Mercurial > repos > iuc > dimet_metabologram

annotate macros.xml @ 7:06f8d9ba09cd draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 6da96d865a3a557cfa3ad09e1cfa830519e73748
author iuc
date Tue, 06 Aug 2024 17:36:05 +0000
parents c7ff01bd331b
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a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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1 <macros>
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2 <token name="@TOOL_VERSION@">0.2.4</token>
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3 <token name="@VERSION_SUFFIX@">4</token>
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4 <xml name="requirements">
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5 <requirements>
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6 <requirement type="package" version="@TOOL_VERSION@">dimet</requirement>
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7 </requirements>
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8 </xml>
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9 <xml name="statistical_test_for_multigroup">
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10 <param name="stat_test" type="select" value="KW" display="radio" label="Select statistical to apply" help="Please enter at max 1 statistical test by file">
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11 <option value="KW">Kruskal-Wallis</option>
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12 </param>
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13 </xml>
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14 <xml name="statistical_test_for_bivariate_analysis">
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15 <param name="stat_test" type="select" value="pearson" display="radio" label="Select statistical to apply" help="Please enter at max 1 statistical test by file">
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16 <option value="pearson">pearson</option>
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17 <option value="spearman">spearman</option>
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18 </param>
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19 </xml>
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20 <xml name="statistical_test">
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21 <conditional name="statistics">
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22 <param name="statistical_test_type" type="select" label="Choose which type of statistical test to perform" help="Choose which type of statistical test to perform">
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23 <option value="parametric">parametric</option>
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24 <option value="non-parametric-rank" selected="true">non-parametric (rank based)</option>
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25 <option value="non-parametric-distribution">non-parametric (distribution based)</option>
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26 </param>
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27 <when value="parametric">
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28 <param name="stat_test" type="select" display="radio" label="Select statistical to apply" help="Please enter at max 1 statistical test by file">
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29 <option value="Tt" selected="true">t-test</option>
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30 </param>
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31 </when>
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32 <when value="non-parametric-rank">
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33 <param name="stat_test" type="select" display="radio" label="Select statistical to apply" help="Please enter at max 1 statistical test by file">
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34 <option value="MW">Mann Whitney</option>
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35 <option value="KW">Kruskal-Wallis</option>
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36 <option value="ranksum" selected="true">Wilcoxon's rank sum test</option>
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37 <option value="Wcox">Wilcoxon signed-rank test</option>
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38 <option value="BrMu">Brunner-Munzel test</option>
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39 </param>
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40 </when>
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41 <when value="non-parametric-distribution">
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42 <param name="stat_test" type="select" display="radio" label="Select statistical to apply" help="Please enter at max 1 statistical test by file">
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43 <option value="prm-scipy" selected="true">permutations test</option>
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44 <option value="disfit">distribution fitting (of the z-score of the ratios), disfit needs several hundreds of metabolites to be trustful.</option>
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45 </param>
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46 </when>
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47 </conditional>
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48
0
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49 </xml>
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50 <xml name="citations">
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51 <citations>
7
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52 <citation type="doi">10.1093/bioinformatics/btae282</citation>
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53 <citation type="bibtex">
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54 @software{Galvis_Rodriguez_DIMet,
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55 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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56 license = {MIT},
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57 title = {{DIMet}},
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58 url = {https://github.com/cbib/DIMet}
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59 }
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60 </citation>
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61 </citations>
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62
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63 </xml>
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64 <xml name="metadata_file_macros">
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65 <param name="metadata_path" type="data" format="tabular" label="metadata file" help="The metadata, a unique file with the description of the samples in your measures' files. This is compulsory, see section Metadata File Information."/>
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66 </xml>
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67 <xml name="abundance_file_macros">
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68 <param name="abundance_file" type="data" format="tabular" label="Metabolite abundance file" help="The total abundances file must be organized as a matrix: - The first column must contain Metabolite IDs that are unique (not repeated) within the file. - The rest of the columns correspond to the samples - The rows correspond to the metabolites - The values must be tab separated, with the first row containing the sample/column labels. (see help below for more details)"/>
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69 </xml>
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70 <xml name="enrichment_file_macros">
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71 <param name="me_or_frac_contrib_file" type="data" format="tabular" label="Metabolite enrichment file" help="The mean enrichment file must be organized as a matrix: - The first column must contain Metabolite IDs that are unique (not repeated) within the file. - The rest of the columns correspond to the samples. - The rows correspond to the metabolites. - The values must be tab separated, with the first row containing the sample/column labels. (see help below for more details)"/>
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72 </xml>
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73 <xml name="isotopologue_prop_file_macros">
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74 <param name="isotop_prop_file" type="data" format="tabular" label="Isotopologues proportion abundance file" help=" The isotopologue proportions file must be organized as a matrix: - The first column must contain isotopologues IDs that are unique (not repeated) within the file. - The rest of the columns correspond to the samples. - The rows correspond to the isotopologues. - The values must be tab separated, with the first row containing the sample/column labels (see help below for more details)."/>
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75 </xml>
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76 <xml name="isotopologue_abs_file_macros">
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77 <param name="isotop_abs_file" type="data" format="tabular" label="Isotopologues absolute abundance file" help="The isotopologue absolute values file must be organized as a matrix: - The first column must contain isotopologues IDs that are unique (not repeated) within the file. - The rest of the columns correspond to the samples. - The rows correspond to the isotopologues. - The values must be tab separated, with the first row containing the sample/column labels (see help below for more details)."/>
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78 </xml>
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79 <xml name="input_parameters_pca">
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80 <expand macro="abundance_file_macros"/>
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81 <param name="me_or_frac_contrib_file" type="data" optional="true" format="tabular" label="Mean enrichment or fraction contribution file"/>
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82 <expand macro="metadata_file_macros"/>
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83 </xml>
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84 <xml name="input_parameters_abundance">
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85 <expand macro="abundance_file_macros"/>
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86 <expand macro="metadata_file_macros"/>
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87 </xml>
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88 <xml name="input_parameters_enrichment">
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89 <expand macro="enrichment_file_macros"/>
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90 <expand macro="metadata_file_macros"/>
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91 </xml>
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92 <xml name="input_parameters_isotopologue">
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93 <expand macro="isotopologue_prop_file_macros"/>
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94 <expand macro="metadata_file_macros"/>
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95 </xml>
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96 <xml name="input_parameters_metabologram">
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97 <conditional name="data_input">
7
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98 <param name="data_input_selector" type="select" label="Abundance or Enrichment quantification files" help="Select between metabolite total abundances and mean enrichment files">
0
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99 <option value="abundance" selected="True">abundance</option>
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100 <option value="mean_enrichment">mean_enrichment</option>
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101 </param>
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102 <when value="abundance">
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103 <expand macro="abundance_file_macros"/>
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104 <expand macro="statistical_test"/>
7
