Mercurial > repos > iuc > dimet_enrichment_plot

annotate macros.xml @ 0:1bfe9f9608e4 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
author iuc
date Fri, 21 Jun 2024 18:45:22 +0000
parents
children 74599e075574
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1 <macros>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
2 <token name="@TOOL_VERSION@">0.2.4</token>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
3 <token name="@VERSION_SUFFIX@">3</token>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
4 <xml name="requirements">
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
5 <requirements>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
6 <requirement type="package" version="@TOOL_VERSION@">dimet</requirement>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
7 </requirements>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
8 </xml>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
9 <xml name="statistical_test_for_multigroup">
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
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">
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
11 <option value="KW">Kruskal-Wallis</option>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
12 </param>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
13 </xml>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
14 <xml name="statistical_test_for_bivariate_analysis">
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
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">
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
16 <option value="pearson">pearson</option>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
17 <option value="spearman">spearman</option>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
18 </param>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
19 </xml>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
20 <xml name="statistical_test">
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
21 <conditional name="statistics">
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
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">
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
23 <option value="parametric">parametric</option>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
24 <option value="non-parametric-rank" selected="true">non-parametric (rank based)</option>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
25 <option value="non-parametric-distribution">non-parametric (distribution based)</option>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
26 </param>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
27 <when value="parametric">
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
28 <param name="stat_test" type="select" display="radio" label="Select statistical to apply" help="Please enter at max 1 statistical test by file">
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
29 <option value="Tt" selected="true">t-test</option>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
30 </param>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
31 </when>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
32 <when value="non-parametric-rank">
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
33 <param name="stat_test" type="select" display="radio" label="Select statistical to apply" help="Please enter at max 1 statistical test by file">
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
34 <option value="MW">Mann Whitney</option>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
35 <option value="KW">Kruskal-Wallis</option>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
36 <option value="ranksum" selected="true">Wilcoxon's rank sum test</option>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
37 <option value="Wcox">Wilcoxon signed-rank test</option>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
38 <option value="BrMu">Brunner-Munzel test</option>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
39 </param>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
40 </when>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
41 <when value="non-parametric-distribution">
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
42 <param name="stat_test" type="select" display="radio" label="Select statistical to apply" help="Please enter at max 1 statistical test by file">
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
43 <option value="prm-scipy" selected="true">permutations test</option>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
44 <option value="disfit">distribution fitting (of the z-score of the ratios), disfit needs several hundreds of metabolites to be trustful.</option>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
45 </param>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
46 </when>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
47 </conditional>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
48
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
49 </xml>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
50 <xml name="citations">
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
51 <citations>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
52 <citation type="bibtex">
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
53 @software{Galvis_Rodriguez_DIMet,
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
54 author = {Galvis Rodriguez, Johanna and Guyon, Joris and Dartigues, Benjamin and Specque, Florian and Daubon, Thomas and Karkar, Slim and Nikolski, Macha},
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
55 license = {MIT},
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
56 title = {{DIMet}},
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
57 url = {https://github.com/cbib/DIMet}
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
58 }
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
59
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
60 </citation>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
61 </citations>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
62
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
63 </xml>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
64 <xml name="metadata_file_macros">
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
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."/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
66 </xml>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
67 <xml name="abundance_file_macros">
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
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)"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
69 </xml>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
70 <xml name="enrichment_file_macros">
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
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)"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
72 </xml>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
73 <xml name="isotopologue_prop_file_macros">
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
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)."/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
75 </xml>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
76 <xml name="isotopologue_abs_file_macros">
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
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)."/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
78 </xml>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
79 <xml name="input_parameters_pca">
1bfe9f9608e4 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"/>
1bfe9f9608e4 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"/>
1bfe9f9608e4 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"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
83 </xml>
1bfe9f9608e4 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">
1bfe9f9608e4 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"/>
1bfe9f9608e4 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"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
87 </xml>
1bfe9f9608e4 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">
1bfe9f9608e4 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"/>
1bfe9f9608e4 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"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
91 </xml>
1bfe9f9608e4 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">
1bfe9f9608e4 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"/>
1bfe9f9608e4 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"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
95 </xml>
1bfe9f9608e4 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">
1bfe9f9608e4 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">
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
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">
1bfe9f9608e4 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>
1bfe9f9608e4 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>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
101 </param>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
102 <when value="abundance">
1bfe9f9608e4 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"/>
1bfe9f9608e4 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"
1bfe9f9608e4 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">
1bfe9f9608e4 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"/>
1bfe9f9608e4 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">
1bfe9f9608e4 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"/>
1bfe9f9608e4 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"/>
1bfe9f9608e4 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"/>
1bfe9f9608e4 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"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
112 </options>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
113 <sanitizer>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
114 <valid initial="default">
1bfe9f9608e4 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"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
116 <add value="\t"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
117 <remove value="&quot;"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
