Mercurial > repos > iuc > dimet_metabologram

annotate macros.xml @ 4:82fb756e71cf draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit afc87f0254b4399b71e53735966032ba1a32434d
author iuc
date Wed, 27 Mar 2024 16:51:14 +0000
parents b6e621c83f94
children 82fbf955bb0f
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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@">1</token>
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4 <token name="@EXECUTABLE@">pca</token>
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5 <xml name="requirements">
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6 <requirements>
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7 <requirement type="package" version="@TOOL_VERSION@">dimet</requirement>
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8 </requirements>
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9 </xml>
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10 <xml name="statistical_test_for_multigroup">
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11 <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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12 <option value="KW">Kruskal-Wallis</option>
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13 </param>
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14 </xml>
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15 <xml name="statistical_test_for_bivariate_analysis">
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16 <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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17 <option value="pearson">pearson</option>
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18 <option value="spearman">spearman</option>
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19 </param>
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20 </xml>
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21 <xml name="statistical_test">
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22 <conditional name="statistics">
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23 <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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24 <option value="parametric">parametric</option>
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25 <option value="non-parametric-rank" selected="true">non-parametric (rank based)</option>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
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26 <option value="non-parametric-distribution">non-parametric (distribution based)</option>
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27 </param>
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28 <when value="parametric">
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29 <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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30 <option value="Tt" selected="true">t-test</option>
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31 </param>
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32 </when>
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33 <when value="non-parametric-rank">
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34 <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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35 <option value="MW">Mann Whitney</option>
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36 <option value="KW">Kruskal-Wallis</option>
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37 <option value="ranksum" selected="true">Wilcoxon's rank sum test</option>
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38 <option value="Wcox">Wilcoxon signed-rank test</option>
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39 <option value="BrMu">Brunner-Munzel test</option>
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40 </param>
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41 </when>
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42 <when value="non-parametric-distribution">
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43 <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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44 <option value="prm-scipy" selected="true">permutations test</option>
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45 <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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46 </param>
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47 </when>
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48 </conditional>
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49
0
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50 </xml>
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51 <xml name="citations">
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52 <citations>
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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
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61 </citation>
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62 </citations>
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63
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64 </xml>
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65 <xml name="metadata_file_macros">
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66 <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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67 </xml>
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68 <xml name="abundance_file_macros">
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69 <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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70 </xml>
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71 <xml name="enrichment_file_macros">
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72 <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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73 </xml>
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74 <xml name="isotopologue_prop_file_macros">
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75 <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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76 </xml>
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77 <xml name="isotopologue_abs_file_macros">
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78 <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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79 </xml>
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80 <xml name="input_parameters_pca">
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81 <expand macro="abundance_file_macros"/>
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82 <param name="me_or_frac_contrib_file" type="data" optional="true" format="tabular" label="Mean enrichment or fraction contribution file"/>
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83 <expand macro="metadata_file_macros"/>
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84 </xml>
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85 <xml name="input_parameters_abundance">
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86 <expand macro="abundance_file_macros"/>
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87 <expand macro="metadata_file_macros"/>
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88 </xml>
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89 <xml name="input_parameters_enrichment">
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90 <expand macro="enrichment_file_macros"/>
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91 <expand macro="metadata_file_macros"/>
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92 </xml>
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93 <xml name="input_parameters_isotopologue">
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94 <expand macro="isotopologue_prop_file_macros"/>
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95 <expand macro="metadata_file_macros"/>
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96 </xml>
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97 <xml name="input_parameters_metabologram">
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98 <conditional name="data_input">
2
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99 <param name="data_input_selector" type="select" label="Abundance, Enrichment or Isotopologues quantification files" help="Select between raw abundance and mean enrichment files">
0
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100 <option value="abundance" selected="True">abundance</option>
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101 <option value="mean_enrichment">mean_enrichment</option>
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102 </param>
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103 <when value="abundance">
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104 <expand macro="abundance_file_macros"/>
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105 <param name="metabolites_list" type="select" optional="false" multiple="true"
2
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106 label="Select Metabolite(s) for condition 1 to plot (1 Min.). You have to load a abundance file prior to have access to metabolite list">
0
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107 <validator type="length" min="1" message="Please enter at max 2 compartments"/>
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108 <options from_dataset="abundance_file">
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109 <column name="metabolite_or_isotopologue" index="0"/>
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110 <column name="value" index="0"/>
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111 <filter type="unique_value" name="metabolite_or_isotopologue" column="0"/>
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112 <filter type="remove_value" value="metabolite_or_isotopologue"/>
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113 </options>
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114 <sanitizer>
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115 <valid initial="default">
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116 <add preset="string.printable"/>
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117 <add value="\t"/>
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118 <remove value="&quot;"/>
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119 <remove value="&apos;"/>
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120 </valid>
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121 </sanitizer>
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122 </param>
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123 <expand macro="statistical_test"/>
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124 </when>
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125 <when value="mean_enrichment">
