Mercurial > repos > iuc > dimet_isotopologues_plot

annotate macros.xml @ 5:89ca62980a2e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit b74312f0a6cb28e204f8633453e493fa0b2c89d8
author iuc
date Tue, 21 May 2024 13:41:17 +0000
parents 16c64719226c
children a7d1d77e7cc3
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1 <macros>
4
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2 <token name="@TOOL_VERSION@">0.2.4</token>
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3 <token name="@VERSION_SUFFIX@">2</token>
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4 <xml name="requirements">
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5 <requirements>
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6 <requirement type="package" version="@TOOL_VERSION@">dimet</requirement>
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7 </requirements>
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8 </xml>
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9 <xml name="statistical_test_for_multigroup">
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10 <param name="stat_test" type="select" value="KW" display="radio" label="Select statistical to apply" help="Please enter at max 1 statistical test by file">
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11 <option value="KW">Kruskal-Wallis</option>
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12 </param>
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13 </xml>
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14 <xml name="statistical_test_for_bivariate_analysis">
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15 <param name="stat_test" type="select" value="pearson" display="radio" label="Select statistical to apply" help="Please enter at max 1 statistical test by file">
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16 <option value="pearson">pearson</option>
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17 <option value="spearman">spearman</option>
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18 </param>
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19 </xml>
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20 <xml name="statistical_test">
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21 <conditional name="statistics">
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22 <param name="statistical_test_type" type="select" label="Choose which type of statistical test to perform" help="Choose which type of statistical test to perform">
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23 <option value="parametric">parametric</option>
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24 <option value="non-parametric-rank" selected="true">non-parametric (rank based)</option>
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25 <option value="non-parametric-distribution">non-parametric (distribution based)</option>
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26 </param>
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27 <when value="parametric">
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28 <param name="stat_test" type="select" display="radio" label="Select statistical to apply" help="Please enter at max 1 statistical test by file">
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29 <option value="Tt" selected="true">t-test</option>
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30 </param>
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31 </when>
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32 <when value="non-parametric-rank">
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33 <param name="stat_test" type="select" display="radio" label="Select statistical to apply" help="Please enter at max 1 statistical test by file">
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34 <option value="MW">Mann Whitney</option>
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35 <option value="KW">Kruskal-Wallis</option>
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36 <option value="ranksum" selected="true">Wilcoxon's rank sum test</option>
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37 <option value="Wcox">Wilcoxon signed-rank test</option>
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38 <option value="BrMu">Brunner-Munzel test</option>
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39 </param>
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40 </when>
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41 <when value="non-parametric-distribution">
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42 <param name="stat_test" type="select" display="radio" label="Select statistical to apply" help="Please enter at max 1 statistical test by file">
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43 <option value="prm-scipy" selected="true">permutations test</option>
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44 <option value="disfit">distribution fitting (of the z-score of the ratios), disfit needs several hundreds of metabolites to be trustful.</option>
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45 </param>
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46 </when>
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47 </conditional>
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48
0
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49 </xml>
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50 <xml name="citations">
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51 <citations>
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52 <citation type="bibtex">
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53 @software{Galvis_Rodriguez_DIMet,
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54 author = {Galvis Rodriguez, Johanna and Guyon, Joris and Dartigues, Benjamin and Specque, Florian and Daubon, Thomas and Karkar, Slim and Nikolski, Macha},
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55 license = {MIT},
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56 title = {{DIMet}},
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57 url = {https://github.com/cbib/DIMet}
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58 }
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59
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60 </citation>
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61 </citations>
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62
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63 </xml>
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64 <xml name="metadata_file_macros">
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65 <param name="metadata_path" type="data" format="tabular" label="metadata file" help="The metadata, a unique file with the description of the samples in your measures' files. This is compulsory, see section Metadata File Information."/>
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66 </xml>
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67 <xml name="abundance_file_macros">
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68 <param name="abundance_file" type="data" format="tabular" label="Metabolite abundance file" help="The total abundances file must be organized as a matrix: - The first column must contain Metabolite IDs that are unique (not repeated) within the file. - The rest of the columns correspond to the samples - The rows correspond to the metabolites - The values must be tab separated, with the first row containing the sample/column labels. (see help below for more details)"/>
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69 </xml>
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70 <xml name="enrichment_file_macros">
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71 <param name="me_or_frac_contrib_file" type="data" format="tabular" label="Metabolite enrichment file" help="The mean enrichment file must be organized as a matrix: - The first column must contain Metabolite IDs that are unique (not repeated) within the file. - The rest of the columns correspond to the samples. - The rows correspond to the metabolites. - The values must be tab separated, with the first row containing the sample/column labels. (see help below for more details)"/>
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72 </xml>
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73 <xml name="isotopologue_prop_file_macros">
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74 <param name="isotop_prop_file" type="data" format="tabular" label="Isotopologues proportion abundance file" help=" The isotopologue proportions file must be organized as a matrix: - The first column must contain isotopologues IDs that are unique (not repeated) within the file. - The rest of the columns correspond to the samples. - The rows correspond to the isotopologues. - The values must be tab separated, with the first row containing the sample/column labels (see help below for more details)."/>
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75 </xml>
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76 <xml name="isotopologue_abs_file_macros">
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77 <param name="isotop_abs_file" type="data" format="tabular" label="Isotopologues absolute abundance file" help="The isotopologue absolute values file must be organized as a matrix: - The first column must contain isotopologues IDs that are unique (not repeated) within the file. - The rest of the columns correspond to the samples. - The rows correspond to the isotopologues. - The values must be tab separated, with the first row containing the sample/column labels (see help below for more details)."/>
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78 </xml>
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79 <xml name="input_parameters_pca">
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80 <expand macro="abundance_file_macros"/>
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81 <param name="me_or_frac_contrib_file" type="data" optional="true" format="tabular" label="Mean enrichment or fraction contribution file"/>
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82 <expand macro="metadata_file_macros"/>
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83 </xml>
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84 <xml name="input_parameters_abundance">
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iuc
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85 <expand macro="abundance_file_macros"/>
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iuc
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86 <expand macro="metadata_file_macros"/>
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87 </xml>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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88 <xml name="input_parameters_enrichment">
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89 <expand macro="enrichment_file_macros"/>
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90 <expand macro="metadata_file_macros"/>
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91 </xml>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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92 <xml name="input_parameters_isotopologue">
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93 <expand macro="isotopologue_prop_file_macros"/>
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94 <expand macro="metadata_file_macros"/>
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95 </xml>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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96 <xml name="input_parameters_metabologram">
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97 <conditional name="data_input">
2
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98 <param name="data_input_selector" type="select" label="Abundance, Enrichment or Isotopologues quantification files" help="Select between raw abundance and mean enrichment files">
0
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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99 <option value="abundance" selected="True">abundance</option>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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100 <option value="mean_enrichment">mean_enrichment</option>
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101 </param>
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102 <when value="abundance">
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103 <expand macro="abundance_file_macros"/>
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104 <param name="metabolites_list" type="select" optional="false" multiple="true"
2
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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">
0
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106 <validator type="length" min="1" message="Please enter at max 2 compartments"/>
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107 <options from_dataset="abundance_file">