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105
0
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106 </when>
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107 <when value="mean_enrichment">
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108 <expand macro="enrichment_file_macros"/>
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109 <expand macro="statistical_test"/>
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110 </when>
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111 </conditional>
7
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112 <expand macro="metadata_file_macros"/>
0
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113 <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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114 <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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115 </xml>
2
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116 <xml name="input_parameters_bivar_analysis">
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117 <conditional name="data_input">
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118 <param name="data_input_selector" type="select" label="Abundance, Enrichment or Isotopologues quantification files" help="Select between raw abundance, mean enrichment or isotopologue files">
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119 <option value="abundance" selected="True">abundance</option>
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120 <option value="mean_enrichment">mean_enrichment</option>
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121 <option value="isotop_prop">isotop_prop</option>
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122 <option value="isotop_abs">isotop_abs</option>
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123 </param>
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124 <when value="abundance">
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125 <expand macro="abundance_file_macros"/>
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126
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127 </when>
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128 <when value="mean_enrichment">
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129 <expand macro="enrichment_file_macros"/>
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130 </when>
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131 <when value="isotop_prop">
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132 <expand macro="isotopologue_prop_file_macros"/>
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133 </when>
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134 <when value="isotop_abs">
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135 <expand macro="isotopologue_abs_file_macros"/>
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136 </when>
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137 </conditional>
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138 <expand macro="metadata_file_macros"/>
4
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139 <expand macro="statistical_test_for_bivariate_analysis"/>
2
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140 </xml>
0
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141 <xml name="input_parameters_diff_analysis">
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142 <conditional name="data_input">
2
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143 <param name="data_input_selector" type="select" label="Abundance, Enrichment or Isotopologues quantification files" help="Select between raw abundance, mean enrichment or isotopologue files">
0
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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144 <option value="abundance" selected="True">abundance</option>
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145 <option value="mean_enrichment">mean_enrichment</option>
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146 <option value="isotop_prop">isotop_prop</option>
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147 <option value="isotop_abs">isotop_abs</option>
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148 </param>
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149 <when value="abundance">
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150 <expand macro="abundance_file_macros"/>
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151 <expand macro="statistical_test"/>
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152
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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153 </when>
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154 <when value="mean_enrichment">
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155 <expand macro="enrichment_file_macros"/>
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156 <expand macro="statistical_test"/>
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157 </when>
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158 <when value="isotop_prop">
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159 <expand macro="isotopologue_prop_file_macros"/>
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160 <expand macro="statistical_test"/>
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161 </when>
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162 <when value="isotop_abs">
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163 <expand macro="isotopologue_abs_file_macros"/>
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164 <expand macro="statistical_test"/>
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165 </when>
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166 </conditional>
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167 <expand macro="metadata_file_macros"/>
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168 </xml>
2
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169 <xml name="input_parameters_multi_diff_analysis">
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170 <conditional name="data_input">
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171 <param name="data_input_selector" type="select" label="Abundance, Enrichment or Isotopologues quantification files" help="Select between raw abundance, mean enrichment or isotopologue files">
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172 <option value="abundance" selected="True">abundance</option>
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173 <option value="mean_enrichment">mean_enrichment</option>
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174 <option value="isotop_prop">isotop_prop</option>
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175 <option value="isotop_abs">isotop_abs</option>
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176 </param>
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177 <when value="abundance">
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178 <expand macro="abundance_file_macros"/>
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179 <expand macro="statistical_test_for_multigroup"/>
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180
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181 </when>
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182 <when value="mean_enrichment">
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183 <expand macro="enrichment_file_macros"/>
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184 <expand macro="statistical_test_for_multigroup"/>
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185 </when>
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186 <when value="isotop_prop">
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187 <expand macro="isotopologue_prop_file_macros"/>
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188 <expand macro="statistical_test_for_multigroup"/>
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189 </when>
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190 <when value="isotop_abs">
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191 <expand macro="isotopologue_abs_file_macros"/>
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192 <expand macro="statistical_test_for_multigroup"/>
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193 </when>
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194 </conditional>
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195 <expand macro="metadata_file_macros"/>
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196 </xml>
0
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197 <xml name="suffix">
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198 <param name="suffix" type="text" optional="false" label="suffix to add to output files" >
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199 <sanitizer invalid_char="">
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200 <valid initial="string.ascii_letters,string.digits">
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201 <add value="_" />
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202 </valid>
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203 </sanitizer>
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204 </param>
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205 </xml>
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206 <xml name="conditions">
2
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207 <param name="conditions" type="select" optional="false" multiple="true" label="Browse conditions from metadata file (1 min. only if two timepoints are set. 2 max.). You have to load a metadata file prior to have access to condition list">
0
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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208 <options from_dataset="metadata_path">
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209 <column name="condition" index="1"/>
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210 <column name="value" index="1"/>
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211 <filter type="unique_value" name="condition" column="condition"/>
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212 <filter type="remove_value" value="condition"/>
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213 </options>
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214 <sanitizer>
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215 <valid initial="default">
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216 <add preset="string.printable"/>
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217 <add value="\t"/>
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218 <remove value="&quot;"/>
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219 <remove value="&apos;"/>
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220 </valid>
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221 </sanitizer>
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222 </param>
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223 </xml>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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224 <xml name="conditions_multigroup">
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225 <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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226 <options from_dataset="metadata_path">
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227 <column name="condition" index="1"/>
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228 <column name="value" index="1"/>
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229 <filter type="unique_value" name="condition" column="condition"/>
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230 <filter type="remove_value" value="condition"/>
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231 </options>
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232 <sanitizer>
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233 <valid initial="default">
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234 <add preset="string.printable"/>
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235 <add value="\t"/>
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236 <remove value="&quot;"/>
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237 <remove value="&apos;"/>
