Mercurial > repos > iuc > dimet_metabologram

annotate macros.xml @ 1:8d8ae3697a65 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 7568e92bfc4560d6e0287e7444455f55c86d135d
author iuc
date Tue, 23 Jan 2024 14:58:39 +0000
parents a7d3e880e74c
children 7ff4f61789de
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1 <macros>
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2 <token name="@TOOL_VERSION@">0.1.4</token>
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3 <token name="@VERSION_SUFFIX@">1</token>
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4 <token name="@EXECUTABLE@">pca</token>
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5 <xml name="factor_repeat">
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6 <repeat name="rep_factorName" title="Factor" min="1">
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7 <param name="factorName" type="text" value="FactorName" label="Specify a factor name, e.g. effects_drug_x or cancer_markers"
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8 help="Only letters, numbers and underscores will be retained in this field">
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9 <sanitizer>
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10 <valid initial="string.letters,string.digits"><add value="_" /></valid>
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11 </sanitizer>
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12 </param>
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13 <repeat name="rep_factorLevel" title="Factor level" min="2" default="2">
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14 <param name="factorLevel" type="text" value="FactorLevel" label="Specify a factor level, typical values could be 'tumor', 'normal', 'treated' or 'control'"
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15 help="Only letters, numbers and underscores will be retained in this field">
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16 <sanitizer>
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17 <valid initial="string.letters,string.digits"><add value="_" /></valid>
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18 </sanitizer>
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19 </param>
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20 <yield/>
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21 </repeat>
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22 </repeat>
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23 </xml>
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24 <xml name="requirements">
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25 <requirements>
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26 <requirement type="package" version="@TOOL_VERSION@">dimet</requirement>
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27 </requirements>
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28 </xml>
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29 <xml name="statistical_test">
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30 <param name="stat_test" type="select" value="Tt" display="radio" label="Select statistical to apply" help="Please enter at max 1 statistical test by file">
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31 <option value="Tt">t-test</option>
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32 <option value="MW">Mann Whitney</option>
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33 <option value="KW">Kruskall Wallis</option>
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34 <option value="ranksum">Wilcoxon's rank sum test</option>
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35 <option value="Wcox">Wilcoxon signed-rank test</option>
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36 <option value="BrMu">Brunner-Munzel test</option>
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37 <option value="prm-scipy">permutations test</option>
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38 <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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39 </param>
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40 </xml>
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41 <xml name="citations">
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42 <citations>
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43 <citation type="bibtex">
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44 @software{Galvis_Rodriguez_DIMet,
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45 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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46 license = {MIT},
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47 title = {{DIMet}},
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48 url = {https://github.com/cbib/DIMet}
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49 }
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50
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51 </citation>
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52 </citations>
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53
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54 </xml>
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55 <xml name="metadata_file_macros">
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56 <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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57 </xml>
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58 <xml name="abundance_file_macros">
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59 <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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60 </xml>
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61 <xml name="enrichment_file_macros">
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62 <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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63 </xml>
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64 <xml name="isotopologue_prop_file_macros">
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65 <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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66 </xml>
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67 <xml name="isotopologue_abs_file_macros">
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68 <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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69 </xml>
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70 <xml name="input_parameters_pca">
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71 <expand macro="abundance_file_macros"/>
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72 <param name="me_or_frac_contrib_file" type="data" optional="true" format="tabular" label="Mean enrichment or fraction contribution file"/>
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73 <expand macro="metadata_file_macros"/>
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74 </xml>
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75 <xml name="input_parameters_abundance">
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76 <expand macro="abundance_file_macros"/>
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77 <expand macro="metadata_file_macros"/>
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78 </xml>
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79 <xml name="input_parameters_enrichment">
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80 <expand macro="enrichment_file_macros"/>
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81 <expand macro="metadata_file_macros"/>
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82 </xml>
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83 <xml name="input_parameters_isotopologue">
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84 <expand macro="isotopologue_prop_file_macros"/>
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85 <expand macro="metadata_file_macros"/>
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86 </xml>
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87 <xml name="input_parameters_metabologram">
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88 <conditional name="data_input">
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89 <param name="data_input_selector" type="select" label="Abundance, Enrichment or Isotopologues count files" help="Select between raw abundance, mean enrichment or isotopologue files">
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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90 <option value="abundance" selected="True">abundance</option>
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91 <option value="mean_enrichment">mean_enrichment</option>
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92 </param>
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93 <when value="abundance">
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94 <expand macro="abundance_file_macros"/>
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95 <param name="metabolites_list" type="select" optional="false" multiple="true"