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108 <column name="metabolite_or_isotopologue" index="0"/>
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109 <column name="value" index="0"/>
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110 <filter type="unique_value" name="metabolite_or_isotopologue" column="0"/>
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111 <filter type="remove_value" value="metabolite_or_isotopologue"/>
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112 </options>
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113 <sanitizer>
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114 <valid initial="default">
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115 <add preset="string.printable"/>
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116 <add value="\t"/>
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117 <remove value="&quot;"/>
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118 <remove value="&apos;"/>
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119 </valid>
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120 </sanitizer>
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121 </param>
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122 <expand macro="statistical_test"/>
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123 </when>
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124 <when value="mean_enrichment">
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125 <expand macro="enrichment_file_macros"/>
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126 <param name="metabolites_list" type="select" optional="false" multiple="true"
2
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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">
0
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128 <validator type="length" min="1" message="Please enter at max 2 compartments"/>
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129 <options from_dataset="me_or_frac_contrib_file">
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130 <column name="metabolite_or_isotopologue" index="0"/>
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131 <column name="value" index="0"/>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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132 <filter type="unique_value" name="metabolite_or_isotopologue" column="0"/>
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iuc
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133 <filter type="remove_value" value="metabolite_or_isotopologue"/>
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134 </options>
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135 <sanitizer>
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136 <valid initial="default">
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iuc
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137 <add preset="string.printable"/>
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138 <add value="\t"/>
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139 <remove value="&quot;"/>
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iuc
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140 <remove value="&apos;"/>
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141 </valid>
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142 </sanitizer>
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143 </param>
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144 <expand macro="statistical_test"/>
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145 </when>
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146 </conditional>
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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)"/>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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148 <param name="path_kegg_transcripts" type="data" format="tabular" label="Pathways kegg transcripts file" help="A file with the pathways and respective gene symbols, which must match with those present in the transcriptomics data. The names of the columns must be the pathways' names, see the minimal data example downloaded from zenodo as explained above. (see help below for more details)"/>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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149 <expand macro="metadata_file_macros"/>
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150 </xml>
2
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151 <xml name="input_parameters_bivar_analysis">
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152 <conditional name="data_input">
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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">
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154 <option value="abundance" selected="True">abundance</option>
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155 <option value="mean_enrichment">mean_enrichment</option>
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156 <option value="isotop_prop">isotop_prop</option>
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157 <option value="isotop_abs">isotop_abs</option>
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158 </param>
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159 <when value="abundance">
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160 <expand macro="abundance_file_macros"/>
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161
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162 </when>
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163 <when value="mean_enrichment">
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164 <expand macro="enrichment_file_macros"/>
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165 </when>
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166 <when value="isotop_prop">
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167 <expand macro="isotopologue_prop_file_macros"/>
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168 </when>
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169 <when value="isotop_abs">
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170 <expand macro="isotopologue_abs_file_macros"/>
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171 </when>
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172 </conditional>
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173 <expand macro="metadata_file_macros"/>
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174 <expand macro="statistical_test_for_bivariate_analysis"/>
2
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175 </xml>
0
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176 <xml name="input_parameters_diff_analysis">
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177 <conditional name="data_input">
2
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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">
0
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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179 <option value="abundance" selected="True">abundance</option>
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180 <option value="mean_enrichment">mean_enrichment</option>
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181 <option value="isotop_prop">isotop_prop</option>
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182 <option value="isotop_abs">isotop_abs</option>
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183 </param>
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184 <when value="abundance">
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185 <expand macro="abundance_file_macros"/>
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186 <expand macro="statistical_test"/>
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187
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188 </when>
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189 <when value="mean_enrichment">
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190 <expand macro="enrichment_file_macros"/>
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191 <expand macro="statistical_test"/>
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192 </when>
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193 <when value="isotop_prop">
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194 <expand macro="isotopologue_prop_file_macros"/>
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195 <expand macro="statistical_test"/>
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196 </when>
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197 <when value="isotop_abs">
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198 <expand macro="isotopologue_abs_file_macros"/>
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199 <expand macro="statistical_test"/>
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200 </when>
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201 </conditional>
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202 <expand macro="metadata_file_macros"/>
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203 </xml>
2
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204 <xml name="input_parameters_multi_diff_analysis">
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205 <conditional name="data_input">
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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">
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
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207 <option value="abundance" selected="True">abundance</option>
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208 <option value="mean_enrichment">mean_enrichment</option>
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209 <option value="isotop_prop">isotop_prop</option>
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210 <option value="isotop_abs">isotop_abs</option>
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211 </param>
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212 <when value="abundance">
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213 <expand macro="abundance_file_macros"/>
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214 <expand macro="statistical_test_for_multigroup"/>
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215
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216 </when>
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217 <when value="mean_enrichment">
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218 <expand macro="enrichment_file_macros"/>
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219 <expand macro="statistical_test_for_multigroup"/>
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220 </when>
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221 <when value="isotop_prop">
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222 <expand macro="isotopologue_prop_file_macros"/>
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223 <expand macro="statistical_test_for_multigroup"/>
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224 </when>
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225 <when value="isotop_abs">
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226 <expand macro="isotopologue_abs_file_macros"/>
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227 <expand macro="statistical_test_for_multigroup"/>
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228 </when>
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229 </conditional>
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230 <expand macro="metadata_file_macros"/>
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231 </xml>
0
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232 <xml name="suffix">
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233 <param name="suffix" type="text" optional="false" label="suffix to add to output files" >
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234 <sanitizer invalid_char="">
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235 <valid initial="string.ascii_letters,string.digits">
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236 <add value="_" />
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237 </valid>
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238 </sanitizer>
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239 </param>
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240 </xml>
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241 <xml name="conditions">
2
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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">
0
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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243 <options from_dataset="metadata_path">
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244 <column name="condition" index="1"/>
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245 <column name="value" index="1"/>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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246 <filter type="unique_value" name="condition" column="condition"/>