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238 </valid>
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239 </sanitizer>
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240 </param>
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241 </xml>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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242 <xml name="timepoint_multigroup">
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243 <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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244 <options from_dataset="metadata_path">
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245 <column name="timepoint" index="2"/>
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246 <column name="value" index="2"/>
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247 <filter type="unique_value" name="timepoint" column="2"/>
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248 <filter type="remove_value" value="timepoint"/>
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249 <filter type="sort_by" name="timepoint" column="1"/>
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250 </options>
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251 <sanitizer>
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252 <valid initial="default">
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253 <add preset="string.printable"/>
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254 <add value="\t"/>
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255 <remove value="&quot;"/>
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256 <remove value="&apos;"/>
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257 </valid>
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258 </sanitizer>
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259 </param>
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260 </xml>
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261 <xml name="timepoint">
2
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262 <param name="timepoint" type="select" optional="false" multiple="true" label="Browse timepoint from metadata file (1 min.)">
0
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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263 <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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264 <column name="timepoint" index="2"/>
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265 <column name="value" index="2"/>
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266 <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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267 <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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268 <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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269 </options>
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270 <sanitizer>
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271 <valid initial="default">
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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272 <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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273 <add value="\t"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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274 <remove value="&quot;"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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275 <remove value="&apos;"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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276 </valid>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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277 </sanitizer>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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278 </param>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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279 </xml>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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280 <xml name="grouping">
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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281 <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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282 <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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283 <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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284 </param>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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285 </xml>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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286 <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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287 <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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288 <option value="bonferroni">bonferroni</option>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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289 <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
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290 <option value="holm">holm</option>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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291 <option value="simes-hochberg">simes-hochberg</option>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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292 <option value="hommel">hommel</option>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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293 <option value="fdr_bh">fdr_bh</option>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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294 <option value="fdr_by">fdr_by</option>
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295 <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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296 <option value="fdr_tsbky">fdr_tsbky</option>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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297 </param>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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298 </xml>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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299 <xml name="compartments_enrichment">
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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300 <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
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301 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
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302 <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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303 <column name="compartment" index="4"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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304 <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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305 <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
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306 <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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307 </options>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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308 <sanitizer>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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309 <valid initial="default">
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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310 <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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311 <add value="\t"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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312 <remove value="&quot;"/>
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 <remove value="&apos;"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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314 </valid>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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315 </sanitizer>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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316 </param>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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317 </xml>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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318 <xml name="compartments_abundance">
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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319 <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
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320 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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321 <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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322 <column name="compartment" index="4"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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diff changeset
323 <column name="value" index="4"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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324 <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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325 <filter type="remove_value" value="compartment"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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326 </options>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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327 <sanitizer>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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328 <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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329 <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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330 <add value="\t"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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diff changeset
331 <remove value="&quot;"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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diff changeset
332 <remove value="&apos;"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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diff changeset
333 </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
334 </sanitizer>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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335 </param>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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336 </xml>
2
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337 <xml name="compartments_metabologram">
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
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338 <param name="compartments" type="select" optional="false" multiple="false"
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
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339 label="Browse compartments from metadata file (1 max.). You have to load a metadata file prior to have access to compartments">
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
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diff changeset
340 <options from_dataset="metadata_path">
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
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diff changeset
341 <column name="compartment" index="4"/>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
342 <column name="value" index="4"/>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
343 <filter type="unique_value" name="compartment" column="4"/>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
344 <filter type="remove_value" value="compartment"/>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
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diff changeset
345 </options>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