118 <remove value="&apos;"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
119 </valid>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
120 </sanitizer>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
121 </param>
1bfe9f9608e4 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"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
123 </when>
1bfe9f9608e4 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">
1bfe9f9608e4 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"/>
1bfe9f9608e4 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"
1bfe9f9608e4 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">
1bfe9f9608e4 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"/>
1bfe9f9608e4 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">
1bfe9f9608e4 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"/>
1bfe9f9608e4 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"/>
1bfe9f9608e4 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"/>
1bfe9f9608e4 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"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
134 </options>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
135 <sanitizer>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
136 <valid initial="default">
1bfe9f9608e4 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"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
138 <add value="\t"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
139 <remove value="&quot;"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
140 <remove value="&apos;"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
141 </valid>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
142 </sanitizer>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
143 </param>
1bfe9f9608e4 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"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
145 </when>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
146 </conditional>
1bfe9f9608e4 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)"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
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)"/>
1bfe9f9608e4 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"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
150 </xml>
1bfe9f9608e4 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">
1bfe9f9608e4 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">
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
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">
1bfe9f9608e4 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>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
155 <option value="mean_enrichment">mean_enrichment</option>
1bfe9f9608e4 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>
1bfe9f9608e4 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>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
158 </param>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
159 <when value="abundance">
1bfe9f9608e4 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"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
161
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
162 </when>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
163 <when value="mean_enrichment">
1bfe9f9608e4 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"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
165 </when>
1bfe9f9608e4 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">
1bfe9f9608e4 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"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
168 </when>
1bfe9f9608e4 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">
1bfe9f9608e4 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"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
171 </when>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
172 </conditional>
1bfe9f9608e4 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"/>
1bfe9f9608e4 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"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
175 </xml>
1bfe9f9608e4 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">
1bfe9f9608e4 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">
1bfe9f9608e4 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">
1bfe9f9608e4 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>
1bfe9f9608e4 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>
1bfe9f9608e4 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>
1bfe9f9608e4 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>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
183 </param>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
184 <when value="abundance">
1bfe9f9608e4 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"/>
1bfe9f9608e4 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"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
187
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
188 </when>
1bfe9f9608e4 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">
1bfe9f9608e4 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"/>
1bfe9f9608e4 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"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
192 </when>
1bfe9f9608e4 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">
1bfe9f9608e4 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"/>
1bfe9f9608e4 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"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
196 </when>
1bfe9f9608e4 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">
1bfe9f9608e4 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"/>
1bfe9f9608e4 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"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
200 </when>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
201 </conditional>
1bfe9f9608e4 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"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
203 </xml>
1bfe9f9608e4 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">
1bfe9f9608e4 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">
1bfe9f9608e4 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">
1bfe9f9608e4 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>
1bfe9f9608e4 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>
1bfe9f9608e4 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>
1bfe9f9608e4 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>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
211 </param>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
212 <when value="abundance">
1bfe9f9608e4 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"/>
1bfe9f9608e4 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"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
215
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
216 </when>
1bfe9f9608e4 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">
1bfe9f9608e4 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"/>
1bfe9f9608e4 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"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
220 </when>
1bfe9f9608e4 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">
1bfe9f9608e4 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"/>
1bfe9f9608e4 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"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
224 </when>
1bfe9f9608e4 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">
1bfe9f9608e4 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"/>
1bfe9f9608e4 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"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
228 </when>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
229 </conditional>
1bfe9f9608e4 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"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
231 </xml>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
232 <xml name="suffix">
1bfe9f9608e4 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" >
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
234 <sanitizer invalid_char="">
1bfe9f9608e4 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">
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
236 <add value="_" />
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
237 </valid>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
238 </sanitizer>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
239 </param>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
240 </xml>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
241 <xml name="conditions">
1bfe9f9608e4 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">
1bfe9f9608e4 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">
1bfe9f9608e4 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"/>
1bfe9f9608e4 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"/>
1bfe9f9608e4 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"/>
1bfe9f9608e4 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"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
248 </options>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
249 <sanitizer>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
250 <valid initial="default">
1bfe9f9608e4 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"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
252 <add value="\t"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
253 <remove value="&quot;"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
254 <remove value="&apos;"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
255 </valid>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
256 </sanitizer>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
257 </param>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
258 </xml>
1bfe9f9608e4 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">
1bfe9f9608e4 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">
1bfe9f9608e4 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">
1bfe9f9608e4 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"/>
1bfe9f9608e4 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"/>
1bfe9f9608e4 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"/>
1bfe9f9608e4 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"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