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247 <filter type="remove_value" value="condition"/>
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248 </options>
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249 <sanitizer>
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250 <valid initial="default">
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251 <add preset="string.printable"/>
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252 <add value="\t"/>
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253 <remove value="&quot;"/>
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254 <remove value="&apos;"/>
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255 </valid>
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256 </sanitizer>
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257 </param>
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258 </xml>
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259 <xml name="conditions_multigroup">
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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">
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261 <options from_dataset="metadata_path">
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262 <column name="condition" index="1"/>
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263 <column name="value" index="1"/>
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264 <filter type="unique_value" name="condition" column="condition"/>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
265 <filter type="remove_value" value="condition"/>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
266 </options>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
267 <sanitizer>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
268 <valid initial="default">
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
269 <add preset="string.printable"/>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
270 <add value="\t"/>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
271 <remove value="&quot;"/>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
272 <remove value="&apos;"/>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
273 </valid>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
274 </sanitizer>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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diff changeset
275 </param>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
276 </xml>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
277 <xml name="timepoint_multigroup">
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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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">
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
279 <options from_dataset="metadata_path">
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
280 <column name="timepoint" index="2"/>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
281 <column name="value" index="2"/>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
282 <filter type="unique_value" name="timepoint" column="2"/>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
283 <filter type="remove_value" value="timepoint"/>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
284 <filter type="sort_by" name="timepoint" column="1"/>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
285 </options>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
286 <sanitizer>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
287 <valid initial="default">
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
288 <add preset="string.printable"/>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
289 <add value="\t"/>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
290 <remove value="&quot;"/>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
291 <remove value="&apos;"/>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
292 </valid>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
293 </sanitizer>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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diff changeset
294 </param>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
295 </xml>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
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296 <xml name="timepoint">
2
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
297 <param name="timepoint" type="select" optional="false" multiple="true" label="Browse timepoint from metadata file (1 min.)">
0
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
298 <options from_dataset="metadata_path">
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
299 <column name="timepoint" index="2"/>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
300 <column name="value" index="2"/>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
301 <filter type="unique_value" name="timepoint" column="2"/>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
302 <filter type="remove_value" value="timepoint"/>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
303 <filter type="sort_by" name="timepoint" column="1"/>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
304 </options>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
305 <sanitizer>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
306 <valid initial="default">
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
307 <add preset="string.printable"/>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
308 <add value="\t"/>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
309 <remove value="&quot;"/>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
310 <remove value="&apos;"/>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
311 </valid>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
312 </sanitizer>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
313 </param>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
314 </xml>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
315 <xml name="grouping">
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
316 <param name="grouping" type="select" optional="false" multiple="true" label="Browse group to compare">
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
317 <option value="condition" selected="true">condition</option>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
318 <option value="timepoint" selected="true">timepoint</option>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
319 </param>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
320 </xml>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
321 <xml name="correction_method">
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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">
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
323 <option value="bonferroni">bonferroni</option>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
324 <option value="holm-sidak">holm-sidak</option>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
325 <option value="holm">holm</option>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
326 <option value="simes-hochberg">simes-hochberg</option>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
327 <option value="hommel">hommel</option>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
328 <option value="fdr_bh">fdr_bh</option>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
329 <option value="fdr_by">fdr_by</option>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
330 <option value="fdr_tsbh">fdr_tsbh</option>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
331 <option value="fdr_tsbky">fdr_tsbky</option>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
332 </param>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
333 </xml>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
334 <xml name="compartments_enrichment">
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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diff changeset
335 <param name="compartments" type="select" optional="false" multiple="true"
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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diff changeset
336 label="Browse compartments from metadata file (All needed). You have to load a metadata file prior to have access to compartments">
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
337 <options from_dataset="metadata_path">
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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diff changeset
338 <column name="compartment" index="4"/>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
339 <column name="value" index="4"/>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
340 <filter type="unique_value" name="compartment" column="4"/>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
341 <filter type="remove_value" value="compartment"/>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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diff changeset
342 </options>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
343 <sanitizer>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
344 <valid initial="default">
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
345 <add preset="string.printable"/>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
346 <add value="\t"/>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
347 <remove value="&quot;"/>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
348 <remove value="&apos;"/>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
349 </valid>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
350 </sanitizer>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
351 </param>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
352 </xml>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
353 <xml name="compartments_abundance">
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
354 <param name="compartments" type="select" optional="false" multiple="true"
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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">
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
356 <options from_dataset="metadata_path">
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
357 <column name="compartment" index="4"/>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
358 <column name="value" index="4"/>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
359 <filter type="unique_value" name="compartment" column="4"/>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
360 <filter type="remove_value" value="compartment"/>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
361 </options>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
362 <sanitizer>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
363 <valid initial="default">
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
364 <add preset="string.printable"/>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
365 <add value="\t"/>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
366 <remove value="&quot;"/>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
367 <remove value="&apos;"/>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
368 </valid>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
369 </sanitizer>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
370 </param>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
371 </xml>
2
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
372 <xml name="compartments_metabologram">
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
373 <param name="compartments" type="select" optional="false" multiple="false"
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
374 label="Browse compartments from metadata file (1 max.). You have to load a metadata file prior to have access to compartments">
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
375 <options from_dataset="metadata_path">
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
376 <column name="compartment" index="4"/>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
377 <column name="value" index="4"/>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
378 <filter type="unique_value" name="compartment" column="4"/>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
379 <filter type="remove_value" value="compartment"/>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
380 </options>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
381 <sanitizer>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
382 <valid initial="default">
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
383 <add preset="string.printable"/>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
384 <add value="\t"/>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
385 <remove value="&quot;"/>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
386 <remove value="&apos;"/>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
387 </valid>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
388 </sanitizer>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
389 </param>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