346 <sanitizer>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
347 <valid initial="default">
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
348 <add preset="string.printable"/>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
349 <add value="\t"/>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
350 <remove value="&quot;"/>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
351 <remove value="&apos;"/>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
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diff changeset
352 </valid>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
353 </sanitizer>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
354 </param>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
355 </xml>
0
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
356 <xml name="compartments">
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
357 <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
parents:
diff changeset
358 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
parents:
diff changeset
359 <options from_dataset="metadata_path">
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
360 <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
361 <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
362 <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
363 <filter type="remove_value" value="compartment"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
364 </options>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
365 <sanitizer>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
366 <valid initial="default">
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
367 <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
368 <add value="\t"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
369 <remove value="&quot;"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
370 <remove value="&apos;"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
371 </valid>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
372 </sanitizer>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
373 </param>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
374 </xml>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
375 <xml name="abundance_metabolites_list">
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
376 <param name="metabolites_list" type="select" optional="false" multiple="true"
2
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
377 label="Select Metabolite(s) for condition 1 to plot (1 min). You have to load a abundance file prior to have access to metabolite list">
0
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
378 <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
379 <options from_dataset="abundance_file">
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
380 <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
381 <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
382 <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
383 <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
parents:
diff changeset
384 </options>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
385 <sanitizer>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
386 <valid initial="default">
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
387 <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
388 <add value="\t"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
389 <remove value="&quot;"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
390 <remove value="&apos;"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
391 </valid>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
392 </sanitizer>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
393 </param>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
394 </xml>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
395 <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
396 <param name="metabolites_list" type="select" optional="false" multiple="true"
2
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
397 label="Select Metabolite(s) for condition 1 to plot (1 Min.). You have to load a abundance file prior to have access to metabolite list">
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
398 <validator type="length" min="1" message="Please enter at min 1 metabolite"/>
0
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
399 <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
400 <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
401 <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
402 <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
403 <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
404 </options>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
405 <sanitizer>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
406 <valid initial="default">
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
407 <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
408 <add value="\t"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
409 <remove value="&quot;"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
410 <remove value="&apos;"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
411 </valid>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
412 </sanitizer>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
413 </param>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
414 </xml>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
415 <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
416 <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
417 label="Select Metabolite(s) to plot (1 Min.). You have to load a abundance file prior to have access to metabolite list">
2
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
418 <validator type="length" min="1" message="Please enter at min 1 metabolite"/>
0
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
419 <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
420 <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
421 <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
422 <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
423 <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
424 </options>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
425 <sanitizer>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
426 <valid initial="default">
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
427 <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
428 <add value="\t"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
429 <remove value="&quot;"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
430 <remove value="&apos;"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
431 </valid>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
432 </sanitizer>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
433 </param>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
434 </xml>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
435 <xml name="deg_list">
2
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
436 <repeat name="deg_list" title="Deregulated gene set" default="1" min="1">
0
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
437 <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
438 <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
439 <param name="valuecol" type="data_column" data_ref="input" label="Column for values" use_header_names="true"/>
2
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
440 <param name="timepoint" type="select" optional="false" multiple="false" label="Browse timepoint from metadata file (1 min.)">
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
441 <options from_dataset="metadata_path">
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
442 <column name="timepoint" index="2"/>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
443 <column name="value" index="2"/>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
444 <filter type="unique_value" name="timepoint" column="2"/>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
445 <filter type="remove_value" value="timepoint"/>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
446 <filter type="sort_by" name="timepoint" column="1"/>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
447 </options>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
448 <sanitizer>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
449 <valid initial="default">
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
450 <add preset="string.printable"/>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
451 <add value="\t"/>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
452 <remove value="&quot;"/>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
453 <remove value="&apos;"/>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
454 </valid>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
455 </sanitizer>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
456 </param>
5
82fbf955bb0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit b74312f0a6cb28e204f8633453e493fa0b2c89d8
iuc
parents: 4
diff changeset
457 <repeat name="factor_list" title="Conditions" default="2" min="2" max="2" help="Specify conditions to compare from metadata file (for each comparison, the last specified condition is the reference). You have to load a metadata file prior to have access to condition list">
2
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
458 <param name="condition" label="Condition" type="select" optional="false" multiple="false">
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
459 <options from_dataset="metadata_path">
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
460 <column name="condition" index="1"/>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
461 <column name="value" index="1"/>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
462 <filter type="unique_value" name="condition" column="condition"/>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
463 <filter type="remove_value" value="condition"/>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
464 </options>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
465 <sanitizer>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
466 <valid initial="default">
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
467 <add preset="string.printable"/>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
468 <add value="\t"/>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
469 <remove value="&quot;"/>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
470 <remove value="&apos;"/>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
471 </valid>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
472 </sanitizer>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
473 </param>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
474 </repeat>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
475
0
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
476 </repeat>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
477 </xml>
2
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
478 <xml name="plot_abundance_factor_list">
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
479 <repeat name="plot_abundance_factor_list" title="Conditions" min="1" help="Specify conditions to compare from metadata file (1 min. only if two timepoints are set. 2 max.). You have to load a metadata file prior to have access to condition list">
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
480 <param name="condition" label="Condition" type="select" optional="false" multiple="false">
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
481 <options from_dataset="metadata_path">
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
482 <column name="condition" index="1"/>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
483 <column name="value" index="1"/>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
484 <filter type="unique_value" name="condition" column="condition"/>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
485 <filter type="remove_value" value="condition"/>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
486 </options>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
487 <sanitizer>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
488 <valid initial="default">
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
489 <add preset="string.printable"/>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