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126 <expand macro="enrichment_file_macros"/>
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127 <param name="metabolites_list" type="select" optional="false" multiple="true"
2
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128 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
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129 <validator type="length" min="1" message="Please enter at max 2 compartments"/>
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130 <options from_dataset="me_or_frac_contrib_file">
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131 <column name="metabolite_or_isotopologue" index="0"/>
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132 <column name="value" index="0"/>
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133 <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
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134 <filter type="remove_value" value="metabolite_or_isotopologue"/>
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135 </options>
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136 <sanitizer>
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137 <valid initial="default">
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138 <add preset="string.printable"/>
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139 <add value="\t"/>
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140 <remove value="&quot;"/>
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141 <remove value="&apos;"/>
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142 </valid>
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143 </sanitizer>
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144 </param>
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145 <expand macro="statistical_test"/>
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146 </when>
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147 </conditional>
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148 <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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149 <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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150 <expand macro="metadata_file_macros"/>
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151 </xml>
2
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152 <xml name="input_parameters_bivar_analysis">
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153 <conditional name="data_input">
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154 <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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155 <option value="abundance" selected="True">abundance</option>
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156 <option value="mean_enrichment">mean_enrichment</option>
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157 <option value="isotop_prop">isotop_prop</option>
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158 <option value="isotop_abs">isotop_abs</option>
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159 </param>
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160 <when value="abundance">
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161 <expand macro="abundance_file_macros"/>
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162
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
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163 </when>
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164 <when value="mean_enrichment">
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165 <expand macro="enrichment_file_macros"/>
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166 </when>
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167 <when value="isotop_prop">
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168 <expand macro="isotopologue_prop_file_macros"/>
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169 </when>
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170 <when value="isotop_abs">
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171 <expand macro="isotopologue_abs_file_macros"/>
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172 </when>
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173 </conditional>
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174 <expand macro="metadata_file_macros"/>
4
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175 <expand macro="statistical_test_for_bivariate_analysis"/>
2
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176 </xml>
0
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177 <xml name="input_parameters_diff_analysis">
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178 <conditional name="data_input">
2
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179 <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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180 <option value="abundance" selected="True">abundance</option>
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181 <option value="mean_enrichment">mean_enrichment</option>
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182 <option value="isotop_prop">isotop_prop</option>
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183 <option value="isotop_abs">isotop_abs</option>
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184 </param>
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185 <when value="abundance">
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186 <expand macro="abundance_file_macros"/>
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187 <expand macro="statistical_test"/>
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188
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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189 </when>
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190 <when value="mean_enrichment">
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191 <expand macro="enrichment_file_macros"/>
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192 <expand macro="statistical_test"/>
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193 </when>
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194 <when value="isotop_prop">
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195 <expand macro="isotopologue_prop_file_macros"/>
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196 <expand macro="statistical_test"/>
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197 </when>
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198 <when value="isotop_abs">
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199 <expand macro="isotopologue_abs_file_macros"/>
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200 <expand macro="statistical_test"/>
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201 </when>
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202 </conditional>
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iuc
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203 <expand macro="metadata_file_macros"/>
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204 </xml>
2
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iuc
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205 <xml name="input_parameters_multi_diff_analysis">
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
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206 <conditional name="data_input">
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207 <param name="data_input_selector" type="select" label="Abundance, Enrichment or Isotopologues quantification files" help="Select between raw abundance, mean enrichment or isotopologue files">
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
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208 <option value="abundance" selected="True">abundance</option>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
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209 <option value="mean_enrichment">mean_enrichment</option>
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iuc
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210 <option value="isotop_prop">isotop_prop</option>
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iuc
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211 <option value="isotop_abs">isotop_abs</option>
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212 </param>
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iuc
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213 <when value="abundance">
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iuc
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214 <expand macro="abundance_file_macros"/>
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iuc
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215 <expand macro="statistical_test_for_multigroup"/>
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iuc
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216
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
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217 </when>
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iuc
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218 <when value="mean_enrichment">
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iuc
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219 <expand macro="enrichment_file_macros"/>
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iuc
parents: 1
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220 <expand macro="statistical_test_for_multigroup"/>
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221 </when>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
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222 <when value="isotop_prop">
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
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223 <expand macro="isotopologue_prop_file_macros"/>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
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224 <expand macro="statistical_test_for_multigroup"/>
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225 </when>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
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226 <when value="isotop_abs">
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227 <expand macro="isotopologue_abs_file_macros"/>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
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228 <expand macro="statistical_test_for_multigroup"/>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
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229 </when>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
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230 </conditional>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
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231 <expand macro="metadata_file_macros"/>
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232 </xml>
0