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96 label="Select Metabolite(s) for factor 1 to plot (1 Min.). You have to load a abundance file prior to have access to metabolite list">
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97 <validator type="length" min="1" message="Please enter at max 2 compartments"/>
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98 <options from_dataset="abundance_file">
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99 <column name="metabolite_or_isotopologue" index="0"/>
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100 <column name="value" index="0"/>
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101 <filter type="unique_value" name="metabolite_or_isotopologue" column="0"/>
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102 <filter type="remove_value" value="metabolite_or_isotopologue"/>
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103 </options>
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104 <sanitizer>
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105 <valid initial="default">
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106 <add preset="string.printable"/>
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107 <add value="\t"/>
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108 <remove value="&quot;"/>
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109 <remove value="&apos;"/>
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110 </valid>
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111 </sanitizer>
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112 </param>
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113 <expand macro="statistical_test"/>
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114 </when>
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115 <when value="mean_enrichment">
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116 <expand macro="enrichment_file_macros"/>
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117 <param name="metabolites_list" type="select" optional="false" multiple="true"
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118 label="Select Metabolite(s) for factor 1 to plot (1 Min.). You have to load a abundance file prior to have access to metabolite list">
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119 <validator type="length" min="1" message="Please enter at max 2 compartments"/>
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120 <options from_dataset="me_or_frac_contrib_file">
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121 <column name="metabolite_or_isotopologue" index="0"/>
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122 <column name="value" index="0"/>
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123 <filter type="unique_value" name="metabolite_or_isotopologue" column="0"/>
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124 <filter type="remove_value" value="metabolite_or_isotopologue"/>
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125 </options>
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126 <sanitizer>
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127 <valid initial="default">
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128 <add preset="string.printable"/>
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129 <add value="\t"/>
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130 <remove value="&quot;"/>
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131 <remove value="&apos;"/>
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132 </valid>
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133 </sanitizer>
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134 </param>
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135 <expand macro="statistical_test"/>
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136 </when>
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137 </conditional>
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138 <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)"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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139 <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)"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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140 <expand macro="metadata_file_macros"/>
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141 </xml>
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142 <xml name="input_parameters_diff_analysis">
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143 <conditional name="data_input">
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144 <param name="data_input_selector" type="select" label="Abundance, Enrichment or Isotopologues count files" help="Select between raw abundance and mean enrichment files">
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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145 <option value="abundance" selected="True">abundance</option>
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146 <option value="mean_enrichment">mean_enrichment</option>
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147 <option value="isotop_prop">isotop_prop</option>
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148 <option value="isotop_abs">isotop_abs</option>
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149 </param>
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150 <when value="abundance">
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151 <expand macro="abundance_file_macros"/>
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152 <expand macro="statistical_test"/>
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153
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154 </when>
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155 <when value="mean_enrichment">
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156 <expand macro="enrichment_file_macros"/>
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157 <expand macro="statistical_test"/>
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158 </when>
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159 <when value="isotop_prop">
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160 <expand macro="isotopologue_prop_file_macros"/>
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161 <expand macro="statistical_test"/>
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162 </when>
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163 <when value="isotop_abs">
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164 <expand macro="isotopologue_abs_file_macros"/>
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165 <expand macro="statistical_test"/>
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166 </when>
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167 </conditional>
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168 <expand macro="metadata_file_macros"/>
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169 </xml>
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170 <xml name="suffix">
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171 <param name="suffix" type="text" optional="false" label="suffix to add to output files" >
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172 <sanitizer invalid_char="">
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173 <valid initial="string.ascii_letters,string.digits">
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174 <add value="_" />
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175 </valid>
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176 </sanitizer>
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177 </param>
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178 </xml>
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179 <xml name="conditions">
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180 <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 metabolite list">
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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181 <options from_dataset="metadata_path">
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182 <column name="condition" index="1"/>
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183 <column name="value" index="1"/>
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184 <filter type="unique_value" name="condition" column="condition"/>
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185 <filter type="remove_value" value="condition"/>
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186 </options>
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187 <sanitizer>
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188 <valid initial="default">
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189 <add preset="string.printable"/>
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190 <add value="\t"/>
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191 <remove value="&quot;"/>
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192 <remove value="&apos;"/>
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193 </valid>
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194 </sanitizer>
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195 </param>