266 </options>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
267 <sanitizer>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
268 <valid initial="default">
1bfe9f9608e4 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"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
270 <add value="\t"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
271 <remove value="&quot;"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
272 <remove value="&apos;"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
273 </valid>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
274 </sanitizer>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
275 </param>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
276 </xml>
1bfe9f9608e4 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">
1bfe9f9608e4 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">
1bfe9f9608e4 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">
1bfe9f9608e4 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"/>
1bfe9f9608e4 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"/>
1bfe9f9608e4 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"/>
1bfe9f9608e4 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"/>
1bfe9f9608e4 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"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
285 </options>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
286 <sanitizer>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
287 <valid initial="default">
1bfe9f9608e4 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"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
289 <add value="\t"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
290 <remove value="&quot;"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
291 <remove value="&apos;"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
292 </valid>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
293 </sanitizer>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
294 </param>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
295 </xml>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
296 <xml name="timepoint">
1bfe9f9608e4 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.)">
1bfe9f9608e4 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">
1bfe9f9608e4 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"/>
1bfe9f9608e4 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"/>
1bfe9f9608e4 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"/>
1bfe9f9608e4 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"/>
1bfe9f9608e4 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"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
304 </options>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
305 <sanitizer>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
306 <valid initial="default">
1bfe9f9608e4 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"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
308 <add value="\t"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
309 <remove value="&quot;"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
310 <remove value="&apos;"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
311 </valid>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
312 </sanitizer>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
313 </param>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
314 </xml>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
315 <xml name="grouping">
1bfe9f9608e4 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">
1bfe9f9608e4 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>
1bfe9f9608e4 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>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
319 </param>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
320 </xml>
1bfe9f9608e4 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">
1bfe9f9608e4 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">
1bfe9f9608e4 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>
1bfe9f9608e4 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>
1bfe9f9608e4 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>
1bfe9f9608e4 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>
1bfe9f9608e4 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>
1bfe9f9608e4 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>
1bfe9f9608e4 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>
1bfe9f9608e4 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>
1bfe9f9608e4 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>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
332 </param>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
333 </xml>
1bfe9f9608e4 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">
1bfe9f9608e4 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"
1bfe9f9608e4 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">
1bfe9f9608e4 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">
1bfe9f9608e4 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"/>
1bfe9f9608e4 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"/>
1bfe9f9608e4 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"/>
1bfe9f9608e4 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"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
342 </options>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
343 <sanitizer>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
344 <valid initial="default">
1bfe9f9608e4 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"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
346 <add value="\t"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
347 <remove value="&quot;"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
348 <remove value="&apos;"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
349 </valid>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
350 </sanitizer>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
351 </param>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
352 </xml>
1bfe9f9608e4 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">
1bfe9f9608e4 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"
1bfe9f9608e4 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">
1bfe9f9608e4 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">
1bfe9f9608e4 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"/>
1bfe9f9608e4 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"/>
1bfe9f9608e4 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"/>
1bfe9f9608e4 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"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
361 </options>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
362 <sanitizer>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
363 <valid initial="default">
1bfe9f9608e4 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"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
365 <add value="\t"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
366 <remove value="&quot;"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
367 <remove value="&apos;"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
368 </valid>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
369 </sanitizer>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
370 </param>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
371 </xml>
1bfe9f9608e4 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">
1bfe9f9608e4 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"
1bfe9f9608e4 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">
1bfe9f9608e4 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">
1bfe9f9608e4 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"/>
1bfe9f9608e4 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"/>
1bfe9f9608e4 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"/>
1bfe9f9608e4 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"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
380 </options>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
381 <sanitizer>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
382 <valid initial="default">
1bfe9f9608e4 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"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
384 <add value="\t"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
385 <remove value="&quot;"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
386 <remove value="&apos;"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
387 </valid>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
388 </sanitizer>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
389 </param>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
390 </xml>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
391 <xml name="compartments">
1bfe9f9608e4 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"
1bfe9f9608e4 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">
1bfe9f9608e4 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">
1bfe9f9608e4 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"/>
1bfe9f9608e4 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"/>
1bfe9f9608e4 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"/>
1bfe9f9608e4 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"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
399 </options>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
400 <sanitizer>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
401 <valid initial="default">
1bfe9f9608e4 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"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
403 <add value="\t"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
404 <remove value="&quot;"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
405 <remove value="&apos;"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
406 </valid>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
407 </sanitizer>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
408 </param>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
409 </xml>
1bfe9f9608e4 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">
1bfe9f9608e4 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"
1bfe9f9608e4 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">