490 <add value="\t"/>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
491 <remove value="&quot;"/>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
492 <remove value="&apos;"/>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
493 </valid>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
494 </sanitizer>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
495 </param>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
496 </repeat>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
497 </xml>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
498 <xml name="plot_factor_list">
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
499 <repeat name="plot_factor_list" title="Conditions" min="2" help="Specify conditions to compare from metadata file (1 min. only if two timepoints are set. 2 max.). You have to load a metadata file prior to have access to condition list">
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
500 <param name="condition" label="Condition" type="select" optional="false" multiple="false">
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
501 <options from_dataset="metadata_path">
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
502 <column name="condition" index="1"/>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
503 <column name="value" index="1"/>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
504 <filter type="unique_value" name="condition" column="condition"/>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
505 <filter type="remove_value" value="condition"/>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
506 </options>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
507 <sanitizer>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
508 <valid initial="default">
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
509 <add preset="string.printable"/>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
510 <add value="\t"/>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
511 <remove value="&quot;"/>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
512 <remove value="&apos;"/>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
513 </valid>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
514 </sanitizer>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
515 </param>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
516 </repeat>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
517 </xml>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
518 <xml name="factor_list">
5
82fbf955bb0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit b74312f0a6cb28e204f8633453e493fa0b2c89d8
iuc
parents: 4
diff changeset
519 <repeat name="factor_list" title="Conditions" min="2" max="2" help="Specify conditions to be taken into account from metadata file (for each comparison, the last specified condition is the reference). You have to load a metadata file prior to have access to condition list">
2
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
520 <param name="condition" label="Condition" type="select" optional="false" multiple="false">
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
521 <options from_dataset="metadata_path">
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
522 <column name="condition" index="1"/>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
523 <column name="value" index="1"/>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
524 <filter type="unique_value" name="condition" column="condition"/>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
525 <filter type="remove_value" value="condition"/>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
526 </options>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
527 <sanitizer>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
528 <valid initial="default">
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
529 <add preset="string.printable"/>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
530 <add value="\t"/>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
531 <remove value="&quot;"/>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
532 <remove value="&apos;"/>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
533 </valid>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
534 </sanitizer>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
535 </param>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
536 </repeat>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
537 </xml>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
538 <xml name="palette">
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
539 <param name="palette" type="select" value="pastel" display="radio" label="Select palette colormap to apply to abundance plot." help="For more information see https://seaborn.pydata.org/tutorial/color_palettes.html">
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
540 <option value="pastel" selected="true">pastel</option>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
541 <option value="deep">deep</option>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
542 <option value="muted">muted</option>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
543 <option value="bright">bright</option>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
544 <option value="dark">dark</option>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
545 <option value="colorblind">colorblind</option>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
546 </param>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
547 </xml>
0
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
548 <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
549 #import json
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
550 #import re
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
551
2
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
552 mkdir -p data &&
0
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
553
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
554 #if $metadata_path:
2
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
555 ln -s '$metadata_path' data/metadata.csv &&
0
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
556 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
557 #if $abundance_file:
2
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
558 ln -s '$abundance_file' data/abundance.csv &&
0
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
559 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
560 #if $me_or_frac_contrib_file:
2
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
561 ln -s '$me_or_frac_contrib_file' data/me_or_frac_contrib.csv &&
0
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
562 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
563
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
564 ]]></token>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
565 <token name="@INIT_CONFIG@"><![CDATA[
6
c7ff01bd331b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents: 5
diff changeset
566 mkdir -p 'config' &&
c7ff01bd331b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents: 5
diff changeset
567 touch 'config/config.yaml' &&
0
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
568 ]]></token>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
569 <token name="@REMOVE_CONFIG@"><![CDATA[
6
c7ff01bd331b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
iuc
parents: 5
diff changeset
570 && rm -r 'config'
0
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
571 ]]></token>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
572 <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
573
2
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
574 mkdir -p data &&
0
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
575 #if $metadata_path:
2
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
576 ln -s '$metadata_path' data/metadata.csv &&
0
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
577 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
578 #if $abundance_file:
2
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
579 ln -s '$abundance_file' data/abundance.csv &&
0
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
580 #end if
5
82fbf955bb0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit b74312f0a6cb28e204f8633453e493fa0b2c89d8
iuc
parents: 4
diff changeset
581 #set $axisx = "condition"
82fbf955bb0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit b74312f0a6cb28e204f8633453e493fa0b2c89d8
iuc
parents: 4
diff changeset
582 #if str( $output_options.bar_color ) == "condition":
82fbf955bb0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit b74312f0a6cb28e204f8633453e493fa0b2c89d8
iuc
parents: 4
diff changeset
583 #set $axisx = "timepoint"
82fbf955bb0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit b74312f0a6cb28e204f8633453e493fa0b2c89d8
iuc
parents: 4
diff changeset
584 #end if
82fbf955bb0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit b74312f0a6cb28e204f8633453e493fa0b2c89d8
iuc
parents: 4
diff changeset
585
0
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
586 ]]></token>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
587 <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
588
2
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
589 mkdir -p data &&
0
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
590
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
591 #if $metadata_path:
2
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
592 ln -s '$metadata_path' data/metadata.csv &&
0
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
593 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
594 #if $me_or_frac_contrib_file:
2
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
595 ln -s '$me_or_frac_contrib_file' data/me_or_frac_contrib.csv &&
0
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
596 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
597 ]]></token>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
598 <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
599
2
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
600 mkdir -p data &&
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
601
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
602 #if $metadata_path:
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
603 ln -s '$metadata_path' data/metadata.csv &&
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
604 #end if
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
605 #if $isotop_prop_file:
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
606 ln -s '$isotop_prop_file' data/isotop_prop.csv &&
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
607 #end if
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
608 ]]></token>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
609 <token name="@INIT_BI_ANALYSIS@"><![CDATA[
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
610
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
611 mkdir -p data &&
0
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
612
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
613 #if $metadata_path:
2
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
614 ln -s '$metadata_path' data/metadata.csv &&
0
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
615 #end if
4
82fb756e71cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit afc87f0254b4399b71e53735966032ba1a32434d
iuc
parents: 3
diff changeset
616
82fb756e71cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit afc87f0254b4399b71e53735966032ba1a32434d
iuc
parents: 3
diff changeset
617
2
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
618 #set conditions_MDV_comparison = {}
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
619 #set timepoints_MDV_comparison = {}
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
620 #set conditions_metabolite_time_profiles = {}
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
621
4
82fb756e71cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit afc87f0254b4399b71e53735966032ba1a32434d
iuc
parents: 3
diff changeset
622 #if str( $stat_test ) == "pearson":
82fb756e71cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit afc87f0254b4399b71e53735966032ba1a32434d
iuc
parents: 3
diff changeset
623 #silent $conditions_MDV_comparison['isotopologue_proportions']='pearson'
82fb756e71cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit afc87f0254b4399b71e53735966032ba1a32434d
