"))
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
821 #end if
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
822 #end if
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
823 ]]></token>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
824 <token name="@INIT_STAT_TEST@"><![CDATA[
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
825 #import re
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
826 #set $statistical_test = {}
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
827 #if str( $data_input.data_input_selector ) == "abundance":
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
828 #if $data_input.abundance_file:
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
829 #silent $statistical_test['abundances']=str($data_input.stat_test)
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
830 #end if
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
831 #elif str( $data_input.data_input_selector ) == "mean_enrichment":
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
832 #if $data_input.me_or_frac_contrib_file:
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
833 #silent $statistical_test['mean_enrichment']=str($data_input.stat_test)
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
834 #end if
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
835 #elif str( $data_input.data_input_selector ) == "isotop_prop":
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
836 #if $data_input.isotop_prop_file:
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
837 #silent $statistical_test['isotopologue_proportions']=str($data_input.stat_test)
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
838 #end if
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
839 #else
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
840 #if $data_input.isotop_abs_file:
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
841 #silent $statistical_test['isotopologues']=str($data_input.stat_test)
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
842 #end if
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
843 #end if
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
844 ]]></token>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
845 <token name="@INIT_CONDITIONS@"><![CDATA[
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
846 #import re
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
847 #set $conds = list()
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
848 #for $co in $conditions:
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
849 $conds.append(re.sub('"', '', str($co)))
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
850 #end for
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
851 ]]></token>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
852 <token name="@INIT_PLOT_CONDITIONS@"><![CDATA[
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
853 #set $conditions = list()
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
854 #for $i, $s in enumerate($plot_factor_list)
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
855 #set $cpt = str($i+1)
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
856 $conditions.append(re.sub('"', '', str($s.condition)))
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
857 #end for
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
858 ]]></token>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
859 <token name="@INIT_ABUNDANCE_PLOT_CONDITIONS@"><![CDATA[
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
860 #set $conditions = list()
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
861 #for $i, $s in enumerate($plot_abundance_factor_list)
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
862 #set $cpt = str($i+1)
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
863 $conditions.append(re.sub('"', '', str($s.condition)))
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
864 #end for
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
865 ]]></token>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
866 <token name="@INIT_TIMEPOINTS@"><![CDATA[
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
867
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
868 #import re
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
869 #set $timepoints = list()
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
870 #for $tp in $timepoint:
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
871 $timepoints.append(re.sub('"', '', str($tp)))
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
872 #end for
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
873 ]]></token>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
874 <token name="@INIT_GROUPS@"><![CDATA[
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
875 #import re
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
876 #set $groups = list()
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
877 $groups.append(re.sub('"', '', str("condition")))
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
878 $groups.append(re.sub('"', '', str("timepoint")))
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
879
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
880 ]]></token>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
881 <token name="@INIT_ENRICHMENT_METABOLITES@"><![CDATA[
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
882 #import json
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
883 #import re
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
884 #set $metabolites = {}
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
885 #for $cp in $compartments:
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
886 #silent $metabolites[re.sub('"', '', str($cp))]=list()
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
887 #for $met in $metabolites_list:
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
888 #set tmp_met=re.sub('\,', '%%',str($met))
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
889 #set tmp_met_bis=str(re.split('_m', str($tmp_met))[0])
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
890 #set tmp_met_ter=re.sub('%%', '\,',str($tmp_met_bis))
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
891 $metabolites[re.sub('"', '', str($cp))].append(re.sub('"', '\'', str(tmp_met_ter)))
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
892 #end for
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
893 #end for
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
894 ]]></token>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
895 <token name="@INIT_ISOTOPOLOGUE_METABOLITES@"><![CDATA[
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
896 #set $metabolites = {}
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
897 #for $cp in $compartments:
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
898 #silent $metabolites[re.sub('"', '', str($cp))]=list()
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
899 #for $met in $metabolites_list:
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
900 #set tmp_met=re.sub('\,', '--',str($met))
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
901 #set tmp_met_bis=str(re.split('_m', str($tmp_met))[0])
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
902 #set tmp_met_ter=re.sub('--', '\,',str($tmp_met_bis))
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
903 $metabolites[re.sub('"', '', str($cp))].append(re.sub('"', '\'', str(tmp_met_ter)))
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
904 #end for
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
905 #end for
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
906 ]]></token>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
907 <token name="@INIT_MULTIGROUP_COMPARISONS@"><![CDATA[
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
908 #set $comparisons = list()
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
909 #for $tp in $timepoint:
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
910 #set $ctrl_found=False
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
911 #set $ctrl=""
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
912
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
913 #for $co in $conditions:
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
914 #set $sub_comparisons = list()
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
915 #if str($co) in ["Control", "control","ctrl"]:
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
916 #set $ctrl_found=True
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
917 #set $ctrl=str($co)
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
918 $sub_comparisons.append(re.sub('"', '', str($co)))
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
919 $sub_comparisons.append(re.sub('"', '', str($tp)))
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