390 </xml>
0
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
391 <xml name="compartments">
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
392 <param name="compartments" type="select" optional="false" multiple="true"
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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">
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
394 <options from_dataset="metadata_path">
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
395 <column name="compartment" index="4"/>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
396 <column name="value" index="4"/>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
397 <filter type="unique_value" name="compartment" column="4"/>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
398 <filter type="remove_value" value="compartment"/>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
399 </options>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
400 <sanitizer>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
401 <valid initial="default">
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
402 <add preset="string.printable"/>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
403 <add value="\t"/>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
404 <remove value="&quot;"/>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
405 <remove value="&apos;"/>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
406 </valid>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
407 </sanitizer>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
408 </param>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
409 </xml>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
410 <xml name="abundance_metabolites_list">
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
411 <param name="metabolites_list" type="select" optional="false" multiple="true"
2
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
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">
0
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
413 <validator type="length" min="1" message="Please enter at max 2 compartments"/>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
414 <options from_dataset="abundance_file">
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
415 <column name="metabolite_or_isotopologue" index="0"/>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
416 <column name="value" index="0"/>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
417 <filter type="unique_value" name="metabolite_or_isotopologue" column="0"/>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
418 <filter type="remove_value" value="metabolite_or_isotopologue"/>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
419 </options>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
420 <sanitizer>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
421 <valid initial="default">
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
422 <add preset="string.printable"/>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
423 <add value="\t"/>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
424 <remove value="&quot;"/>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
425 <remove value="&apos;"/>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
426 </valid>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
427 </sanitizer>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
428 </param>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
429 </xml>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
430 <xml name="enrichment_metabolites_list">
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
431 <param name="metabolites_list" type="select" optional="false" multiple="true"
2
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
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">
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
433 <validator type="length" min="1" message="Please enter at min 1 metabolite"/>
0
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
434 <options from_dataset="me_or_frac_contrib_file">
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
435 <column name="ID" index="0"/>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
436 <column name="value" index="0"/>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
437 <filter type="unique_value" name="ID" column="0"/>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
438 <filter type="remove_value" value="ID"/>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
439 </options>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
440 <sanitizer>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
441 <valid initial="default">
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
442 <add preset="string.printable"/>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
443 <add value="\t"/>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
444 <remove value="&quot;"/>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
445 <remove value="&apos;"/>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
446 </valid>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
447 </sanitizer>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
448 </param>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
449 </xml>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
450 <xml name="isotopologue_metabolites_list">
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
451 <param name="metabolites_list" type="select" optional="false" multiple="true"
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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">
2
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
453 <validator type="length" min="1" message="Please enter at min 1 metabolite"/>
0
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
454 <options from_dataset="isotop_prop_file">
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
455 <column name="ID" index="0"/>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
456 <column name="value" index="0"/>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
457 <filter type="unique_value" name="ID" column="0"/>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
458 <filter type="remove_value" value="ID"/>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
459 </options>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
460 <sanitizer>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
461 <valid initial="default">
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
462 <add preset="string.printable"/>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
463 <add value="\t"/>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
464 <remove value="&quot;"/>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
465 <remove value="&apos;"/>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
466 </valid>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
467 </sanitizer>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
468 </param>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
469 </xml>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
470 <xml name="deg_list">
2
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
471 <repeat name="deg_list" title="Deregulated gene set" default="1" min="1">
0
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
472 <param name="input" type="data" format="tabular" label="Deregulated genes set"/>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
473 <param name="idcol" type="data_column" data_ref="input" label="Column for id" use_header_names="true"/>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
474 <param name="valuecol" type="data_column" data_ref="input" label="Column for values" use_header_names="true"/>
2
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
475 <param name="timepoint" type="select" optional="false" multiple="false" label="Browse timepoint from metadata file (1 min.)">
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
476 <options from_dataset="metadata_path">
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
477 <column name="timepoint" index="2"/>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
478 <column name="value" index="2"/>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
479 <filter type="unique_value" name="timepoint" column="2"/>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
480 <filter type="remove_value" value="timepoint"/>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
481 <filter type="sort_by" name="timepoint" column="1"/>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
482 </options>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
483 <sanitizer>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
484 <valid initial="default">
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
485 <add preset="string.printable"/>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
486 <add value="\t"/>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
487 <remove value="&quot;"/>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
488 <remove value="&apos;"/>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
489 </valid>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
490 </sanitizer>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
491 </param>
5
89ca62980a2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit b74312f0a6cb28e204f8633453e493fa0b2c89d8
iuc
parents: 4
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">
2
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
493 <param name="condition" label="Condition" type="select" optional="false" multiple="false">
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
494 <options from_dataset="metadata_path">
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
495 <column name="condition" index="1"/>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
496 <column name="value" index="1"/>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
497 <filter type="unique_value" name="condition" column="condition"/>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
498 <filter type="remove_value" value="condition"/>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
499 </options>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
500 <sanitizer>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
501 <valid initial="default">
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
502 <add preset="string.printable"/>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
503 <add value="\t"/>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
504 <remove value="&quot;"/>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
505 <remove value="&apos;"/>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
506 </valid>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
507 </sanitizer>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
508 </param>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
509 </repeat>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
510
0
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
511 </repeat>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
512 </xml>
2
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
513 <xml name="plot_abundance_factor_list">
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
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">
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
515 <param name="condition" label="Condition" type="select" optional="false" multiple="false">
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
516 <options from_dataset="metadata_path">
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
517 <column name="condition" index="1"/>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
518 <column name="value" index="1"/>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
519 <filter type="unique_value" name="condition" column="condition"/>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
520 <filter type="remove_value" value="condition"/>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
521 </options>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
522 <sanitizer>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
523 <valid initial="default">
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
524 <add preset="string.printable"/>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
525 <add value="\t"/>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
526 <remove value="&quot;"/>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
527 <remove value="&apos;"/>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
528 </valid>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
529 </sanitizer>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
530 </param>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
531 </repeat>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
532 </xml>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
533 <xml name="plot_factor_list">
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
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">
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