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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233 <xml name="suffix">
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234 <param name="suffix" type="text" optional="false" label="suffix to add to output files" >
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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235 <sanitizer invalid_char="">
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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236 <valid initial="string.ascii_letters,string.digits">
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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237 <add value="_" />
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238 </valid>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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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="conditions">
2
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243 <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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244 <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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245 <column name="condition" index="1"/>
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246 <column name="value" index="1"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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247 <filter type="unique_value" name="condition" column="condition"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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248 <filter type="remove_value" value="condition"/>
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249 </options>
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250 <sanitizer>
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251 <valid initial="default">
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252 <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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253 <add value="\t"/>
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254 <remove value="&quot;"/>
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255 <remove value="&apos;"/>
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256 </valid>
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257 </sanitizer>
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258 </param>
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259 </xml>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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260 <xml name="conditions_multigroup">
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261 <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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262 <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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263 <column name="condition" index="1"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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264 <column name="value" index="1"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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265 <filter type="unique_value" name="condition" column="condition"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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266 <filter type="remove_value" value="condition"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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267 </options>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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268 <sanitizer>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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269 <valid initial="default">
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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270 <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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271 <add value="\t"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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272 <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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273 <remove value="&apos;"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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274 </valid>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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275 </sanitizer>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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276 </param>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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277 </xml>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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278 <xml name="timepoint_multigroup">
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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279 <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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280 <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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281 <column name="timepoint" index="2"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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282 <column name="value" index="2"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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283 <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
iuc
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284 <filter type="remove_value" value="timepoint"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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285 <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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286 </options>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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287 <sanitizer>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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288 <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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289 <add preset="string.printable"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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diff changeset
290 <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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291 <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
292 <remove value="&apos;"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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293 </valid>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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294 </sanitizer>
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diff changeset
295 </param>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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296 </xml>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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297 <xml name="timepoint">
2
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
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298 <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
iuc
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299 <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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300 <column name="timepoint" index="2"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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diff changeset
301 <column name="value" index="2"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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diff changeset
302 <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
iuc
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diff changeset
303 <filter type="remove_value" value="timepoint"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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diff changeset
304 <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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diff changeset
305 </options>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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306 <sanitizer>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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diff changeset
307 <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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diff changeset
308 <add preset="string.printable"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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diff changeset
309 <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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diff changeset
310 <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
311 <remove value="&apos;"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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diff changeset
312 </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
313 </sanitizer>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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diff changeset
314 </param>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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diff changeset
315 </xml>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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316 <xml name="grouping">
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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317 <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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318 <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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319 <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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320 </param>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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diff changeset