920 #else:
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
921 $sub_comparisons.append(re.sub('"', '', str($co)))
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
922 $sub_comparisons.append(re.sub('"', '', str($tp)))
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
923
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
924 #end if
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
925 $comparisons.append($sub_comparisons)
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
926 #end for
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
927 #end for
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
928 ]]></token>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
929 <token name="@INIT_CONDITIONS_TIMECOURSE@"><![CDATA[
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
930 #import re
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
931 #set $conditions = list()
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
932 #for $i, $s in enumerate($factor_list)
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
933 #set $cpt = str($i+1)
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
934 $conditions.append(re.sub('"', '', str($s.condition)))
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
935 #end for
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
936
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
937 ]]></token>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
938 <token name="@INIT_BIVAR_COMPARISONS@"><![CDATA[
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
939 #import re
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
940 #set $conditions = list()
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
941 #for $i, $s in enumerate($plot_factor_list)
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
942 #set $cpt = str($i+1)
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
943 $conditions.append(re.sub('"', '', str($s.condition)))
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
944 #end for
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
945 ]]></token>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
946 <token name="@INIT_COMPARISONS_METABOLOGRAM@"><![CDATA[
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
947 #import re
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
948 #set $conditions = list()
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
949 #set $timepoints = list()
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
950 #set $comparisons = list()
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
951 #for $i, $s in enumerate($deg_list)
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
952 #set $cpt = str($i+1)
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
953 #set $comparisons_bis = list()
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
954 #for $j, $t in enumerate($s.factor_list)
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
955 #set $sub_comparisons = list()
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
956 #if str($t.condition) not in $conditions:
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
957 $conditions.append(re.sub('"', '', str($t.condition)))
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
958 #end if
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
959 $sub_comparisons.append(re.sub('"', '', str($t.condition)))
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
960 $sub_comparisons.append(re.sub('"', '', str($s.timepoint)))
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
961 $comparisons_bis.append($sub_comparisons)
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
962 #end for
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
963 $timepoints.append(re.sub('"', '', str($s.timepoint)))
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
964 $comparisons.append($comparisons_bis)
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
965 #end for
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
966
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
967
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
968
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
969 ]]></token>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
970 <token name="@INIT_COMPARISONS@"><![CDATA[
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
971 #import re
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
972 #set $conds = list()
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
973 #for $co in $conditions:
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
974 $conds.append(re.sub('"', '', str($co)))
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
975 #end for
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
976 #set $timepoints = list()
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
977 #for $tp in $timepoint:
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
978 $timepoints.append(re.sub('"', '', str($tp)))
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
979 #end for
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
980
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
981 #set $comparisons = list()
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
982 #if len($conds) > 1:
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
983 #if len($timepoints) > 0:
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
984 #for $tp in $timepoint:
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
985 #set $ctrl_found=False
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
986 #set $ctrl=""
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
987 #set $comparisons_bis = list()
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
988 #for $co in $conditions:
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
989 #set $sub_comparisons = list()
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
990 #if str($co) in ["'Control'", "'control'", "'ctrl'"]:
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
991 #set $ctrl_found=True
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
992 #set $ctrl=str($co)
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
993 #else:
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
994 $sub_comparisons.append(re.sub('"', '', str($co)))
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
995 $sub_comparisons.append(re.sub('"', '', str($tp)))
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
996
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
997 #end if
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
998 $comparisons_bis.append($sub_comparisons)
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
999 #end for
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1000
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1001 #if $ctrl_found:
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1002 $sub_comparisons.append(str($ctrl))
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1003 $sub_comparisons.append(str($tp))
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1004 $comparisons_bis.append($sub_comparisons)
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1005 #end if
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1006
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1007 $comparisons.append($comparisons_bis)
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1008 #end for
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1009 #else
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1010 #for $co in $conditions:
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1011 $comparisons.append(re.sub('"', '', str($co)))
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1012 #end for
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1013 #end if
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1014
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1015 #else
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1016 #if len($conds) > 0:
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1017 #if len($timepoints) > 1:
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1018 #for $co in $conditions:
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1019 #set $comparisons_bis = list()
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1020 #for $tp in $timepoint:
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1021 #set $sub_comparisons = list()
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1022 $sub_comparisons.append(re.sub('"', '', str($co)))
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1023 $sub_comparisons.append(re.sub('"', '', str($tp)))
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1024 $comparisons_bis.append($sub_comparisons)
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1025 #end for
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1026 $comparisons.append($comparisons_bis)