535 <param name="condition" label="Condition" type="select" optional="false" multiple="false">
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
536 <options from_dataset="metadata_path">
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
537 <column name="condition" index="1"/>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
538 <column name="value" index="1"/>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
539 <filter type="unique_value" name="condition" column="condition"/>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
540 <filter type="remove_value" value="condition"/>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
541 </options>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
542 <sanitizer>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
543 <valid initial="default">
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
544 <add preset="string.printable"/>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
545 <add value="\t"/>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
546 <remove value="&quot;"/>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
547 <remove value="&apos;"/>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
548 </valid>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
549 </sanitizer>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
550 </param>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
551 </repeat>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
552 </xml>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
553 <xml name="factor_list">
5
89ca62980a2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit b74312f0a6cb28e204f8633453e493fa0b2c89d8
iuc
parents: 4
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">
2
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
555 <param name="condition" label="Condition" type="select" optional="false" multiple="false">
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
556 <options from_dataset="metadata_path">
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
557 <column name="condition" index="1"/>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
558 <column name="value" index="1"/>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
559 <filter type="unique_value" name="condition" column="condition"/>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
560 <filter type="remove_value" value="condition"/>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
561 </options>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
562 <sanitizer>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
563 <valid initial="default">
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
564 <add preset="string.printable"/>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
565 <add value="\t"/>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
566 <remove value="&quot;"/>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
567 <remove value="&apos;"/>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
568 </valid>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
569 </sanitizer>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
570 </param>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
571 </repeat>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
572 </xml>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
573 <xml name="palette">
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
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">
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
575 <option value="pastel" selected="true">pastel</option>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
576 <option value="deep">deep</option>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
577 <option value="muted">muted</option>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
578 <option value="bright">bright</option>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
579 <option value="dark">dark</option>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
580 <option value="colorblind">colorblind</option>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
581 </param>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
582 </xml>
0
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
583 <token name="@INIT_PCA@"><![CDATA[
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
584 #import json
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
585 #import re
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
586
2
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
587 mkdir -p data &&
0
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
588
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
589 #if $metadata_path:
2
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
590 ln -s '$metadata_path' data/metadata.csv &&
0
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
591 #end if
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
592 #if $abundance_file:
2
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
593 ln -s '$abundance_file' data/abundance.csv &&
0
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
594 #end if
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
595 #if $me_or_frac_contrib_file:
2
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
596 ln -s '$me_or_frac_contrib_file' data/me_or_frac_contrib.csv &&
0
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
597 #end if
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
598
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
599 ]]></token>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
600 <token name="@INIT_CONFIG@"><![CDATA[
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
601 mkdir -p '$__new_file_path__/config' &&
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
602 touch '$__new_file_path__/config/config.yaml' &&
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
603 ]]></token>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
604 <token name="@REMOVE_CONFIG@"><![CDATA[
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
605 && rm -r '$__new_file_path__/config'
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
606 ]]></token>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
607 <token name="@INIT_ABUNDANCE_PLOT@"><![CDATA[
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
608
2
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
609 mkdir -p data &&
0
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
610
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
611 #if $metadata_path:
2
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
612 ln -s '$metadata_path' data/metadata.csv &&
0
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
613 #end if
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
614 #if $abundance_file:
2
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
615 ln -s '$abundance_file' data/abundance.csv &&
0
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
616 #end if
5
89ca62980a2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit b74312f0a6cb28e204f8633453e493fa0b2c89d8
iuc
parents: 4
diff changeset
617 #set $axisx = "condition"
89ca62980a2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit b74312f0a6cb28e204f8633453e493fa0b2c89d8
iuc
parents: 4
diff changeset
618 #if str( $output_options.bar_color ) == "condition":
89ca62980a2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit b74312f0a6cb28e204f8633453e493fa0b2c89d8
iuc
parents: 4
diff changeset
619 #set $axisx = "timepoint"
89ca62980a2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit b74312f0a6cb28e204f8633453e493fa0b2c89d8
iuc
parents: 4
diff changeset
620 #end if
89ca62980a2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit b74312f0a6cb28e204f8633453e493fa0b2c89d8
iuc
parents: 4
diff changeset
621
0
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
622 ]]></token>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
623 <token name="@INIT_ENRICHMENT_PLOT@"><![CDATA[
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
624
2
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
625 mkdir -p data &&
0
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
626
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
627 #if $metadata_path:
2
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
628 ln -s '$metadata_path' data/metadata.csv &&
0
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
629 #end if
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
630 #if $me_or_frac_contrib_file:
2
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
631 ln -s '$me_or_frac_contrib_file' data/me_or_frac_contrib.csv &&
0
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
632 #end if
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
633 ]]></token>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
634 <token name="@INIT_ISOTOPOLOGUE_PLOT@"><![CDATA[
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
635
2
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
636 mkdir -p data &&
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
637
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
638 #if $metadata_path:
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
639 ln -s '$metadata_path' data/metadata.csv &&
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
640 #end if
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
641 #if $isotop_prop_file:
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
642 ln -s '$isotop_prop_file' data/isotop_prop.csv &&
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
643 #end if
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
644 ]]></token>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
645 <token name="@INIT_BI_ANALYSIS@"><![CDATA[
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
646
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
647 mkdir -p data &&
0
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
648
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
649 #if $metadata_path:
2
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
650 ln -s '$metadata_path' data/metadata.csv &&
0
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
651 #end if
4
16c64719226c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit afc87f0254b4399b71e53735966032ba1a32434d
iuc
parents: 3
diff changeset
652
16c64719226c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit afc87f0254b4399b71e53735966032ba1a32434d
iuc
parents: 3
diff changeset
653
2
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
654 #set conditions_MDV_comparison = {}
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
655 #set timepoints_MDV_comparison = {}
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
656 #set conditions_metabolite_time_profiles = {}
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
657
4
16c64719226c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit afc87f0254b4399b71e53735966032ba1a32434d
iuc
parents: 3
diff changeset
658 #if str( $stat_test ) == "pearson":
16c64719226c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit afc87f0254b4399b71e53735966032ba1a32434d
iuc
parents: 3
diff changeset
659 #silent $conditions_MDV_comparison['isotopologue_proportions']='pearson'
16c64719226c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit afc87f0254b4399b71e53735966032ba1a32434d
iuc
parents: 3
diff changeset
660 #silent $timepoints_MDV_comparison['isotopologue_proportions']='pearson'
16c64719226c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit afc87f0254b4399b71e53735966032ba1a32434d
iuc
parents: 3
diff changeset
661 #silent $conditions_metabolite_time_profiles['abundances']='pearson'
16c64719226c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit afc87f0254b4399b71e53735966032ba1a32434d
iuc
parents: 3
diff changeset
662 #silent $conditions_metabolite_time_profiles['mean_enrichment']='pearson'
16c64719226c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit afc87f0254b4399b71e53735966032ba1a32434d
iuc
parents: 3
diff changeset
663 #else
16c64719226c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit afc87f0254b4399b71e53735966032ba1a32434d
iuc
parents: 3
diff changeset
664 #silent $conditions_MDV_comparison['isotopologue_proportions']='spearman'
16c64719226c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit afc87f0254b4399b71e53735966032ba1a32434d
iuc
parents: 3
diff changeset
665 #silent $timepoints_MDV_comparison['isotopologue_proportions']='spearman'
16c64719226c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit afc87f0254b4399b71e53735966032ba1a32434d
iuc
parents: 3
diff changeset
666 #silent $conditions_metabolite_time_profiles['abundances']='spearman'
16c64719226c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit afc87f0254b4399b71e53735966032ba1a32434d
iuc
parents: 3
diff changeset
667 #silent $conditions_metabolite_time_profiles['mean_enrichment']='spearman'
16c64719226c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit afc87f0254b4399b71e53735966032ba1a32434d
iuc
parents: 3
diff changeset
668 #end if
2
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
669 #set $impute_values = {}
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
670 #if str( $data_input.data_input_selector ) == "abundance":
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