321 </xml>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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322 <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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323 <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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324 <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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325 <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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326 <option value="holm">holm</option>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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327 <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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328 <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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329 <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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330 <option value="fdr_by">fdr_by</option>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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331 <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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332 <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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333 </param>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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334 </xml>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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335 <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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336 <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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337 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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338 <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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339 <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
340 <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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diff changeset
341 <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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342 <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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343 </options>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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344 <sanitizer>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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345 <valid initial="default">
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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diff changeset
346 <add preset="string.printable"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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diff changeset
347 <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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diff changeset
348 <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
349 <remove value="&apos;"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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350 </valid>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
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diff changeset
351 </sanitizer>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
352 </param>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
353 </xml>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
354 <xml name="compartments_abundance">
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
355 <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
356 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
parents:
diff changeset
357 <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
358 <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
359 <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
360 <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
361 <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
362 </options>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
363 <sanitizer>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
364 <valid initial="default">
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
365 <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
366 <add value="\t"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
367 <remove value="&quot;"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
368 <remove value="&apos;"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
369 </valid>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
370 </sanitizer>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
371 </param>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
372 </xml>
2
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
373 <xml name="compartments_metabologram">
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
374 <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
iuc
parents: 1
diff changeset
375 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
parents: 1
diff changeset
376 <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
377 <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
378 <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
379 <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
380 <filter type="remove_value" value="compartment"/>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
381 </options>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
382 <sanitizer>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
383 <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
384 <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
385 <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
386 <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
387 <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
388 </valid>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
389 </sanitizer>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
390 </param>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
391 </xml>
0
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
392 <xml name="compartments">
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
393 <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
394 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
395 <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
396 <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
397 <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
398 <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
399 <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
400 </options>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
401 <sanitizer>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
402 <valid initial="default">
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
403 <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
404 <add value="\t"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
405 <remove value="&quot;"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
406 <remove value="&apos;"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
407 </valid>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
408 </sanitizer>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
409 </param>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
410 </xml>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
411 <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
412 <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
413 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
414 <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
415 <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
416 <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
417 <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
418 <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
419 <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
420 </options>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
421 <sanitizer>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
422 <valid initial="default">
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
423 <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
424 <add value="\t"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
425 <remove value="&quot;"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
426 <remove value="&apos;"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
427 </valid>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
428 </sanitizer>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
429 </param>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
430 </xml>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
431 <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
432 <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
433 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
434 <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
435 <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
436 <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
437 <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
438 <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
439 <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
440 </options>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
441 <sanitizer>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
442 <valid initial="default">
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
443 <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
444 <add value="\t"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
445 <remove value="&quot;"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
446 <remove value="&apos;"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
447 </valid>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
448 </sanitizer>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
449 </param>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
450 </xml>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
451 <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
452 <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
453 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
454 <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
455 <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
456 <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
457 <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
458 <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
459 <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
460 </options>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
461 <sanitizer>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
462 <valid initial="default">
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
463 <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
464 <add value="\t"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
465 <remove value="&quot;"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
466 <remove value="&apos;"/>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
467 </valid>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
468 </sanitizer>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
469 </param>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
470 </xml>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
471 <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
472 <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
473 <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
474 <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
475 <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
476 <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
477 <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
478 <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
479 <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
480 <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
481 <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