1bfe9f9608e4 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"/>
1bfe9f9608e4 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">
1bfe9f9608e4 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"/>
1bfe9f9608e4 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"/>
1bfe9f9608e4 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"/>
1bfe9f9608e4 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"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
419 </options>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
420 <sanitizer>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
421 <valid initial="default">
1bfe9f9608e4 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"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
423 <add value="\t"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
424 <remove value="&quot;"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
425 <remove value="&apos;"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
426 </valid>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
427 </sanitizer>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
428 </param>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
429 </xml>
1bfe9f9608e4 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">
1bfe9f9608e4 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"
1bfe9f9608e4 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">
1bfe9f9608e4 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"/>
1bfe9f9608e4 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">
1bfe9f9608e4 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"/>
1bfe9f9608e4 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"/>
1bfe9f9608e4 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"/>
1bfe9f9608e4 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"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
439 </options>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
440 <sanitizer>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
441 <valid initial="default">
1bfe9f9608e4 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"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
443 <add value="\t"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
444 <remove value="&quot;"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
445 <remove value="&apos;"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
446 </valid>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
447 </sanitizer>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
448 </param>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
449 </xml>
1bfe9f9608e4 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">
1bfe9f9608e4 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"
1bfe9f9608e4 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">
1bfe9f9608e4 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"/>
1bfe9f9608e4 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">
1bfe9f9608e4 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"/>
1bfe9f9608e4 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"/>
1bfe9f9608e4 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"/>
1bfe9f9608e4 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"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
459 </options>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
460 <sanitizer>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
461 <valid initial="default">
1bfe9f9608e4 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"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
463 <add value="\t"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
464 <remove value="&quot;"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
465 <remove value="&apos;"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
466 </valid>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
467 </sanitizer>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
468 </param>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
469 </xml>
1bfe9f9608e4 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">
1bfe9f9608e4 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">
1bfe9f9608e4 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"/>
1bfe9f9608e4 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"/>
1bfe9f9608e4 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"/>
1bfe9f9608e4 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.)">
1bfe9f9608e4 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">
1bfe9f9608e4 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"/>
1bfe9f9608e4 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"/>
1bfe9f9608e4 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"/>
1bfe9f9608e4 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"/>
1bfe9f9608e4 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"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
482 </options>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
483 <sanitizer>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
484 <valid initial="default">
1bfe9f9608e4 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"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
486 <add value="\t"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
487 <remove value="&quot;"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
488 <remove value="&apos;"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
489 </valid>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
490 </sanitizer>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
491 </param>
1bfe9f9608e4 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">
1bfe9f9608e4 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">
1bfe9f9608e4 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">
1bfe9f9608e4 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"/>
1bfe9f9608e4 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"/>
1bfe9f9608e4 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"/>
1bfe9f9608e4 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"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
499 </options>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
500 <sanitizer>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
501 <valid initial="default">
1bfe9f9608e4 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"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
503 <add value="\t"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
504 <remove value="&quot;"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
505 <remove value="&apos;"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
506 </valid>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
507 </sanitizer>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
508 </param>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
509 </repeat>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
510
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
511 </repeat>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
512 </xml>
1bfe9f9608e4 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">
1bfe9f9608e4 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">
1bfe9f9608e4 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">
1bfe9f9608e4 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">
1bfe9f9608e4 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"/>
1bfe9f9608e4 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"/>
1bfe9f9608e4 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"/>
1bfe9f9608e4 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"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
521 </options>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
522 <sanitizer>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
523 <valid initial="default">
1bfe9f9608e4 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"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
525 <add value="\t"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
526 <remove value="&quot;"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
527 <remove value="&apos;"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
528 </valid>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
529 </sanitizer>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
530 </param>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
531 </repeat>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
532 </xml>
1bfe9f9608e4 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">
1bfe9f9608e4 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">
1bfe9f9608e4 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">
1bfe9f9608e4 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">
1bfe9f9608e4 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"/>
1bfe9f9608e4 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"/>
1bfe9f9608e4 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"/>
1bfe9f9608e4 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"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
541 </options>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
542 <sanitizer>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
543 <valid initial="default">
1bfe9f9608e4 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"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
545 <add value="\t"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
546 <remove value="&quot;"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
547 <remove value="&apos;"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
548 </valid>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
549 </sanitizer>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
550 </param>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
551 </repeat>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
552 </xml>
1bfe9f9608e4 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">
1bfe9f9608e4 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">
1bfe9f9608e4 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">
1bfe9f9608e4 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">
1bfe9f9608e4 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"/>
1bfe9f9608e4 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"/>
1bfe9f9608e4 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"/>