671 #if $data_input.abundance_file:
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
672 ln -s '$data_input.abundance_file' data/abundance.csv &&
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
673 #silent $impute_values['abundances']='min'
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
674 #end if
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
675 #elif str( $data_input.data_input_selector ) == "mean_enrichment":
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
676 #if $data_input.me_or_frac_contrib_file:
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
677 ln -s '$data_input.me_or_frac_contrib_file' data/me_or_frac_contrib.csv &&
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
678 #silent $impute_values['mean_enrichment']='min'
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
679 #end if
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
680 #elif str( $data_input.data_input_selector ) == "isotop_prop":
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
681 #if $data_input.isotop_prop_file:
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
682 ln -s '$data_input.isotop_prop_file' data/isotop_prop.csv &&
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
683 #silent $impute_values['isotopologue_proportions']='min'
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
684 #end if
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
685 #else
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
686 #if $data_input.isotop_abs_file:
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
687 ln -s '$data_input.isotop_abs_file' data/isotop_abs.csv &&
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
688 #silent $impute_values['isotopologues']='min'
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
689 #end if
0
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
690 #end if
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
691 ]]></token>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
692 <token name="@INIT_DIFF_ANALYSIS@"><![CDATA[
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
693
2
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
694 mkdir -p data &&
0
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
695
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
696 #if $metadata_path:
2
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
697 ln -s '$metadata_path' data/metadata.csv &&
0
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
698 #end if
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
699
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
700 #set $impute_values = {}
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
701 #if str( $data_input.data_input_selector ) == "abundance":
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
702 #if $data_input.abundance_file:
2
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
703 ln -s '$data_input.abundance_file' data/abundance.csv &&
0
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
704 #silent $impute_values['abundances']='min'
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
705 #end if
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
706 #elif str( $data_input.data_input_selector ) == "mean_enrichment":
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
707 #if $data_input.me_or_frac_contrib_file:
2
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
708 ln -s '$data_input.me_or_frac_contrib_file' data/me_or_frac_contrib.csv &&
0
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
709 #silent $impute_values['mean_enrichment']='min'
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
710 #end if
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
711 #elif str( $data_input.data_input_selector ) == "isotop_prop":
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
712 #if $data_input.isotop_prop_file:
2
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
713 ln -s '$data_input.isotop_prop_file' data/isotop_prop.csv &&
0
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
714 #silent $impute_values['isotopologue_proportions']='min'
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
715 #end if
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
716 #else
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
717 #if $data_input.isotop_abs_file:
2
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
718 ln -s '$data_input.isotop_abs_file' data/isotop_abs.csv &&
0
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
719 #silent $impute_values['isotopologues']='min'
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
720 #end if
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
721 #end if
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
722 ]]></token>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
723 <token name="@INIT_METABOLOGRAM@"><![CDATA[
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
724 #import json
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
725 #import re
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
726 #import os
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
727 #import csv
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
728 #import subprocess
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
729
2
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
730 mkdir -p data &&
0
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
731
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
732 #if $path_kegg_metabolites:
2
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
733 ln -s '$path_kegg_metabolites' data/pathways_kegg_metabolites.csv &&
0
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
734 #end if
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
735 #if $path_kegg_transcripts:
2
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
736 ln -s '$path_kegg_transcripts' data/pathways_kegg_transcripts.csv &&
0
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
737 #end if
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
738
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
739 #if $metadata_path:
2
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
740 ln -s '$metadata_path' data/metadata.csv &&
0
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
741 #end if
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
742
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
743 #set $impute_values = {}
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
744 #if str( $data_input.data_input_selector ) == "abundance":
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
745 #if $data_input.abundance_file:
2
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
746 ln -s '$data_input.abundance_file' data/abundance.csv &&
0
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
747 #silent $impute_values['abundances']='min'
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
748 #end if
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
749 #else:
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
750 #if $data_input.me_or_frac_contrib_file:
2
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
751 ln -s '$data_input.me_or_frac_contrib_file' data/me_or_frac_contrib.csv &&
0
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
752 #silent $impute_values['mean_enrichment']='min'
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
753 #end if
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
754 #end if
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
755
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
756 #for $i, $s in enumerate($deg_list)
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
757 #set $cpt = str($i+1)
2
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
758 ln -s '${s.input}' data/DEG_comparison'${cpt}'.csv &&
0
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
759 #end for
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
760
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
761
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
762 ]]></token>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
763 <token name="@INIT_DIFF_MULTIGROUP_ANALYSIS@"><![CDATA[
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
764
2
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
765 mkdir -p data &&
0
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
766
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
767 #if $metadata_path:
2
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
768 ln -s '$metadata_path' data/metadata.csv &&
0
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
769 #end if
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
770
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
771 #set $impute_values = {}
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
772 #if str( $data_input.data_input_selector ) == "abundance":
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
773 #if $data_input.abundance_file:
2
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
774 ln -s '$data_input.abundance_file' data/abundance.csv &&
0
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
775 #silent $impute_values['abundances']='min'
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
776 #end if
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
777 #elif str( $data_input.data_input_selector ) == "mean_enrichment":
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
778 #if $data_input.me_or_frac_contrib_file:
2
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
779 ln -s '$data_input.me_or_frac_contrib_file' data/me_or_frac_contrib.csv &&
0
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
780 #silent $impute_values['mean_enrichment']='min'
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
781 #end if
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
782 #elif str( $data_input.data_input_selector ) == "isotop_prop":
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
783 #if $data_input.isotop_prop_file:
2
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
784 ln -s '$data_input.isotop_prop_file' data/isotop_prop.csv &&
0
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
785 #silent $impute_values['isotopologue_proportions']='min'
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
786 #end if
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
787 #else
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
788 #if $data_input.isotop_abs_file:
2
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
789 ln -s '$data_input.isotop_abs_file' data/isotop_abs.csv &&
0
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
790 #silent $impute_values['isotopologues']='min'
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
791 #end if
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
792 #end if
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
793 ]]></token>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
794 <token name="@INIT_IMPUTE_VALUES@"><![CDATA[
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
795 #import re
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
796 #set $impute_values = {}
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
797 #if $abundance_file:
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
798 #silent $impute_values['abundances']='min'
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
799 #end if
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
800 #if $me_or_frac_contrib_file:
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
801 #silent $impute_values['mean_enrichment']='min'
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
802 #end if
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
803 ]]></token>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
804 <token name="@INIT_DATATYPES@"><![CDATA[
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
805 #import re
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
806 #set $datatypes_avail = list()
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
807 #if str( $data_input.data_input_selector ) == "abundance":
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
808 #if $data_input.abundance_file:
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
809 $datatypes_avail.append(re.sub('"', '', "abundances"))
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
810 #end if
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
811 #elif str( $data_input.data_input_selector ) == "mean_enrichment":
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
812 #if $data_input.me_or_frac_contrib_file:
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
813 $datatypes_avail.append(re.sub('"', '', "mean_enrichment"))
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
814 #end if
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
815 #elif str( $data_input.data_input_selector ) == "isotop_prop":
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
816 #if $data_input.isotop_prop_file:
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
817 $datatypes_avail.append(re.sub('"', '', "isotopologue_proportions"))
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
818 #end if
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
819 #else