482 <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
483 </options>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
484 <sanitizer>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
485 <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
486 <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
487 <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
488 <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
489 <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
490 </valid>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
491 </sanitizer>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
492 </param>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
493 <repeat name="factor_list" title="Conditions" default="2" min="2" max="2" help="Specify conditions to compare from metadata file (for each comparison, the first specified condition is the reference). 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
494 <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
495 <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
496 <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
497 <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
498 <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
499 <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
500 </options>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
501 <sanitizer>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
502 <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
503 <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
504 <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
505 <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
506 <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
507 </valid>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
508 </sanitizer>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
509 </param>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
510 </repeat>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
511
0
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
512 </repeat>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
513 </xml>
2
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
514 <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
515 <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
516 <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
517 <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
518 <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
519 <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
520 <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
521 <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
522 </options>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
523 <sanitizer>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
524 <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
525 <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
526 <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
527 <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
528 <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
529 </valid>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
530 </sanitizer>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
531 </param>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
532 </repeat>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
533 </xml>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
534 <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
535 <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
536 <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
537 <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
538 <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
539 <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
540 <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
541 <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
542 </options>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
543 <sanitizer>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
544 <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
545 <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
546 <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
547 <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
548 <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
549 </valid>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
550 </sanitizer>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
551 </param>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
552 </repeat>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
553 </xml>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
554 <xml name="factor_list">
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
555 <repeat name="factor_list" title="Conditions" min="2" max="2" help="Specify conditions to compare from metadata file (for each comparison, the first specified condition is the reference). 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
556 <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
557 <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
558 <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
559 <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
560 <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
561 <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
562 </options>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
563 <sanitizer>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
564 <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
565 <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
566 <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
567 <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
568 <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
569 </valid>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
570 </sanitizer>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
571 </param>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
572 </repeat>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
573 </xml>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
574 <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
575 <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
576 <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
577 <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
578 <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
579 <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
580 <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
581 <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
582 </param>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
583 </xml>
0
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
584 <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
585 #import json
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
586 #import re
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
587
2
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
588 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
589
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
590 #if $metadata_path:
2
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
591 ln -s '$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
592 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
593 #if $abundance_file:
2
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
594 ln -s '$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
595 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
596 #if $me_or_frac_contrib_file:
2
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
597 ln -s '$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
598 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
599
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
600 ]]></token>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
601 <token name="@INIT_CONFIG@"><![CDATA[
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
602 mkdir -p '$__new_file_path__/config' &&
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
603 touch '$__new_file_path__/config/config.yaml' &&
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
604 ]]></token>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
605 <token name="@REMOVE_CONFIG@"><![CDATA[
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
606 && rm -r '$__new_file_path__/config'
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
607 ]]></token>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
608 <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
609
2
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
610 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
611
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
612 #if $metadata_path:
2
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
613 ln -s '$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
614 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
615 #if $abundance_file:
2
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
616 ln -s '$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
617 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
618 ]]></token>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
619 <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
620
2
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
621 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
622
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
623 #if $metadata_path:
2
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
624 ln -s '$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
625 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
626 #if $me_or_frac_contrib_file:
2
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
627 ln -s '$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
628 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
629 ]]></token>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
630 <token name="@INIT_ISOTOPOLOGUE_PLOT@"><![CDATA[
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
631
2
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
632 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
633
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
634 #if $metadata_path:
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
635 ln -s '$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
636 #end if
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
637 #if $isotop_prop_file:
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
638 ln -s '$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
639 #end if
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
640 ]]></token>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
641 <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
642
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
643 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
644
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
645 #if $metadata_path:
2
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
646 ln -s '$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
647 #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