1bfe9f9608e4 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"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
561 </options>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
562 <sanitizer>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
563 <valid initial="default">
1bfe9f9608e4 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"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
565 <add value="\t"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
566 <remove value="&quot;"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
567 <remove value="&apos;"/>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
568 </valid>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
569 </sanitizer>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
570 </param>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
571 </repeat>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
572 </xml>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
573 <xml name="palette">
1bfe9f9608e4 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">
1bfe9f9608e4 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>
1bfe9f9608e4 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>
1bfe9f9608e4 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>
1bfe9f9608e4 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>
1bfe9f9608e4 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>
1bfe9f9608e4 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>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
581 </param>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
582 </xml>
1bfe9f9608e4 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[
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
584 #import json
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
585 #import re
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
586
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
587 mkdir -p data &&
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
588
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
589 #if $metadata_path:
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
590 ln -s '$metadata_path' data/metadata.csv &&
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
591 #end if
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
592 #if $abundance_file:
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
593 ln -s '$abundance_file' data/abundance.csv &&
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
594 #end if
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
595 #if $me_or_frac_contrib_file:
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
596 ln -s '$me_or_frac_contrib_file' data/me_or_frac_contrib.csv &&
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
597 #end if
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
598
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
599 ]]></token>
1bfe9f9608e4 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[
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
601 mkdir -p 'config' &&
1bfe9f9608e4 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' &&
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
603 ]]></token>
1bfe9f9608e4 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[
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
605 && rm -r 'config'
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
606 ]]></token>
1bfe9f9608e4 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[
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
608
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
609 mkdir -p data &&
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
610 #if $metadata_path:
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
611 ln -s '$metadata_path' data/metadata.csv &&
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
612 #end if
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
613 #if $abundance_file:
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
614 ln -s '$abundance_file' data/abundance.csv &&
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
615 #end if
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
616 #set $axisx = "condition"
1bfe9f9608e4 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":
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
618 #set $axisx = "timepoint"
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
619 #end if
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
620
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
621 ]]></token>
1bfe9f9608e4 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[
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
623
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
624 mkdir -p data &&
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
625
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
626 #if $metadata_path:
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
627 ln -s '$metadata_path' data/metadata.csv &&
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
628 #end if
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
629 #if $me_or_frac_contrib_file:
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
630 ln -s '$me_or_frac_contrib_file' data/me_or_frac_contrib.csv &&
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
631 #end if
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
632 ]]></token>
1bfe9f9608e4 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[
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
634
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
635 mkdir -p data &&
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
636
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
637 #if $metadata_path:
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
638 ln -s '$metadata_path' data/metadata.csv &&
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
639 #end if
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
640 #if $isotop_prop_file:
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
641 ln -s '$isotop_prop_file' data/isotop_prop.csv &&
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
642 #end if
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
643 ]]></token>
1bfe9f9608e4 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[
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
645
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
646 mkdir -p data &&
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
647
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
648 #if $metadata_path:
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
649 ln -s '$metadata_path' data/metadata.csv &&
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
650 #end if
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
651
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
652
1bfe9f9608e4 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 = {}
1bfe9f9608e4 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 = {}
1bfe9f9608e4 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 = {}
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
656
1bfe9f9608e4 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":
1bfe9f9608e4 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'
1bfe9f9608e4 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'
1bfe9f9608e4 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'
1bfe9f9608e4 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'
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
662 #else
1bfe9f9608e4 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'
1bfe9f9608e4 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'
1bfe9f9608e4 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'
1bfe9f9608e4 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'
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
667 #end if
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
668 #set $impute_values = {}
1bfe9f9608e4 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":
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
670 #if $data_input.abundance_file:
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
671 ln -s '$data_input.abundance_file' data/abundance.csv &&
1bfe9f9608e4 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'
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
673 #end if
1bfe9f9608e4 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":
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
675 #if $data_input.me_or_frac_contrib_file:
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
676 ln -s '$data_input.me_or_frac_contrib_file' data/me_or_frac_contrib.csv &&
1bfe9f9608e4 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'
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
678 #end if
1bfe9f9608e4 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":
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
680 #if $data_input.isotop_prop_file:
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
681 ln -s '$data_input.isotop_prop_file' data/isotop_prop.csv &&
1bfe9f9608e4 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'
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
683 #end if
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
684 #else
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
685 #if $data_input.isotop_abs_file:
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
686 ln -s '$data_input.isotop_abs_file' data/isotop_abs.csv &&
1bfe9f9608e4 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'
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
688 #end if
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
689 #end if
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
690 ]]></token>
1bfe9f9608e4 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[
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
692
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
693 mkdir -p data &&
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
694
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
695 #if $metadata_path:
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
696 ln -s '$metadata_path' data/metadata.csv &&
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
697 #end if
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
698
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