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
820 #if $data_input.isotop_abs_file:
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
821 $datatypes_avail.append(re.sub('"', '', "isotopologues"))
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
822 #end if
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
823 #end if
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
824 ]]></token>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
825 <token name="@INIT_STAT_TEST@"><![CDATA[
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
826 #import re
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
827 #set $statistical_test = {}
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
828 #if str( $data_input.data_input_selector ) == "abundance":
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
829 #if $data_input.abundance_file:
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
830 #silent $statistical_test['abundances']=str($data_input.stat_test)
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
831 #end if
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
832 #elif str( $data_input.data_input_selector ) == "mean_enrichment":
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
833 #if $data_input.me_or_frac_contrib_file:
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
834 #silent $statistical_test['mean_enrichment']=str($data_input.stat_test)
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
835 #end if
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
836 #elif str( $data_input.data_input_selector ) == "isotop_prop":
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
837 #if $data_input.isotop_prop_file:
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
838 #silent $statistical_test['isotopologue_proportions']=str($data_input.stat_test)
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
839 #end if
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
840 #else
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
841 #if $data_input.isotop_abs_file:
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
842 #silent $statistical_test['isotopologues']=str($data_input.stat_test)
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
843 #end if
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
844 #end if
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
845 ]]></token>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
846 <token name="@INIT_CONDITIONS@"><![CDATA[
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
847 #import re
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
848 #set $conds = list()
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
849 #for $co in $conditions:
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
850 $conds.append(re.sub('"', '', str($co)))
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
851 #end for
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
852 ]]></token>
2
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
853 <token name="@INIT_PLOT_CONDITIONS@"><![CDATA[
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
854 #set $conditions = list()
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
855 #for $i, $s in enumerate($plot_factor_list)
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
856 #set $cpt = str($i+1)
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
857 $conditions.append(re.sub('"', '', str($s.condition)))
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
858 #end for
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
859 ]]></token>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
860 <token name="@INIT_ABUNDANCE_PLOT_CONDITIONS@"><![CDATA[
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
861 #set $conditions = list()
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
862 #for $i, $s in enumerate($plot_abundance_factor_list)
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
863 #set $cpt = str($i+1)
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
864 $conditions.append(re.sub('"', '', str($s.condition)))
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
865 #end for
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
866 ]]></token>
0
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
867 <token name="@INIT_TIMEPOINTS@"><![CDATA[
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
868
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
869 #import re
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
870 #set $timepoints = list()
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
871 #for $tp in $timepoint:
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
872 $timepoints.append(re.sub('"', '', str($tp)))
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
873 #end for
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
874 ]]></token>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
875 <token name="@INIT_GROUPS@"><![CDATA[
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
876 #import re
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
877 #set $groups = list()
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
878 $groups.append(re.sub('"', '', str("condition")))
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
879 $groups.append(re.sub('"', '', str("timepoint")))
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
880
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
881 ]]></token>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
882 <token name="@INIT_ENRICHMENT_METABOLITES@"><![CDATA[
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
883 #import json
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
884 #import re
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
885 #set $metabolites = {}
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
886 #for $cp in $compartments:
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
887 #silent $metabolites[re.sub('"', '', str($cp))]=list()
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
888 #for $met in $metabolites_list:
2
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
889 #set tmp_met=re.sub('\,', '%%',str($met))
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
890 #set tmp_met_bis=str(re.split('_m', str($tmp_met))[0])
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
891 #set tmp_met_ter=re.sub('%%', '\,',str($tmp_met_bis))
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
892 $metabolites[re.sub('"', '', str($cp))].append(re.sub('"', '\'', str(tmp_met_ter)))
0
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
893 #end for
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
894 #end for
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
895 ]]></token>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
896 <token name="@INIT_ISOTOPOLOGUE_METABOLITES@"><![CDATA[
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
897 #set $metabolites = {}
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
898 #for $cp in $compartments:
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
899 #silent $metabolites[re.sub('"', '', str($cp))]=list()
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
900 #for $met in $metabolites_list:
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
901 #set tmp_met=re.sub('\,', '--',str($met))
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
902 #set tmp_met_bis=str(re.split('_m', str($tmp_met))[0])
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
903 #set tmp_met_ter=re.sub('--', '\,',str($tmp_met_bis))
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
904 $metabolites[re.sub('"', '', str($cp))].append(re.sub('"', '\'', str(tmp_met_ter)))
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
905 #end for
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
906 #end for
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
907 ]]></token>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
908 <token name="@INIT_MULTIGROUP_COMPARISONS@"><![CDATA[
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
909 #set $comparisons = list()
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
910 #for $tp in $timepoint:
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
911 #set $ctrl_found=False
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
912 #set $ctrl=""
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
913
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
914 #for $co in $conditions:
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
915 #set $sub_comparisons = list()
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
916 #if str($co) in ["Control", "control","ctrl"]:
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
917 #set $ctrl_found=True
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
918 #set $ctrl=str($co)
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
919 $sub_comparisons.append(re.sub('"', '', str($co)))
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
920 $sub_comparisons.append(re.sub('"', '', str($tp)))
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
921 #else:
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
922 $sub_comparisons.append(re.sub('"', '', str($co)))
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
923 $sub_comparisons.append(re.sub('"', '', str($tp)))
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
924
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
925 #end if
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
926 $comparisons.append($sub_comparisons)
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
927 #end for
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
928 #end for
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
929 ]]></token>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
930 <token name="@INIT_CONDITIONS_TIMECOURSE@"><![CDATA[
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
931 #import re
2
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
932 #set $conditions = list()
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
933 #for $i, $s in enumerate($factor_list)
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
934 #set $cpt = str($i+1)
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
935 $conditions.append(re.sub('"', '', str($s.condition)))
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
936 #end for
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
937
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
938 ]]></token>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
939 <token name="@INIT_BIVAR_COMPARISONS@"><![CDATA[
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
940 #import re
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
941 #set $conditions = list()
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
942 #for $i, $s in enumerate($plot_factor_list)
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
943 #set $cpt = str($i+1)
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
944 $conditions.append(re.sub('"', '', str($s.condition)))
0
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
945 #end for
2
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
946 ]]></token>
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
947 <token name="@INIT_COMPARISONS_METABOLOGRAM@"><![CDATA[
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
948 #import re
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
949 #set $conditions = list()
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
950 #set $timepoints = list()
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
951 #set $comparisons = list()
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
952 #for $i, $s in enumerate($deg_list)
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
953 #set $cpt = str($i+1)
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
954 #set $comparisons_bis = list()
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
955 #for $j, $t in enumerate($s.factor_list)
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
956 #set $sub_comparisons = list()
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
957 #if str($t.condition) not in $conditions:
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
958 $conditions.append(re.sub('"', '', str($t.condition)))
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
959 #end if
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
960 $sub_comparisons.append(re.sub('"', '', str($t.condition)))
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
961 $sub_comparisons.append(re.sub('"', '', str($s.timepoint)))
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
962 $comparisons_bis.append($sub_comparisons)
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
963 #end for
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
964 $timepoints.append(re.sub('"', '', str($s.timepoint)))
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
965 $comparisons.append($comparisons_bis)
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
966 #end for
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
967
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
968
0
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
969
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