iuc
parents: 3
diff changeset
624 #silent $timepoints_MDV_comparison['isotopologue_proportions']='pearson'
82fb756e71cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit afc87f0254b4399b71e53735966032ba1a32434d
iuc
parents: 3
diff changeset
625 #silent $conditions_metabolite_time_profiles['abundances']='pearson'
82fb756e71cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit afc87f0254b4399b71e53735966032ba1a32434d
iuc
parents: 3
diff changeset
626 #silent $conditions_metabolite_time_profiles['mean_enrichment']='pearson'
82fb756e71cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit afc87f0254b4399b71e53735966032ba1a32434d
iuc
parents: 3
diff changeset
627 #else
82fb756e71cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit afc87f0254b4399b71e53735966032ba1a32434d
iuc
parents: 3
diff changeset
628 #silent $conditions_MDV_comparison['isotopologue_proportions']='spearman'
82fb756e71cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit afc87f0254b4399b71e53735966032ba1a32434d
iuc
parents: 3
diff changeset
629 #silent $timepoints_MDV_comparison['isotopologue_proportions']='spearman'
82fb756e71cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit afc87f0254b4399b71e53735966032ba1a32434d
iuc
parents: 3
diff changeset
630 #silent $conditions_metabolite_time_profiles['abundances']='spearman'
82fb756e71cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit afc87f0254b4399b71e53735966032ba1a32434d
iuc
parents: 3
diff changeset
631 #silent $conditions_metabolite_time_profiles['mean_enrichment']='spearman'
82fb756e71cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit afc87f0254b4399b71e53735966032ba1a32434d
iuc
parents: 3
diff changeset
632 #end if
2
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
633 #set $impute_values = {}
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
634 #if str( $data_input.data_input_selector ) == "abundance":
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
635 #if $data_input.abundance_file:
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
636 ln -s '$data_input.abundance_file' data/abundance.csv &&
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
637 #silent $impute_values['abundances']='min'
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
638 #end if
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
639 #elif str( $data_input.data_input_selector ) == "mean_enrichment":
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
640 #if $data_input.me_or_frac_contrib_file:
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
641 ln -s '$data_input.me_or_frac_contrib_file' data/me_or_frac_contrib.csv &&
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
642 #silent $impute_values['mean_enrichment']='min'
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
643 #end if
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
644 #elif str( $data_input.data_input_selector ) == "isotop_prop":
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
645 #if $data_input.isotop_prop_file:
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
646 ln -s '$data_input.isotop_prop_file' data/isotop_prop.csv &&
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
647 #silent $impute_values['isotopologue_proportions']='min'
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
648 #end if
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
649 #else
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
650 #if $data_input.isotop_abs_file:
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
651 ln -s '$data_input.isotop_abs_file' data/isotop_abs.csv &&
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
652 #silent $impute_values['isotopologues']='min'
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
653 #end if
0
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
654 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
655 ]]></token>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
656 <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
657
2
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
658 mkdir -p data &&
0
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
659
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
660 #if $metadata_path:
2
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
661 ln -s '$metadata_path' data/metadata.csv &&
0
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
662 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
663
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
664 #set $impute_values = {}
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
665 #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
666 #if $data_input.abundance_file:
2
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
667 ln -s '$data_input.abundance_file' data/abundance.csv &&
0
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
668 #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
669 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
670 #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
671 #if $data_input.me_or_frac_contrib_file:
2
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
672 ln -s '$data_input.me_or_frac_contrib_file' data/me_or_frac_contrib.csv &&
0
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
673 #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
674 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
675 #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
676 #if $data_input.isotop_prop_file:
2
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
677 ln -s '$data_input.isotop_prop_file' data/isotop_prop.csv &&
0
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
678 #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
679 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
680 #else
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
681 #if $data_input.isotop_abs_file:
2
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
682 ln -s '$data_input.isotop_abs_file' data/isotop_abs.csv &&
0
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
683 #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
684 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
685 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
686 ]]></token>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
687 <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
688 #import json
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
689 #import re
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
690 #import os
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
691 #import csv
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
692 #import subprocess
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
693
2
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
694 mkdir -p data &&
0
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
695
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
696 #if $path_kegg_metabolites:
2
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
697 ln -s '$path_kegg_metabolites' data/pathways_kegg_metabolites.csv &&
0
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
698 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
699 #if $path_kegg_transcripts:
2
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
700 ln -s '$path_kegg_transcripts' data/pathways_kegg_transcripts.csv &&
0
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
701 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
702
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
703 #if $metadata_path:
2
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
704 ln -s '$metadata_path' data/metadata.csv &&
0
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
705 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
706
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
707 #set $impute_values = {}
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
708 #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
709 #if $data_input.abundance_file:
2
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
710 ln -s '$data_input.abundance_file' data/abundance.csv &&
0
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
711 #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
712 #end if
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 #if $data_input.me_or_frac_contrib_file:
2
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
715 ln -s '$data_input.me_or_frac_contrib_file' data/me_or_frac_contrib.csv &&
0
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
716 #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
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 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
719
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
720 #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
721 #set $cpt = str($i+1)
2
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
722 ln -s '${s.input}' data/DEG_comparison'${cpt}'.csv &&
0
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
723 #end for
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
724
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
725
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
726 ]]></token>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
727 <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
728
2
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
729 mkdir -p data &&
0
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
730
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
731 #if $metadata_path:
2
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
732 ln -s '$metadata_path' data/metadata.csv &&
0
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 #set $impute_values = {}
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
736 #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
737 #if $data_input.abundance_file:
2
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
738 ln -s '$data_input.abundance_file' data/abundance.csv &&
0
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
739 #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
740 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
741 #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
742 #if $data_input.me_or_frac_contrib_file:
2
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
743 ln -s '$data_input.me_or_frac_contrib_file' data/me_or_frac_contrib.csv &&
0
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
744 #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
745 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
746 #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
747 #if $data_input.isotop_prop_file:
2
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
748 ln -s '$data_input.isotop_prop_file' data/isotop_prop.csv &&
0
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
749 #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
750 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
751 #else
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
752 #if $data_input.isotop_abs_file:
2
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
753 ln -s '$data_input.isotop_abs_file' data/isotop_abs.csv &&
0
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
754 #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
755 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
756 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
757 ]]></token>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
758 <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
759 #import re
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
760 #set $impute_values = {}
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
761 #if $abundance_file:
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
762 #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
763 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
764 #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
765 #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
766 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
767 ]]></token>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
768 <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
769 #import re
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
770 #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
771 #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
772 #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
773 $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