699 #set $impute_values = {}
1bfe9f9608e4 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":
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
701 #if $data_input.abundance_file:
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
702 ln -s '$data_input.abundance_file' data/abundance.csv &&
1bfe9f9608e4 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'
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
704 #end if
1bfe9f9608e4 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":
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
706 #if $data_input.me_or_frac_contrib_file:
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
707 ln -s '$data_input.me_or_frac_contrib_file' data/me_or_frac_contrib.csv &&
1bfe9f9608e4 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'
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
709 #end if
1bfe9f9608e4 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":
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
711 #if $data_input.isotop_prop_file:
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
712 ln -s '$data_input.isotop_prop_file' data/isotop_prop.csv &&
1bfe9f9608e4 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'
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
714 #end if
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
715 #else
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
716 #if $data_input.isotop_abs_file:
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
717 ln -s '$data_input.isotop_abs_file' data/isotop_abs.csv &&
1bfe9f9608e4 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'
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
719 #end if
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
720 #end if
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
721 ]]></token>
1bfe9f9608e4 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[
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
723 #import json
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
724 #import re
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
725 #import os
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
726 #import csv
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
727 #import subprocess
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
728
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
729 mkdir -p data &&
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
730
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
731 #if $path_kegg_metabolites:
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
732 ln -s '$path_kegg_metabolites' data/pathways_kegg_metabolites.csv &&
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
733 #end if
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
734 #if $path_kegg_transcripts:
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
735 ln -s '$path_kegg_transcripts' data/pathways_kegg_transcripts.csv &&
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
736 #end if
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
737
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
738 #if $metadata_path:
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
739 ln -s '$metadata_path' data/metadata.csv &&
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
740 #end if
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
741
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
742 #set $impute_values = {}
1bfe9f9608e4 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":
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
744 #if $data_input.abundance_file:
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
745 ln -s '$data_input.abundance_file' data/abundance.csv &&
1bfe9f9608e4 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'
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
747 #end if
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
748 #else:
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
749 #if $data_input.me_or_frac_contrib_file:
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
750 ln -s '$data_input.me_or_frac_contrib_file' data/me_or_frac_contrib.csv &&
1bfe9f9608e4 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'
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
752 #end if
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
753 #end if
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
754
1bfe9f9608e4 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)
1bfe9f9608e4 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)
1bfe9f9608e4 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 &&
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
758 #end for
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
759
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
760
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
761 ]]></token>
1bfe9f9608e4 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[
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
763
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
764 mkdir -p data &&
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
765
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
766 #if $metadata_path:
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
767 ln -s '$metadata_path' data/metadata.csv &&
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
768 #end if
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
769
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
770 #set $impute_values = {}
1bfe9f9608e4 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":
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
772 #if $data_input.abundance_file:
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
773 ln -s '$data_input.abundance_file' data/abundance.csv &&
1bfe9f9608e4 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'
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
775 #end if
1bfe9f9608e4 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":
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
777 #if $data_input.me_or_frac_contrib_file:
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
778 ln -s '$data_input.me_or_frac_contrib_file' data/me_or_frac_contrib.csv &&
1bfe9f9608e4 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'
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
780 #end if
1bfe9f9608e4 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":
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
782 #if $data_input.isotop_prop_file:
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
783 ln -s '$data_input.isotop_prop_file' data/isotop_prop.csv &&
1bfe9f9608e4 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'
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
785 #end if
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
786 #else
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
787 #if $data_input.isotop_abs_file:
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
788 ln -s '$data_input.isotop_abs_file' data/isotop_abs.csv &&
1bfe9f9608e4 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'
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
790 #end if
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
791 #end if
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
792 ]]></token>
1bfe9f9608e4 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[
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
794 #import re
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
795 #set $impute_values = {}
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
796 #if $abundance_file:
1bfe9f9608e4 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'
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
798 #end if
1bfe9f9608e4 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:
1bfe9f9608e4 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'
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
801 #end if
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
802 ]]></token>
1bfe9f9608e4 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[
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
804 #import re
1bfe9f9608e4 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()
1bfe9f9608e4 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":
1bfe9f9608e4 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:
1bfe9f9608e4 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"))
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
809 #end if
1bfe9f9608e4 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":
1bfe9f9608e4 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:
1bfe9f9608e4 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"))
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
813 #end if
1bfe9f9608e4 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":
1bfe9f9608e4 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:
1bfe9f9608e4 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"))
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
817 #end if
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
818 #else
1bfe9f9608e4 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:
1bfe9f9608e4 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"))
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
821 #end if
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
822 #end if
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
823 ]]></token>
1bfe9f9608e4 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[
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
825 #import re
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
826 #set $statistical_test = {}
1bfe9f9608e4 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":
1bfe9f9608e4 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:
1bfe9f9608e4 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)
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
830 #end if
1bfe9f9608e4 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":
1bfe9f9608e4 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:
1bfe9f9608e4 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)
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
834 #end if
1bfe9f9608e4 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":
1bfe9f9608e4 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:
1bfe9f9608e4 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)
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
838 #end if
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
839 #else
1bfe9f9608e4 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:
1bfe9f9608e4 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)
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
842 #end if
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
843 #end if
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
844 ]]></token>
1bfe9f9608e4 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[
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
846 #import re
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
847 #set $conds = list()
1bfe9f9608e4 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:
1bfe9f9608e4 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)))
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
850 #end for
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
851 ]]></token>
1bfe9f9608e4 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[
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
853 #set $conditions = list()
1bfe9f9608e4 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)
1bfe9f9608e4 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)
1bfe9f9608e4 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)))
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
857 #end for
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
858 ]]></token>
1bfe9f9608e4 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[
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
860 #set $conditions = list()
1bfe9f9608e4 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)
1bfe9f9608e4 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)
1bfe9f9608e4 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)))
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
864 #end for
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
865 ]]></token>
1bfe9f9608e4 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[
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
867
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
868 #import re
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
869 #set $timepoints = list()
1bfe9f9608e4 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:
1bfe9f9608e4 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)))
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
872 #end for
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
873 ]]></token>
1bfe9f9608e4 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[
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
875 #import re
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
876 #set $groups = list()
1bfe9f9608e4 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")))
1bfe9f9608e4 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")))
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
879
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
880 ]]></token>
1bfe9f9608e4 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[
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
882 #import json
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
883 #import re
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
884 #set $metabolites = {}
1bfe9f9608e4 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:
1bfe9f9608e4 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()
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
887 #for $met in $metabolites_list:
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
888 #set tmp_met=re.sub('\,', '%%',str($met))
1bfe9f9608e4 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($tmp_met))[0])
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
890 #set tmp_met_ter=re.sub('%%', '\,',str($tmp_met_bis))
1bfe9f9608e4 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)))
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
892 #end for
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
893 #end for
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
894 ]]></token>
1bfe9f9608e4 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[
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
896 #set $metabolites = {}
1bfe9f9608e4 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:
1bfe9f9608e4 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()
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
899 #for $met in $metabolites_list:
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
900 #set tmp_met=re.sub('\,', '--',str($met))
1bfe9f9608e4 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($tmp_met))[0])
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
902 #set tmp_met_ter=re.sub('--', '\,',str($tmp_met_bis))
1bfe9f9608e4 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)))
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
904 #end for
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
905 #end for
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
906 ]]></token>
1bfe9f9608e4 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[
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
908 #set $comparisons = list()
1bfe9f9608e4 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:
1bfe9f9608e4 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
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
911 #set $ctrl=""
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
912
1bfe9f9608e4 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:
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
914 #set $sub_comparisons = list()
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
915 #if str($co) in ["Control", "control","ctrl"]:
1bfe9f9608e4 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
1bfe9f9608e4 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)
1bfe9f9608e4 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)))
1bfe9f9608e4 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)))
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
920 #else:
1bfe9f9608e4 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)))
1bfe9f9608e4 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)))
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
923
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
924 #end if
1bfe9f9608e4 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)
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
926 #end for
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
927 #end for
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
928 ]]></token>
1bfe9f9608e4 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[
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
930 #import re
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
931 #set $conditions = list()
1bfe9f9608e4 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)
1bfe9f9608e4 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)
1bfe9f9608e4 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)))
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
935 #end for
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
936
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
937 ]]></token>
1bfe9f9608e4 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[
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
939 #import re
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
940 #set $conditions = list()
1bfe9f9608e4 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)
1bfe9f9608e4 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)
1bfe9f9608e4 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)))
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
944 #end for
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
945 ]]></token>
1bfe9f9608e4 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[
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
947 #import re
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
948 #set $conditions = list()
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
949 #set $timepoints = list()
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
950 #set $comparisons = list()
1bfe9f9608e4 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)
1bfe9f9608e4 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)
1bfe9f9608e4 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()
1bfe9f9608e4 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)
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
955 #set $sub_comparisons = list()
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
956 #if str($t.condition) not in $conditions:
1bfe9f9608e4 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)))
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
958 #end if
1bfe9f9608e4 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)))
1bfe9f9608e4 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)))
1bfe9f9608e4 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)
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
962 #end for
1bfe9f9608e4 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)))
1bfe9f9608e4 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)
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
965 #end for
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
966
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
967
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
968
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
969 ]]></token>
1bfe9f9608e4 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[
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
971 #import re
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
972 #set $conds = list()
1bfe9f9608e4 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:
1bfe9f9608e4 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)))
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
975 #end for
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
976 #set $timepoints = list()
1bfe9f9608e4 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:
1bfe9f9608e4 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)))
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
979 #end for
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
980