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196 </xml>
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197 <xml name="conditions_multigroup">
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198 <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">
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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199 <options from_dataset="metadata_path">
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200 <column name="condition" index="1"/>
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201 <column name="value" index="1"/>
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202 <filter type="unique_value" name="condition" column="condition"/>
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203 <filter type="remove_value" value="condition"/>
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204 </options>
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205 <sanitizer>
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206 <valid initial="default">
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207 <add preset="string.printable"/>
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208 <add value="\t"/>
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209 <remove value="&quot;"/>
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210 <remove value="&apos;"/>
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211 </valid>
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212 </sanitizer>
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213 </param>
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214 </xml>
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215 <xml name="timepoint_multigroup">
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216 <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">
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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217 <options from_dataset="metadata_path">
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218 <column name="timepoint" index="2"/>
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219 <column name="value" index="2"/>
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220 <filter type="unique_value" name="timepoint" column="2"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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221 <filter type="remove_value" value="timepoint"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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222 <filter type="sort_by" name="timepoint" column="1"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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223 </options>
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224 <sanitizer>
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225 <valid initial="default">
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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226 <add preset="string.printable"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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227 <add value="\t"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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228 <remove value="&quot;"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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229 <remove value="&apos;"/>
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230 </valid>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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231 </sanitizer>
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232 </param>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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233 </xml>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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234 <xml name="timepoint">
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235 <param name="timepoint" type="select" optional="true" multiple="true" label="Browse timepoint from metadata file (1 min. only if two conditions are set.)">
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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236 <options from_dataset="metadata_path">
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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237 <column name="timepoint" index="2"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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238 <column name="value" index="2"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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239 <filter type="unique_value" name="timepoint" column="2"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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240 <filter type="remove_value" value="timepoint"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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241 <filter type="sort_by" name="timepoint" column="1"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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242 </options>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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243 <sanitizer>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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244 <valid initial="default">
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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245 <add preset="string.printable"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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246 <add value="\t"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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247 <remove value="&quot;"/>
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248 <remove value="&apos;"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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249 </valid>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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250 </sanitizer>
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251 </param>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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252 </xml>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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253 <xml name="grouping">
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254 <param name="grouping" type="select" optional="false" multiple="true" label="Browse group to compare">
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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255 <option value="condition" selected="true">condition</option>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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256 <option value="timepoint" selected="true">timepoint</option>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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257 </param>
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258 </xml>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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259 <xml name="correction_method">
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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260 <param name="correction_method" type="select" value="bonferroni" display="radio" label="Select multiple test correction to apply" help="Please enter at max 1 method">
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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261 <option value="bonferroni">bonferroni</option>
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262 <option value="holm-sidak">holm-sidak</option>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
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263 <option value="holm">holm</option>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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264 <option value="simes-hochberg">simes-hochberg</option>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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265 <option value="hommel">hommel</option>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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266 <option value="fdr_bh">fdr_bh</option>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
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267 <option value="fdr_by">fdr_by</option>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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268 <option value="fdr_tsbh">fdr_tsbh</option>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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269 <option value="fdr_tsbky">fdr_tsbky</option>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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270 </param>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
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271 </xml>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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272 <xml name="compartments_enrichment">