648
82fb756e71cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit afc87f0254b4399b71e53735966032ba1a32434d
iuc
parents: 3
diff changeset
649
2
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
650 #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
651 #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
652 #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
653
4
82fb756e71cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit afc87f0254b4399b71e53735966032ba1a32434d
iuc
parents: 3
diff changeset
654 #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
655 #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
656 #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
657 #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
658 #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
659 #else
82fb756e71cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit afc87f0254b4399b71e53735966032ba1a32434d
iuc
parents: 3
diff changeset
660 #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
661 #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
662 #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
663 #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
664 #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
665 #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
666 #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
667 #if $data_input.abundance_file:
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
668 ln -s '$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
669 #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
670 #end if
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
671 #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
672 #if $data_input.me_or_frac_contrib_file:
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
673 ln -s '$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
674 #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
675 #end if
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
676 #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
677 #if $data_input.isotop_prop_file:
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
678 ln -s '$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
679 #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
680 #end if
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
681 #else
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
682 #if $data_input.isotop_abs_file:
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
683 ln -s '$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
684 #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
685 #end if
0
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
686 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
687 ]]></token>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
688 <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
689
2
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
690 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
691
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
692 #if $metadata_path:
2
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
693 ln -s '$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
694 #end if
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 #set $impute_values = {}
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
697 #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
698 #if $data_input.abundance_file:
2
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
699 ln -s '$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
700 #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
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 #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
703 #if $data_input.me_or_frac_contrib_file:
2
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
704 ln -s '$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
705 #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
706 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
707 #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
708 #if $data_input.isotop_prop_file:
2
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
709 ln -s '$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
710 #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
711 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
712 #else
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
713 #if $data_input.isotop_abs_file:
2
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
714 ln -s '$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
715 #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
716 #end if
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 ]]></token>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
719 <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
720 #import json
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
721 #import re
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
722 #import os
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
723 #import csv
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
724 #import subprocess
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
725
2
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
726 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
727
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
728 #if $path_kegg_metabolites:
2
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
729 ln -s '$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
730 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
731 #if $path_kegg_transcripts:
2
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
732 ln -s '$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
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 #if $metadata_path:
2
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
736 ln -s '$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
737 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
738
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
739 #set $impute_values = {}
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
740 #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
741 #if $data_input.abundance_file:
2
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
742 ln -s '$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
743 #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
744 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
745 #else:
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
746 #if $data_input.me_or_frac_contrib_file:
2
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
747 ln -s '$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
748 #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
749 #end if
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
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
752 #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
753 #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
754 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
755 #end for
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
756
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
757
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
758 ]]></token>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
759 <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
760
2
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
761 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
762
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
763 #if $metadata_path:
2
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
764 ln -s '$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
765 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
766
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
767 #set $impute_values = {}
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
768 #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
769 #if $data_input.abundance_file:
2
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
770 ln -s '$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
771 #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
772 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
773 #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
774 #if $data_input.me_or_frac_contrib_file:
2
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
775 ln -s '$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
776 #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
777 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
778 #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
779 #if $data_input.isotop_prop_file:
2
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
780 ln -s '$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
781 #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
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 $data_input.isotop_abs_file:
2
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
785 ln -s '$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
786 #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
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 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
789 ]]></token>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
790 <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
791 #import re
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
792 #set $impute_values = {}
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
793 #if $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 $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
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 #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
797 #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
798 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
799 ]]></token>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
800 <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
801 #import re
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
802 #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
803 #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
804 #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
805 $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
806 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
807 #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
808 #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
809 $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
810 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
811 #elif str( $data_input.data_input_selector ) == "isotop_prop":
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
812 #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
813 $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
814 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
815 #else
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
816 #if $data_input.isotop_abs_file:
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
817 $datatypes_avail.append(re.sub('"', '', "isotopologues"))
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