774 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
775 #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
776 #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
777 $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
778 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
779 #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
780 #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
781 $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
782 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
783 #else
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
784 #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
785 $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
786 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
787 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
788 ]]></token>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
789 <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
790 #import re
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
791 #set $statistical_test = {}
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
792 #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
793 #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
794 #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
795 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
796 #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
797 #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
798 #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
799 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
800 #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
801 #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
802 #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
803 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
804 #else
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
805 #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
806 #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
807 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
808 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
809 ]]></token>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
810 <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
811 #import re
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
812 #set $conds = list()
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
813 #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
814 $conds.append(re.sub('"', '', str($co)))
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
815 #end for
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
816 ]]></token>
2
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
817 <token name="@INIT_PLOT_CONDITIONS@"><![CDATA[
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
818 #set $conditions = list()
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
819 #for $i, $s in enumerate($plot_factor_list)
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
820 #set $cpt = str($i+1)
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
821 $conditions.append(re.sub('"', '', str($s.condition)))
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
822 #end for
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
823 ]]></token>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
824 <token name="@INIT_ABUNDANCE_PLOT_CONDITIONS@"><![CDATA[
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
825 #set $conditions = list()
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
826 #for $i, $s in enumerate($plot_abundance_factor_list)
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
827 #set $cpt = str($i+1)
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
828 $conditions.append(re.sub('"', '', str($s.condition)))
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
829 #end for
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
830 ]]></token>
0
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
831 <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
832
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
833 #import re
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
834 #set $timepoints = list()
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
835 #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
836 $timepoints.append(re.sub('"', '', str($tp)))
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
837 #end for
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
838 ]]></token>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
839 <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
840 #import re
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
841 #set $groups = list()
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
842 $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
843 $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
844
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
845 ]]></token>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
846 <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
847 #import json
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
848 #import re
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
849 #set $metabolites = {}
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
850 #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
851 #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
852 #for $met in $metabolites_list:
2
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
853 #set tmp_met=re.sub('\,', '%%',str($met))
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
854 #set tmp_met_bis=str(re.split('_m', str($tmp_met))[0])
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
855 #set tmp_met_ter=re.sub('%%', '\,',str($tmp_met_bis))
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
856 $metabolites[re.sub('"', '', str($cp))].append(re.sub('"', '\'', str(tmp_met_ter)))
0
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
857 #end for
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
858 #end for
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
859 ]]></token>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
860 <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
861 #set $metabolites = {}
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
862 #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
863 #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
864 #for $met in $metabolites_list:
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
865 #set tmp_met=re.sub('\,', '--',str($met))
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
866 #set tmp_met_bis=str(re.split('_m', str($tmp_met))[0])
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
867 #set tmp_met_ter=re.sub('--', '\,',str($tmp_met_bis))
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
868 $metabolites[re.sub('"', '', str($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
869 #end for
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
870 #end for
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
871 ]]></token>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
872 <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
873 #set $comparisons = list()
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
874 #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
875 #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
876 #set $ctrl=""
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
877
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
878 #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
879 #set $sub_comparisons = list()
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
880 #if str($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
881 #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
882 #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
883 $sub_comparisons.append(re.sub('"', '', str($co)))
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
884 $sub_comparisons.append(re.sub('"', '', str($tp)))
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
885 #else:
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
886 $sub_comparisons.append(re.sub('"', '', str($co)))
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
887 $sub_comparisons.append(re.sub('"', '', str($tp)))
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
888
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
889 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
890 $comparisons.append($sub_comparisons)
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
891 #end for
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
892 #end for
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
893 ]]></token>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
894 <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
895 #import re
2
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
896 #set $conditions = list()
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
897 #for $i, $s in enumerate($factor_list)
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
898 #set $cpt = str($i+1)
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
899 $conditions.append(re.sub('"', '', str($s.condition)))
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
900 #end for
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
901
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
902 ]]></token>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
903 <token name="@INIT_BIVAR_COMPARISONS@"><![CDATA[
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
904 #import re
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
905 #set $conditions = list()
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
906 #for $i, $s in enumerate($plot_factor_list)
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
907 #set $cpt = str($i+1)
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
908 $conditions.append(re.sub('"', '', str($s.condition)))
0
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
909 #end for
2
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
910 ]]></token>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
911 <token name="@INIT_COMPARISONS_METABOLOGRAM@"><![CDATA[
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
912 #import re
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
913 #set $conditions = list()
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
914 #set $timepoints = list()
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
915 #set $comparisons = list()
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
916 #for $i, $s in enumerate($deg_list)
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
917 #set $cpt = str($i+1)
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
918 #set $comparisons_bis = list()
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
919 #for $j, $t in enumerate($s.factor_list)
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
920 #set $sub_comparisons = list()
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
921 #if str($t.condition) not in $conditions:
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
922 $conditions.append(re.sub('"', '', str($t.condition)))
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
923 #end if
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
924 $sub_comparisons.append(re.sub('"', '', str($t.condition)))
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
925 $sub_comparisons.append(re.sub('"', '', str($s.timepoint)))
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
926 $comparisons_bis.append($sub_comparisons)
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
927 #end for
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
928 $timepoints.append(re.sub('"', '', str($s.timepoint)))
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
929 $comparisons.append($comparisons_bis)
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
930 #end for
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
931
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
932
0
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
933
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
934 ]]></token>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
935 <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
936 #import re
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
937 #set $conds = list()
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