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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273 <param name="compartments" type="select" optional="false" multiple="true"
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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274 label="Browse compartments from metadata file (All needed). You have to load a metadata file prior to have access to compartments">
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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275 <options from_dataset="metadata_path">
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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276 <column name="compartment" index="4"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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277 <column name="value" index="4"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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278 <filter type="unique_value" name="compartment" column="4"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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279 <filter type="remove_value" value="compartment"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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280 </options>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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281 <sanitizer>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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282 <valid initial="default">
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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283 <add preset="string.printable"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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diff changeset
284 <add value="\t"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
285 <remove value="&quot;"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
286 <remove value="&apos;"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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287 </valid>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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288 </sanitizer>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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289 </param>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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290 </xml>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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291 <xml name="compartments_abundance">
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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292 <param name="compartments" type="select" optional="false" multiple="true"
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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293 label="Browse compartments from metadata file (All needed). You have to load a metadata file prior to have access to compartments">
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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294 <options from_dataset="metadata_path">
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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295 <column name="compartment" index="4"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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diff changeset
296 <column name="value" index="4"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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diff changeset
297 <filter type="unique_value" name="compartment" column="4"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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298 <filter type="remove_value" value="compartment"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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diff changeset
299 </options>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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300 <sanitizer>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
301 <valid initial="default">
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
302 <add preset="string.printable"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
303 <add value="\t"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
304 <remove value="&quot;"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
305 <remove value="&apos;"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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diff changeset
306 </valid>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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diff changeset
307 </sanitizer>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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diff changeset
308 </param>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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diff changeset
309 </xml>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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diff changeset
310 <xml name="compartments">
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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311 <param name="compartments" type="select" optional="false" multiple="true"
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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312 label="Browse compartments from metadata file (1 min.). You have to load a metadata file prior to have access to compartments">
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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diff changeset
313 <options from_dataset="metadata_path">
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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diff changeset
314 <column name="compartment" index="4"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
315 <column name="value" index="4"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
316 <filter type="unique_value" name="compartment" column="4"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
317 <filter type="remove_value" value="compartment"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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diff changeset
318 </options>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
319 <sanitizer>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
320 <valid initial="default">
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
321 <add preset="string.printable"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
322 <add value="\t"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
323 <remove value="&quot;"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
324 <remove value="&apos;"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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diff changeset
325 </valid>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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diff changeset
326 </sanitizer>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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diff changeset
327 </param>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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328 </xml>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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329 <xml name="abundance_metabolites_list">
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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330 <param name="metabolites_list" type="select" optional="false" multiple="true"
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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diff changeset
331 label="Select Metabolite(s) for factor 1 to plot (1 min). You have to load a abundance file prior to have access to metabolite list">
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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332 <validator type="length" min="1" message="Please enter at max 2 compartments"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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diff changeset
333 <options from_dataset="abundance_file">
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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diff changeset
334 <column name="metabolite_or_isotopologue" index="0"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
335 <column name="value" index="0"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
336 <filter type="unique_value" name="metabolite_or_isotopologue" column="0"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
337 <filter type="remove_value" value="metabolite_or_isotopologue"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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diff changeset
338 </options>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
339 <sanitizer>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
340 <valid initial="default">
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
341 <add preset="string.printable"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
342 <add value="\t"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
343 <remove value="&quot;"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