818 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
819 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
820 ]]></token>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
821 <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
822 #import re
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
823 #set $statistical_test = {}
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
824 #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
825 #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
826 #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
827 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
828 #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
829 #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
830 #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
831 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
832 #elif str( $data_input.data_input_selector ) == "isotop_prop":
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
833 #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
834 #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
835 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
836 #else
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
837 #if $data_input.isotop_abs_file:
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
838 #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
839 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
840 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
841 ]]></token>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
842 <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
843 #import re
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
844 #set $conds = list()
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
845 #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
846 $conds.append(re.sub('"', '', str($co)))
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
847 #end for
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
848 ]]></token>
2
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
849 <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
850 #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
851 #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
852 #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
853 $conditions.append(re.sub('"', '', str($s.condition)))
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
854 #end for
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
855 ]]></token>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
856 <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
857 #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
858 #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
859 #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
860 $conditions.append(re.sub('"', '', str($s.condition)))
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
861 #end for
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
862 ]]></token>
0
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
863 <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
864
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
865 #import re
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
866 #set $timepoints = list()
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
867 #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
868 $timepoints.append(re.sub('"', '', str($tp)))
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
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 ]]></token>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
871 <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
872 #import re
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
873 #set $groups = list()
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
874 $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
875 $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
876
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
877 ]]></token>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
878 <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
879 #import json
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
880 #import re
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
881 #set $metabolites = {}
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
882 #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
883 #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
884 #for $met in $metabolites_list:
2
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
885 #set tmp_met=re.sub('\,', '%%',str($met))
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
886 #set tmp_met_bis=str(re.split('_m', str($tmp_met))[0])
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
887 #set tmp_met_ter=re.sub('%%', '\,',str($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
888 $metabolites[re.sub('"', '', str($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
889 #end for
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
890 #end for
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
891 ]]></token>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
892 <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
893 #set $metabolites = {}
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
894 #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
895 #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
896 #for $met in $metabolites_list:
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
897 #set tmp_met=re.sub('\,', '--',str($met))
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
898 #set tmp_met_bis=str(re.split('_m', str($tmp_met))[0])
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
899 #set tmp_met_ter=re.sub('--', '\,',str($tmp_met_bis))
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
900 $metabolites[re.sub('"', '', str($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
901 #end for
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
902 #end for
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
903 ]]></token>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
904 <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
905 #set $comparisons = list()
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
906 #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
907 #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
908 #set $ctrl=""
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
909
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
910 #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
911 #set $sub_comparisons = list()
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
912 #if str($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
913 #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
914 #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
915 $sub_comparisons.append(re.sub('"', '', str($co)))
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
916 $sub_comparisons.append(re.sub('"', '', str($tp)))
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
917 #else:
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
918 $sub_comparisons.append(re.sub('"', '', str($co)))
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
919 $sub_comparisons.append(re.sub('"', '', str($tp)))
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
920
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
921 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
922 $comparisons.append($sub_comparisons)
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
923 #end for
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
924 #end for
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
925 ]]></token>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
926 <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
927 #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
928 #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
929 #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
930 #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
931 $conditions.append(re.sub('"', '', str($s.condition)))
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
932 #end for
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
933
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
934 ]]></token>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
935 <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
936 #import re
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
937 #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
938 #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
939 #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
940 $conditions.append(re.sub('"', '', str($s.condition)))
0
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
941 #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
942 ]]></token>
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
943 <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
944 #import re
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
945 #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
946 #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
947 #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
948 #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
949 #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
950 #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
951 #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
952 #set $sub_comparisons = list()
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
953 #if str($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
954 $conditions.append(re.sub('"', '', str($t.condition)))
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
955 #end if
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
956 $sub_comparisons.append(re.sub('"', '', str($t.condition)))
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
957 $sub_comparisons.append(re.sub('"', '', str($s.timepoint)))
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
958 $comparisons_bis.append($sub_comparisons)
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
959 #end for
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
960 $timepoints.append(re.sub('"', '', str($s.timepoint)))
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
961 $comparisons.append($comparisons_bis)
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
962 #end for
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
963
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
964
0
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 ]]></token>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
967 <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
968 #import re
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
969 #set $conds = list()
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
970 #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
971 $conds.append(re.sub('"', '', str($co)))
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
972 #end for
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
973 #set $timepoints = list()
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