938 #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
939 $conds.append(re.sub('"', '', str($co)))
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
940 #end for
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
941 #set $timepoints = list()
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
942 #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
943 $timepoints.append(re.sub('"', '', str($tp)))
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
944 #end for
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
945
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
946 #set $comparisons = list()
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
947 #if len($conds) > 1:
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
948 #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
949 #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
950 #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
951 #set $ctrl=""
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
952 #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
953 #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
954 #set $sub_comparisons = list()
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
955 #if str($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
956 #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
957 #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
958 #else:
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
959 $sub_comparisons.append(re.sub('"', '', str($co)))
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
960 $sub_comparisons.append(re.sub('"', '', str($tp)))
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
961
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
962 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
963 $comparisons_bis.append($sub_comparisons)
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
964 #end for
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
965
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
966 #if $ctrl_found:
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
967 $sub_comparisons.append(str($ctrl))
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
968 $sub_comparisons.append(str($tp))
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
969 $comparisons_bis.append($sub_comparisons)
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
970 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
971
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
972 $comparisons.append($comparisons_bis)
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
973 #end for
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
974 #else
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
975 #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
976 $comparisons.append(re.sub('"', '', str($co)))
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
977 #end for
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
978 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
979
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
980 #else
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
981 #if len($conds) > 0:
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
982 #if len($timepoints) > 1:
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
983 #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
984 #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
985 #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
986 #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
987 $sub_comparisons.append(re.sub('"', '', str($co)))
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
988 $sub_comparisons.append(re.sub('"', '', str($tp)))
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
989 $comparisons_bis.append($sub_comparisons)
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
990 #end for
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
991 $comparisons.append($comparisons_bis)
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
992 #end for
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
993 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
994 #else
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
995 #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
996 $comparisons.append(re.sub('"', '', str($tp)))
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
997 #end for
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
998 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
999 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1000 ]]></token>
2
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1001 <token name="@INIT_DIFF_ANALYSIS_COMPARISONS@"><![CDATA[
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1002 #import re
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1003 #set $conditions = list()
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1004 #for $i, $s in enumerate($factor_list)
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1005 #set $cpt = str($i+1)
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1006 $conditions.append(re.sub('"', '', str($s.condition)))
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1007 #end for
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1008
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1009 #set $timepoints = list()
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1010 #for $tp in $timepoint:
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1011 $timepoints.append(re.sub('"', '', str($tp)))
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1012 #end for
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1013
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1014 #set $comparisons = list()
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1015 #if len($conditions) > 1:
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1016 #if len($timepoints) > 0:
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1017 #for $tp in $timepoint:
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1018 #set $ctrl_found=False
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1019 #set $ctrl=""
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1020 #set $comparisons_bis = list()
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1021
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1022 #for $co in $conditions:
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1023 #set $sub_comparisons = list()
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1024 #if str($co) in ["'Control'", "'control'", "'ctrl'"]:
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1025 #set $ctrl_found=True
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1026 #set $ctrl=str($co)
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1027 #else:
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1028 $sub_comparisons.append(re.sub('"', '', str($co)))
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1029 $sub_comparisons.append(re.sub('"', '', str($tp)))
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1030
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1031 #end if
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1032 $comparisons_bis.append($sub_comparisons)
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1033 #end for
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1034
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1035 #if $ctrl_found:
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1036 $sub_comparisons.append(str($ctrl))
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1037 $sub_comparisons.append(str($tp))
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1038 $comparisons_bis.append($sub_comparisons)
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1039 #end if
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1040
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1041 $comparisons.append($comparisons_bis)
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1042 #end for
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1043 #else
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1044 #for $co in $conditions:
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1045 $comparisons.append(re.sub('"', '', str($co)))
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1046 #end for
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1047 #end if
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1048
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1049 #else
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1050 #if len($conditions) > 0:
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1051 #if len($timepoints) > 1:
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1052 #for $co in $conditions:
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1053 #set $comparisons_bis = list()
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1054 #for $tp in $timepoint:
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1055 #set $sub_comparisons = list()
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1056 $sub_comparisons.append(re.sub('"', '', str($co)))
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1057 $sub_comparisons.append(re.sub('"', '', str($tp)))
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1058 $comparisons_bis.append($sub_comparisons)
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1059 #end for
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1060 $comparisons.append($comparisons_bis)
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1061 #end for
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1062 #end if
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1063 #else
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1064 #for $tp in $timepoint:
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1065 $comparisons.append(re.sub('"', '', str($tp)))
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1066 #end for
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1067 #end if
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1068 #end if
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1069 ]]></token>
0
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1070 <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
1071 #import re
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1072 #import os
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1073 #import subprocess
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1074 #set $transcripts = list()
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1075
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1076 #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
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1077 #set $cpt = str($i+1)
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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diff changeset
1078 $transcripts.append(re.sub('"', '', "DEG_comparison"+str($i+1)))
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1079 #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
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1080 #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
1081 #end for
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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1082 ]]></token>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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1083 <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
1084 #set $pathways = {}
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
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1085 #if $path_kegg_metabolites:
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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1086 #silent $pathways['metabolites']='pathways_kegg_metabolites'
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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1087 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1088 #if $path_kegg_transcripts:
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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1089 #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:
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1090 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
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1091 ]]></token>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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1092 </macros>