344 <remove value="&apos;"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
345 </valid>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
346 </sanitizer>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
347 </param>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
348 </xml>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
349 <xml name="enrichment_metabolites_list">
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
350 <param name="metabolites_list" type="select" optional="false" multiple="true"
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
351 label="Select Metabolite(s) for factor 1 to plot (1 Min.). You have to load a abundance file prior to have access to metabolite list">
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
352 <validator type="length" min="1" message="Please enter at max 2 compartments"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
353 <options from_dataset="me_or_frac_contrib_file">
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
354 <column name="ID" index="0"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
355 <column name="value" index="0"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
356 <filter type="unique_value" name="ID" column="0"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
357 <filter type="remove_value" value="ID"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
358 </options>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
359 <sanitizer>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
360 <valid initial="default">
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
361 <add preset="string.printable"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
362 <add value="\t"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
363 <remove value="&quot;"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
364 <remove value="&apos;"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
365 </valid>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
366 </sanitizer>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
367 </param>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
368 </xml>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
369 <xml name="isotopologue_metabolites_list">
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
370 <param name="metabolites_list" type="select" optional="false" multiple="true"
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
371 label="Select Metabolite(s) to plot (1 Min.). You have to load a abundance file prior to have access to metabolite list">
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
372 <validator type="length" min="1" message="Please enter at max 2 compartments"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
373 <options from_dataset="isotop_prop_file">
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
374 <column name="ID" index="0"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
375 <column name="value" index="0"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
376 <filter type="unique_value" name="ID" column="0"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
377 <filter type="remove_value" value="ID"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
378 </options>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
379 <sanitizer>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
380 <valid initial="default">
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
381 <add preset="string.printable"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
382 <add value="\t"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
383 <remove value="&quot;"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
384 <remove value="&apos;"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
385 </valid>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
386 </sanitizer>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
387 </param>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
388 </xml>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
389 <xml name="deg_list">
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
390 <repeat name="deg_list" title="Deregulated gene set">
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
391 <param name="input" type="data" format="tabular" label="Deregulated genes set"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
392 <param name="idcol" type="data_column" data_ref="input" label="Column for id" use_header_names="true"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
393 <param name="valuecol" type="data_column" data_ref="input" label="Column for values" use_header_names="true"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
394 </repeat>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
395 </xml>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
396 <token name="@INIT_PCA@"><![CDATA[
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
397 #import json
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
398 #import re
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
399
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
400 mkdir -p data/raw &&
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
401 mkdir -p data/processed &&
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
402
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
403 #if $metadata_path:
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
404 ln -s '$metadata_path' data/raw/metadata.csv &&
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
405 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
406 #if $abundance_file:
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
407 ln -s '$abundance_file' data/raw/abundance.csv &&
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
408 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
409 #if $me_or_frac_contrib_file:
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
410 ln -s '$me_or_frac_contrib_file' data/raw/me_or_frac_contrib.csv &&
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
411 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
412
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
413 ]]></token>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
414 <token name="@INIT_CONFIG@"><![CDATA[
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
415 mkdir -p '$__new_file_path__/config' &&
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
416 touch '$__new_file_path__/config/config.yaml' &&
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
417 ]]></token>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
418 <token name="@REMOVE_CONFIG@"><![CDATA[
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
419 && rm -r '$__new_file_path__/config'
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
420 ]]></token>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
421 <token name="@INIT_ABUNDANCE_PLOT@"><![CDATA[
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
422
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
423 mkdir -p data/raw &&
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
424 mkdir -p data/processed &&
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
425
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
426 #if $metadata_path:
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
427 ln -s '$metadata_path' data/raw/metadata.csv &&
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
428 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
429 #if $abundance_file:
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
430 ln -s '$abundance_file' data/raw/abundance.csv &&
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
431 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
432 ]]></token>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
433 <token name="@INIT_ENRICHMENT_PLOT@"><![CDATA[
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
434
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
435 mkdir -p data/raw &&
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
436 mkdir -p data/processed &&
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
437
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
438 #if $metadata_path:
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
439 ln -s '$metadata_path' data/raw/metadata.csv &&
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
440 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
441 #if $me_or_frac_contrib_file:
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
442 ln -s '$me_or_frac_contrib_file' data/raw/me_or_frac_contrib.csv &&
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
443 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
444 ]]></token>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
445 <token name="@INIT_ISOTOPOLOGUE_PLOT@"><![CDATA[
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
446
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
447 mkdir -p data/raw &&
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
448 mkdir -p data/processed &&
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
449
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
450 #if $metadata_path:
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
451 ln -s '$metadata_path' data/raw/metadata.csv &&