974 #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
975 $timepoints.append(re.sub('"', '', str($tp)))
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
976 #end for
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
977
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
978 #set $comparisons = list()
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
979 #if len($conds) > 1:
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
980 #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
981 #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
982 #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
983 #set $ctrl=""
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 $co in $conditions:
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
986 #set $sub_comparisons = list()
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
987 #if str($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
988 #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
989 #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
990 #else:
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
991 $sub_comparisons.append(re.sub('"', '', str($co)))
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
992 $sub_comparisons.append(re.sub('"', '', str($tp)))
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
993
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
994 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
995 $comparisons_bis.append($sub_comparisons)
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
996 #end for
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
997
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
998 #if $ctrl_found:
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
999 $sub_comparisons.append(str($ctrl))
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1000 $sub_comparisons.append(str($tp))
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1001 $comparisons_bis.append($sub_comparisons)
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1002 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1003
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1004 $comparisons.append($comparisons_bis)
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1005 #end for
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1006 #else
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1007 #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
1008 $comparisons.append(re.sub('"', '', str($co)))
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1009 #end for
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1010 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1011
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1012 #else
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1013 #if len($conds) > 0:
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1014 #if len($timepoints) > 1:
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1015 #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
1016 #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
1017 #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
1018 #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
1019 $sub_comparisons.append(re.sub('"', '', str($co)))
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1020 $sub_comparisons.append(re.sub('"', '', str($tp)))
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1021 $comparisons_bis.append($sub_comparisons)
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1022 #end for
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1023 $comparisons.append($comparisons_bis)
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1024 #end for
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1025 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1026 #else
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1027 #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
1028 $comparisons.append(re.sub('"', '', str($tp)))
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1029 #end for
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1030 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1031 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1032 ]]></token>
2
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1033 <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
1034 #import re
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1035 #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
1036 #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
1037 #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
1038 $conditions.append(re.sub('"', '', str($s.condition)))
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1039 #end for
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 #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
1042 #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
1043 $timepoints.append(re.sub('"', '', str($tp)))
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1044 #end for
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1045
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1046 #set $comparisons = list()
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1047 #if len($conditions) > 1:
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1048 #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
1049 #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
1050 #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
1051 #set $ctrl=""
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1052 #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
1053
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1054 #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
1055 #set $sub_comparisons = list()
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1056 #if str($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
1057 #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
1058 #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
1059 #else:
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1060 $sub_comparisons.append(re.sub('"', '', str($co)))
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1061 $sub_comparisons.append(re.sub('"', '', str($tp)))
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1062
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1063 #end if
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1064 $comparisons_bis.append($sub_comparisons)
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1065 #end for
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1066
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1067 #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
1068 $sub_comparisons.append(str($ctrl))
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1069 $sub_comparisons.append(str($tp))
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1070 $comparisons_bis.append($sub_comparisons)
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1071 #end if
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1072
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1073 $comparisons.append($comparisons_bis)
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1074 #end for
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1075 #else
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1076 #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
1077 $comparisons.append(re.sub('"', '', str($co)))
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1078 #end for
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1079 #end if
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1080
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1081 #else
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1082 #if len($conditions) > 0:
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1083 #if len($timepoints) > 1:
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1084 #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
1085 #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
1086 #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
1087 #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
1088 $sub_comparisons.append(re.sub('"', '', str($co)))
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1089 $sub_comparisons.append(re.sub('"', '', str($tp)))
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1090 $comparisons_bis.append($sub_comparisons)
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1091 #end for
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1092 $comparisons.append($comparisons_bis)
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1093 #end for
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1094 #end if
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1095 #else
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1096 #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
1097 $comparisons.append(re.sub('"', '', str($tp)))
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1098 #end for
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1099 #end if
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1100 #end if
7ff4f61789de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
iuc
parents: 1
diff changeset
1101 ]]></token>
0
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1102 <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
1103 #import re
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1104 #import os
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1105 #import subprocess
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1106 #set $transcripts = list()
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1107
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1108 #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
1109 #set $cpt = str($i+1)
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1110 $transcripts.append(re.sub('"', '', "DEG_comparison"+str($i+1)))
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1111 #set $deg_one_values = os.fsdecode(subprocess.check_output('head -n1 ' + str($s.input) + '| cut -f' + str($s.valuecol), shell=True))
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1112 #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
1113 #end for
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1114 ]]></token>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1115 <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
1116 #set $pathways = {}
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1117 #if $path_kegg_metabolites:
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1118 #silent $pathways['metabolites']='pathways_kegg_metabolites'
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1119 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1120 #if $path_kegg_transcripts:
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1121 #silent $pathways['transcripts']='pathways_kegg_transcripts'
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1122 #end if
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1123 ]]></token>
a7d3e880e74c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
diff changeset
1124 </macros>