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
981 #set $comparisons = list()
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
982 #if len($conds) > 1:
1bfe9f9608e4 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:
1bfe9f9608e4 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:
1bfe9f9608e4 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
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
986 #set $ctrl=""
1bfe9f9608e4 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()
1bfe9f9608e4 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:
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
989 #set $sub_comparisons = list()
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
990 #if str($co) in ["'Control'", "'control'", "'ctrl'"]:
1bfe9f9608e4 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
1bfe9f9608e4 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)
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
993 #else:
1bfe9f9608e4 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)))
1bfe9f9608e4 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)))
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
996
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
997 #end if
1bfe9f9608e4 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)
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
999 #end for
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1000
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1001 #if $ctrl_found:
1bfe9f9608e4 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))
1bfe9f9608e4 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))
1bfe9f9608e4 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)
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1005 #end if
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1006
1bfe9f9608e4 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)
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1008 #end for
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1009 #else
1bfe9f9608e4 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:
1bfe9f9608e4 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)))
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1012 #end for
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1013 #end if
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1014
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1015 #else
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1016 #if len($conds) > 0:
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1017 #if len($timepoints) > 1:
1bfe9f9608e4 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:
1bfe9f9608e4 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()
1bfe9f9608e4 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:
1bfe9f9608e4 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()
1bfe9f9608e4 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)))
1bfe9f9608e4 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)))
1bfe9f9608e4 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)
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1025 #end for
1bfe9f9608e4 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)
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1027 #end for
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1028 #end if
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1029 #else
1bfe9f9608e4 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:
1bfe9f9608e4 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)))
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1032 #end for
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1033 #end if
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1034 #end if
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1035 ]]></token>
1bfe9f9608e4 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[
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1037 #import re
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1038 #set $conditions = list()
1bfe9f9608e4 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)
1bfe9f9608e4 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)
1bfe9f9608e4 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)))
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1042 #end for
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1043
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1044 #set $timepoints = list()
1bfe9f9608e4 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:
1bfe9f9608e4 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)))
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1047 #end for
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1048
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1049 #set $comparisons = list()
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1050 #if len($conditions) > 1:
1bfe9f9608e4 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:
1bfe9f9608e4 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:
1bfe9f9608e4 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
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1054 #set $ctrl=""
1bfe9f9608e4 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()
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1056
1bfe9f9608e4 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:
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1058 #set $sub_comparisons = list()
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1059 #if str($co) in ["'Control'", "'control'", "'ctrl'"]:
1bfe9f9608e4 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
1bfe9f9608e4 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)
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1062 #else:
1bfe9f9608e4 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)))
1bfe9f9608e4 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)))
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1065
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1066 #end if
1bfe9f9608e4 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)
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1068 #end for
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1069
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1070 #if $ctrl_found:
1bfe9f9608e4 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))
1bfe9f9608e4 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))
1bfe9f9608e4 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)
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1074 #end if
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1075
1bfe9f9608e4 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)
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1077 #end for
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1078 #else
1bfe9f9608e4 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:
1bfe9f9608e4 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)))
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1081 #end for
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1082 #end if
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1083
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1084 #else
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1085 #if len($conditions) > 0:
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1086 #if len($timepoints) > 1:
1bfe9f9608e4 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:
1bfe9f9608e4 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()
1bfe9f9608e4 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:
1bfe9f9608e4 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()
1bfe9f9608e4 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)))
1bfe9f9608e4 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)))
1bfe9f9608e4 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)
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1094 #end for
1bfe9f9608e4 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)
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1096 #end for
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1097 #end if
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1098 #else
1bfe9f9608e4 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:
1bfe9f9608e4 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)))
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1101 #end for
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1102 #end if
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1103 #end if
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1104 ]]></token>
1bfe9f9608e4 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[
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1106 #import re
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1107 #import os
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1108 #import subprocess
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1109 #set $transcripts = list()
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1110
1bfe9f9608e4 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)
1bfe9f9608e4 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)
1bfe9f9608e4 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)))
1bfe9f9608e4 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))
1bfe9f9608e4 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))
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1116 #end for
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1117 ]]></token>
1bfe9f9608e4 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[
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1119 #set $pathways = {}
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1120 #if $path_kegg_metabolites:
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1121 #silent $pathways['metabolites']='pathways_kegg_metabolites'
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1122 #end if
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1123 #if $path_kegg_transcripts:
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1124 #silent $pathways['transcripts']='pathways_kegg_transcripts'
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1125 #end if
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1126 ]]></token>
1bfe9f9608e4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents:
diff changeset
1127 </macros>