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
452 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
453 #if $isotop_prop_file:
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
454 ln -s '$isotop_prop_file' data/raw/isotop_prop.csv &&
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
455 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
456 ]]></token>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
457 <token name="@INIT_DIFF_ANALYSIS@"><![CDATA[
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
458
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
459 mkdir -p data/raw &&
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
460 mkdir -p data/processed &&
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
461
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
462 #if $metadata_path:
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
463 ln -s '$metadata_path' data/raw/metadata.csv &&
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
464 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
465
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
466 #set $impute_values = {}
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
467 #if str( $data_input.data_input_selector ) == "abundance":
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
468 #if $data_input.abundance_file:
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
469 ln -s '$data_input.abundance_file' data/raw/abundance.csv &&
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
470 #silent $impute_values['abundances']='min'
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
471 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
472 #elif str( $data_input.data_input_selector ) == "mean_enrichment":
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
473 #if $data_input.me_or_frac_contrib_file:
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
474 ln -s '$data_input.me_or_frac_contrib_file' data/raw/me_or_frac_contrib.csv &&
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
475 #silent $impute_values['mean_enrichment']='min'
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
476 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
477 #elif str( $data_input.data_input_selector ) == "isotop_prop":
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
478 #if $data_input.isotop_prop_file:
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
479 ln -s '$data_input.isotop_prop_file' data/raw/isotop_prop.csv &&
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
480 #silent $impute_values['isotopologue_proportions']='min'
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
481 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
482 #else
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
483 #if $data_input.isotop_abs_file:
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
484 ln -s '$data_input.isotop_abs_file' data/raw/isotop_abs.csv &&
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
485 #silent $impute_values['isotopologues']='min'
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
486 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
487 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
488 ]]></token>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
489 <token name="@INIT_METABOLOGRAM@"><![CDATA[
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
490 #import json
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
491 #import re
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
492 #import os
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
493 #import csv
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
494 #import subprocess
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
495
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
496 mkdir -p data/raw &&
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
497 mkdir -p data/processed &&
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
498 mkdir -p data/integration_files &&
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
499
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
500 #if $path_kegg_metabolites:
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
501 ln -s '$path_kegg_metabolites' data/integration_files/pathways_kegg_metabolites.csv &&
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
502 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
503 #if $path_kegg_transcripts:
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
504 ln -s '$path_kegg_transcripts' data/integration_files/pathways_kegg_transcripts.csv &&
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
505 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
506
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
507 #if $metadata_path:
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
508 ln -s '$metadata_path' data/raw/metadata.csv &&
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
509 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
510
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
511 #set $impute_values = {}
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
512 #if str( $data_input.data_input_selector ) == "abundance":
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
513 #if $data_input.abundance_file:
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
514 ln -s '$data_input.abundance_file' data/raw/abundance.csv &&
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
515 #silent $impute_values['abundances']='min'
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
516 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
517 #else:
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
518 #if $data_input.me_or_frac_contrib_file:
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
519 ln -s '$data_input.me_or_frac_contrib_file' data/raw/me_or_frac_contrib.csv &&
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
520 #silent $impute_values['mean_enrichment']='min'
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
521 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
522 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
523
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
524 #for $i, $s in enumerate($deg_list)
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
525 #set $cpt = str($i+1)
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
526 ln -s '${s.input}' data/integration_files/DEG_comparison'${cpt}'.csv &&
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
527 #end for
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
528
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
529
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
530 ]]></token>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
531 <token name="@INIT_DIFF_MULTIGROUP_ANALYSIS@"><![CDATA[
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
532
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
533 mkdir -p data/raw &&
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
534 mkdir -p data/processed &&
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
535
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
536 #if $metadata_path:
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
537 ln -s '$metadata_path' data/raw/metadata.csv &&
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
538 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
539
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
540 #set $impute_values = {}
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
541 #if str( $data_input.data_input_selector ) == "abundance":
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
542 #if $data_input.abundance_file:
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
543 ln -s '$data_input.abundance_file' data/raw/abundance.csv &&
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
544 #silent $impute_values['abundances']='min'
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
545 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
546 #elif str( $data_input.data_input_selector ) == "mean_enrichment":
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
547 #if $data_input.me_or_frac_contrib_file:
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
548 ln -s '$data_input.me_or_frac_contrib_file' data/raw/me_or_frac_contrib.csv &&
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
549 #silent $impute_values['mean_enrichment']='min'
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
550 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
551 #elif str( $data_input.data_input_selector ) == "isotop_prop":
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
552 #if $data_input.isotop_prop_file:
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
553 ln -s '$data_input.isotop_prop_file' data/raw/isotop_prop.csv &&
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
554 #silent $impute_values['isotopologue_proportions']='min'
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
555 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
556 #else
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
557 #if $data_input.isotop_abs_file:
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
558 ln -s '$data_input.isotop_abs_file' data/raw/isotop_abs.csv &&
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