970 ]]></token>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
971 <token name="@INIT_COMPARISONS@"><![CDATA[
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
972 #import re
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
973 #set $conds = list()
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
974 #for $co in $conditions:
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
975 $conds.append(re.sub('"', '', str($co)))
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
976 #end for
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
977 #set $timepoints = list()
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
978 #for $tp in $timepoint:
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
979 $timepoints.append(re.sub('"', '', str($tp)))
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
980 #end for
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
981
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
982 #set $comparisons = list()
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
983 #if len($conds) > 1:
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
984 #if len($timepoints) > 0:
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
985 #for $tp in $timepoint:
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
986 #set $ctrl_found=False
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
987 #set $ctrl=""
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
988 #set $comparisons_bis = list()
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
989 #for $co in $conditions:
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
990 #set $sub_comparisons = list()
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
991 #if str($co) in ["'Control'", "'control'", "'ctrl'"]:
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
992 #set $ctrl_found=True
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
993 #set $ctrl=str($co)
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
994 #else:
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
995 $sub_comparisons.append(re.sub('"', '', str($co)))
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
996 $sub_comparisons.append(re.sub('"', '', str($tp)))
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
997
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
998 #end if
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
999 $comparisons_bis.append($sub_comparisons)
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1000 #end for
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1001
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1002 #if $ctrl_found:
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1003 $sub_comparisons.append(str($ctrl))
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1004 $sub_comparisons.append(str($tp))
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1005 $comparisons_bis.append($sub_comparisons)
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1006 #end if
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1007
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1008 $comparisons.append($comparisons_bis)
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1009 #end for
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1010 #else
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1011 #for $co in $conditions:
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1012 $comparisons.append(re.sub('"', '', str($co)))
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1013 #end for
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1014 #end if
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1015
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1016 #else
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1017 #if len($conds) > 0:
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1018 #if len($timepoints) > 1:
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1019 #for $co in $conditions:
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1020 #set $comparisons_bis = list()
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1021 #for $tp in $timepoint:
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1022 #set $sub_comparisons = list()
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1023 $sub_comparisons.append(re.sub('"', '', str($co)))
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1024 $sub_comparisons.append(re.sub('"', '', str($tp)))
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1025 $comparisons_bis.append($sub_comparisons)
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1026 #end for
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1027 $comparisons.append($comparisons_bis)
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1028 #end for
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1029 #end if
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1030 #else
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1031 #for $tp in $timepoint:
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1032 $comparisons.append(re.sub('"', '', str($tp)))
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1033 #end for
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1034 #end if
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1035 #end if
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1036 ]]></token>
2
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1037 <token name="@INIT_DIFF_ANALYSIS_COMPARISONS@"><![CDATA[
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1038 #import re
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1039 #set $conditions = list()
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1040 #for $i, $s in enumerate($factor_list)
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1041 #set $cpt = str($i+1)
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1042 $conditions.append(re.sub('"', '', str($s.condition)))
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1043 #end for
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1044
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1045 #set $timepoints = list()
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1046 #for $tp in $timepoint:
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1047 $timepoints.append(re.sub('"', '', str($tp)))
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1048 #end for
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1049
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1050 #set $comparisons = list()
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1051 #if len($conditions) > 1:
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1052 #if len($timepoints) > 0:
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1053 #for $tp in $timepoint:
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1054 #set $ctrl_found=False
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1055 #set $ctrl=""
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1056 #set $comparisons_bis = list()
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1057
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1058 #for $co in $conditions:
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1059 #set $sub_comparisons = list()
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1060 #if str($co) in ["'Control'", "'control'", "'ctrl'"]:
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1061 #set $ctrl_found=True
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1062 #set $ctrl=str($co)
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1063 #else:
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1064 $sub_comparisons.append(re.sub('"', '', str($co)))
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1065 $sub_comparisons.append(re.sub('"', '', str($tp)))
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1066
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1067 #end if
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1068 $comparisons_bis.append($sub_comparisons)
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1069 #end for
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1070
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1071 #if $ctrl_found:
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1072 $sub_comparisons.append(str($ctrl))
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1073 $sub_comparisons.append(str($tp))
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1074 $comparisons_bis.append($sub_comparisons)
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1075 #end if
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1076
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1077 $comparisons.append($comparisons_bis)
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1078 #end for
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1079 #else
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1080 #for $co in $conditions:
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1081 $comparisons.append(re.sub('"', '', str($co)))
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1082 #end for
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1083 #end if
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1084
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1085 #else
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1086 #if len($conditions) > 0:
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1087 #if len($timepoints) > 1:
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1088 #for $co in $conditions:
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1089 #set $comparisons_bis = list()
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1090 #for $tp in $timepoint:
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
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diff changeset
1091 #set $sub_comparisons = list()
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1092 $sub_comparisons.append(re.sub('"', '', str($co)))
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1093 $sub_comparisons.append(re.sub('"', '', str($tp)))
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1094 $comparisons_bis.append($sub_comparisons)
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1095 #end for
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1096 $comparisons.append($comparisons_bis)
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1097 #end for
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1098 #end if
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1099 #else
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1100 #for $tp in $timepoint:
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
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diff changeset
1101 $comparisons.append(re.sub('"', '', str($tp)))
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1102 #end for
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1103 #end if
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1104 #end if
31b19ad28c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1105 ]]></token>
0
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1106 <token name="@INIT_TRANSCRIPTS@"><![CDATA[
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1107 #import re
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1108 #import os
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1109 #import subprocess
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1110 #set $transcripts = list()
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1111
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1112 #for $i, $s in enumerate($deg_list)
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1113 #set $cpt = str($i+1)
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1114 $transcripts.append(re.sub('"', '', "DEG_comparison"+str($i+1)))
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1115 #set $deg_one_values = os.fsdecode(subprocess.check_output('head -n1 ' + str($s.input) + '| cut -f' + str($s.valuecol), shell=True))
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1116 #set $deg_one_id = os.fsdecode(subprocess.check_output('head -n1 ' + str($s.input) + '| cut -f' + str($s.idcol), shell=True))
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1117 #end for
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1118 ]]></token>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1119 <token name="@INIT_PATHWAYS@"><![CDATA[
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1120 #set $pathways = {}
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1121 #if $path_kegg_metabolites:
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1122 #silent $pathways['metabolites']='pathways_kegg_metabolites'
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1123 #end if
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1124 #if $path_kegg_transcripts:
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1125 #silent $pathways['transcripts']='pathways_kegg_transcripts'
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1126 #end if
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1127 ]]></token>
a3349c105bd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1128 </macros>