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1027 #end for
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1028 #end if
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1029 #else
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1030 #for $tp in $timepoint:
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1031 $comparisons.append(re.sub('"', '', str($tp)))
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1032 #end for
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1033 #end if
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1034 #end if
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1035 ]]></token>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1036 <token name="@INIT_DIFF_ANALYSIS_COMPARISONS@"><![CDATA[
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1037 #import re
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1038 #set $conditions = list()
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1039 #for $i, $s in enumerate($factor_list)
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1040 #set $cpt = str($i+1)
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1041 $conditions.append(re.sub('"', '', str($s.condition)))
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1042 #end for
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1043
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1044 #set $timepoints = list()
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1045 #for $tp in $timepoint:
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1046 $timepoints.append(re.sub('"', '', str($tp)))
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1047 #end for
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1048
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1049 #set $comparisons = list()
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1050 #if len($conditions) > 1:
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1051 #if len($timepoints) > 0:
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1052 #for $tp in $timepoint:
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1053 #set $ctrl_found=False
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1054 #set $ctrl=""
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1055 #set $comparisons_bis = list()
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1056
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1057 #for $co in $conditions:
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1058 #set $sub_comparisons = list()
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1059 #if str($co) in ["'Control'", "'control'", "'ctrl'"]:
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1060 #set $ctrl_found=True
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1061 #set $ctrl=str($co)
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1062 #else:
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1063 $sub_comparisons.append(re.sub('"', '', str($co)))
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1064 $sub_comparisons.append(re.sub('"', '', str($tp)))
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1065
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1066 #end if
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1067 $comparisons_bis.append($sub_comparisons)
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1068 #end for
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1069
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1070 #if $ctrl_found:
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1071 $sub_comparisons.append(str($ctrl))
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1072 $sub_comparisons.append(str($tp))
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1073 $comparisons_bis.append($sub_comparisons)
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1074 #end if
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1075
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1076 $comparisons.append($comparisons_bis)
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1077 #end for
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1078 #else
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1079 #for $co in $conditions:
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1080 $comparisons.append(re.sub('"', '', str($co)))
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1081 #end for
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1082 #end if
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1083
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1084 #else
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1085 #if len($conditions) > 0:
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1086 #if len($timepoints) > 1:
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1087 #for $co in $conditions:
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1088 #set $comparisons_bis = list()
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1089 #for $tp in $timepoint:
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1090 #set $sub_comparisons = list()
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1091 $sub_comparisons.append(re.sub('"', '', str($co)))
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1092 $sub_comparisons.append(re.sub('"', '', str($tp)))
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1093 $comparisons_bis.append($sub_comparisons)
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1094 #end for
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1095 $comparisons.append($comparisons_bis)
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1096 #end for
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1097 #end if
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1098 #else
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1099 #for $tp in $timepoint:
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1100 $comparisons.append(re.sub('"', '', str($tp)))
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1101 #end for
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1102 #end if
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1103 #end if
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1104 ]]></token>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1105 <token name="@INIT_TRANSCRIPTS@"><![CDATA[
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1106 #import re
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1107 #import os
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1108 #import subprocess
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1109 #set $transcripts = list()
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1110
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1111 #for $i, $s in enumerate($deg_list)
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1112 #set $cpt = str($i+1)
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1113 $transcripts.append(re.sub('"', '', "DEG_comparison"+str($i+1)))
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1114 #set $deg_one_values = os.fsdecode(subprocess.check_output('head -n1 ' + str($s.input) + '| cut -f' + str($s.valuecol), shell=True))
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1115 #set $deg_one_id = os.fsdecode(subprocess.check_output('head -n1 ' + str($s.input) + '| cut -f' + str($s.idcol), shell=True))
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1116 #end for
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1117 ]]></token>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1118 <token name="@INIT_PATHWAYS@"><![CDATA[
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
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1119 #set $pathways = {}
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
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1120 #if $path_kegg_metabolites:
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
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1121 #silent $pathways['metabolites']='pathways_kegg_metabolites'
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
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1122 #end if
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
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1123 #if $path_kegg_transcripts:
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
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1124 #silent $pathways['transcripts']='pathways_kegg_transcripts'
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
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1125 #end if
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
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1126 ]]></token>
d9e56e80a153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
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1127 </macros>