559 #silent $impute_values['isotopologues']='min'
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
560 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
561 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
562 ]]></token>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
563 <token name="@INIT_IMPUTE_VALUES@"><![CDATA[
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
564 #import re
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
565 #set $impute_values = {}
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
566 #if $abundance_file:
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
567 #silent $impute_values['abundances']='min'
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
568 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
569 #if $me_or_frac_contrib_file:
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
570 #silent $impute_values['mean_enrichment']='min'
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
571 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
572 ]]></token>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
573 <token name="@INIT_DATATYPES@"><![CDATA[
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
574 #import re
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
575 #set $datatypes_avail = list()
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
576 #if str( $data_input.data_input_selector ) == "abundance":
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
577 #if $data_input.abundance_file:
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
578 $datatypes_avail.append(re.sub('"', '', "abundances"))
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
579 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
580 #elif str( $data_input.data_input_selector ) == "mean_enrichment":
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
581 #if $data_input.me_or_frac_contrib_file:
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
582 $datatypes_avail.append(re.sub('"', '', "mean_enrichment"))
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
583 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
584 #elif str( $data_input.data_input_selector ) == "isotop_prop":
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
585 #if $data_input.isotop_prop_file:
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
586 $datatypes_avail.append(re.sub('"', '', "isotopologue_proportions"))
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
587 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
588 #else
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
589 #if $data_input.isotop_abs_file:
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
590 $datatypes_avail.append(re.sub('"', '', "isotopologues"))
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
591 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
592 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
593 ]]></token>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
594 <token name="@INIT_STAT_TEST@"><![CDATA[
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
595 #import re
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
596 #set $statistical_test = {}
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
597 #if str( $data_input.data_input_selector ) == "abundance":
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
598 #if $data_input.abundance_file:
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
599 #silent $statistical_test['abundances']=str($data_input.stat_test)
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
600 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
601 #elif str( $data_input.data_input_selector ) == "mean_enrichment":
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
602 #if $data_input.me_or_frac_contrib_file:
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
603 #silent $statistical_test['mean_enrichment']=str($data_input.stat_test)
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
604 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
605 #elif str( $data_input.data_input_selector ) == "isotop_prop":
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
606 #if $data_input.isotop_prop_file:
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
607 #silent $statistical_test['isotopologue_proportions']=str($data_input.stat_test)
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
608 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
609 #else
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
610 #if $data_input.isotop_abs_file:
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
611 #silent $statistical_test['isotopologues']=str($data_input.stat_test)
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
612 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
613 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
614 ]]></token>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
615 <token name="@INIT_CONDITIONS@"><![CDATA[
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
616 #import re
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
617 #set $conds = list()
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
618 #for $co in $conditions:
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
619 $conds.append(re.sub('"', '', str($co)))
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
620 #end for
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
621 ]]></token>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
622 <token name="@INIT_TIMEPOINTS@"><![CDATA[
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
623
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
624 #import re
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
625 #set $timepoints = list()
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
626 #for $tp in $timepoint:
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
627 $timepoints.append(re.sub('"', '', str($tp)))
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
628 #end for
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
629 ]]></token>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
630 <token name="@INIT_GROUPS@"><![CDATA[
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
631 #import re
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
632 #set $groups = list()
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
633 $groups.append(re.sub('"', '', str("condition")))
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
634 $groups.append(re.sub('"', '', str("timepoint")))
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
635
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
636 ]]></token>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
637 <token name="@INIT_ENRICHMENT_METABOLITES@"><![CDATA[
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
638 #import json
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
639 #import re
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
640 #set $metabolites = {}
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
641 #for $cp in $compartments:
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
642 #silent $metabolites[re.sub('"', '', str($cp))]=list()
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
643 #for $met in $metabolites_list:
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
644 $metabolites[re.sub('"', '', str($cp))].append(re.sub('"', '\'', str($met)))
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
645 #end for
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
646 #end for
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
647 ]]></token>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
648 <token name="@INIT_ISOTOPOLOGUE_METABOLITES@"><![CDATA[
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
649 #set $metabolites = {}
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
650 #for $cp in $compartments:
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
651 #silent $metabolites[re.sub('"', '', str($cp))]=list()
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
652 #for $met in $metabolites_list:
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
653 #set tmp_met=re.sub('\,', '--',str($met))
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
654 #set tmp_met_bis=str(re.split('_m', str($tmp_met))[0])
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
655 #set tmp_met_ter=re.sub('--', '\,',str($tmp_met_bis))
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
656 $metabolites[re.sub('"', '', str($cp))].append(re.sub('"', '\'', str(tmp_met_ter)))
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
657 #end for
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
658 #end for
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
659 ]]></token>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
660 <token name="@INIT_MULTIGROUP_COMPARISONS@"><![CDATA[
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
661 #set $comparisons = list()
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
662 #for $tp in $timepoint:
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
663 #set $ctrl_found=False
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
664 #set $ctrl=""
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
665
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
666 #for $co in $conditions:
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
667 #set $sub_comparisons = list()
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
668 #if str($co) in ["Control", "control","ctrl"]:
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
669 #set $ctrl_found=True
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
670 #set $ctrl=str($co)
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
671 $sub_comparisons.append(re.sub('"', '', str($co)))
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
672 $sub_comparisons.append(re.sub('"', '', str($tp)))
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
673 #else:
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
674 $sub_comparisons.append(re.sub('"', '', str($co)))
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
675 $sub_comparisons.append(re.sub('"', '', str($tp)))
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
676
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
677 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
678 $comparisons.append($sub_comparisons)
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
679 #end for
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
680 #end for
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
681 ]]></token>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
682 <token name="@INIT_CONDITIONS_TIMECOURSE@"><![CDATA[
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
683 #import re
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
684 #set $conds = list()
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
685 #for $co in $conditions:
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
686 $conds.append(re.sub('"', '', str($co)))
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
687 #end for
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
688
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
689 ]]></token>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
690 <token name="@INIT_COMPARISONS@"><![CDATA[
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
691 #import re
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
692 #set $conds = list()
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
693 #for $co in $conditions:
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
694 $conds.append(re.sub('"', '', str($co)))
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
695 #end for
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
696 #set $timepoints = list()
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
697 #for $tp in $timepoint:
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
698 $timepoints.append(re.sub('"', '', str($tp)))
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
699 #end for
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
700
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
701 #set $comparisons = list()
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
702 #if len($conds) > 1:
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
703 #if len($timepoints) > 0:
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
704 #for $tp in $timepoint:
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
705 #set $ctrl_found=False
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
706 #set $ctrl=""
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
707 #set $comparisons_bis = list()
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
708 #for $co in $conditions:
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
709 #set $sub_comparisons = list()
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
710 #if str($co) in ["'Control'", "'control'", "'ctrl'"]:
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
711 #set $ctrl_found=True
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
712 #set $ctrl=str($co)
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
713 #else:
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
714 $sub_comparisons.append(re.sub('"', '', str($co)))
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
715 $sub_comparisons.append(re.sub('"', '', str($tp)))
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
716
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
717 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
718 $comparisons_bis.append($sub_comparisons)
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
719 #end for
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
720
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
721 #if $ctrl_found:
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
722 $sub_comparisons.append(str($ctrl))
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
723 $sub_comparisons.append(str($tp))
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
724 $comparisons_bis.append($sub_comparisons)
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
725 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
726
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
727 $comparisons.append($comparisons_bis)
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
728 #end for
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
729 #else
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
730 #for $co in $conditions:
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
731 $comparisons.append(re.sub('"', '', str($co)))
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
732 #end for
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
733 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
734
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
735 #else
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
736 #if len($conds) > 0:
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
737 #if len($timepoints) > 1:
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
738 #for $co in $conditions:
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
739 #set $comparisons_bis = list()
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
740 #for $tp in $timepoint:
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
741 #set $sub_comparisons = list()
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
742 $sub_comparisons.append(re.sub('"', '', str($co)))
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
743 $sub_comparisons.append(re.sub('"', '', str($tp)))
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
744 $comparisons_bis.append($sub_comparisons)
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
745 #end for
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
746 $comparisons.append($comparisons_bis)
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
747 #end for
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
748 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
749 #else
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
750 #for $tp in $timepoint:
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
751 $comparisons.append(re.sub('"', '', str($tp)))
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
752 #end for
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
753 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
754 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
755 ]]></token>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
756 <token name="@INIT_TRANSCRIPTS@"><![CDATA[
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
757 #import re
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
758 #import os
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
759 #import subprocess
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
760 #set $transcripts = list()
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
761
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
762 #for $i, $s in enumerate($deg_list)
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
763 #set $cpt = str($i+1)
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
764 $transcripts.append(re.sub('"', '', "DEG_comparison"+str($i+1)))
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
765 #set $deg_one_values = os.fsdecode(subprocess.check_output('head -n1 ' + str($s.input) + '| cut -f' + str($s.valuecol), shell=True))
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
766 #set $deg_one_id = os.fsdecode(subprocess.check_output('head -n1 ' + str($s.input) + '| cut -f' + str($s.idcol), shell=True))
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
767 #end for
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
768 ]]></token>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
769 <token name="@INIT_PATHWAYS@"><![CDATA[
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
770 #set $pathways = {}
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
771 #if $path_kegg_metabolites:
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
772 #silent $pathways['metabolites']='pathways_kegg_metabolites'
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
773 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
774 #if $path_kegg_transcripts:
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
775 #silent $pathways['transcripts']='pathways_kegg_transcripts'
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
776 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
777 ]]></token>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
778 </macros>