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1 <tool id="MaREA_cluester" name="MaREA cluster analysis" version="1.0.0">
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2 <description>of Reaction Activity Scores</description>
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3 <macros>
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4 <import>marea_macros.xml</import>
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5 </macros>
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6 <requirements>
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7 <requirement type="package">pandas</requirement>
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8 <requirement type="package">scipy</requirement>
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9 <requirement type="package">cobra</requirement>
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10 <requirement type="package">python-libsbml</requirement>
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11 <requirement type="package">scikit-learn</requirement>
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12 <requirement type="package">matplotlib</requirement>
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13 </requirements>
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14 <command detect_errors="exit_code">
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15 <![CDATA[
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16 python $__tool_directory__/marea_cluster.py
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17 --rules_selector $cond_rule.rules_selector
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18 #if $cond_rule.rules_selector == 'Custom':
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19 --custom ${cond_rule.Custom_rules}
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20 #end if
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21 --cond_hier $cond_hier.hier
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22 #if $cond_hier.hier == 'yes':
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23 --linkage ${cond_hier.linkage}
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24 --dendro $dendrogram
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25 #end if
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26 --k_max $k_max
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27 --k_min $k_min
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28 --data $input
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29 --name $name
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30 --none $None
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31 --tool_dir $__tool_directory__
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32 --out_log $log
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33 --elbow $elbow
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34 ]]>
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35 </command>
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36 <inputs>
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37 <conditional name="cond_rule">
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38 <expand macro="options"/>
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39 <when value="Custom">
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40 <param name="Custom_rules" type="data" format="tabular, csv, tsv, xml" label="Custom rules" />
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41 </when>
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42 <when value="HMRcore">
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43 </when>
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44 <when value="Recon">
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45 </when>
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46 </conditional>
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47 <param name="input" argument="--data" type="data" format="tabular, csv, tsv" label="RNAseq of all samples" />
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48 <param name="name" argument="--name" type="text" label="Output name prefix" value="dataset" />
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49 <param name="k_min" argument="--k_min" type="integer" size="20" value="3" min="2" max="30" label="Min number of clusters (k) to be tested (k-means)"/>
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50 <param name="k_max" argument="--k_max" type="integer" size="20" value="3" min="2" max="30" label="Max number of clusters (k) to be tested (k-means)"/>
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51 <param name="None" argument="--none" type="boolean" truevalue="true" falsevalue="false" checked="true" label="(A and NaN) solved as (A)?" help="If NO is selected, (A and NaN) is solved as (NaN)" />
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52 <conditional name="cond_hier">
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53 <param name="hier" argument="--cond_hier" type="select" label="Produce dendrogram (hierarchical clustering):">
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54 <option value="no" selected="true">no</option>
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55 <option value="yes">yes</option>
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56 </param>
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57 <when value="yes">
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58 <param name="linkage" argument="--linkage" type="select" label="Linkage type:">
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59 <option value="single" selected="true">Single: minimum distance between all observations of two sets</option>
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60 <option value="complete">Complete: maximum distance between all observations of two sets</option>
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61 <option value="average">Average: average distance between all observations of two sets</option>
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62 </param>
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63 </when>
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64 <when value="no">
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65 </when>
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66 </conditional>
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67 </inputs>
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68
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69 <outputs>
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70 <data format="txt" name="log" label="Log" />
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71 <data format="pdf" name="dendrogram" label="$name dendrogram">
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72 <filter>cond_hier['hier'] == 'yes'</filter>
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73 </data>
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74 <data format="pdf" name="elbow" label="$name elbow evaluation method" />
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75 <collection name="cluster_out" type="list" label="Clusters $k_min - $k_max">
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76 <discover_datasets pattern="__name_and_ext__" directory="cluster_out" />
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77 </collection>
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78 </outputs>
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79 <tests>
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80 <test>
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81 <param name="k_min" value="4"/>
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82 <output name="log" file="log.txt"/>
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83 </test>
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84 </tests>
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85 <help>
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86 <![CDATA[
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87
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88 What it does
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89 -------------
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90
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91 This tool performs cluster analysis of RNA-seq dataset(s) based of Graudenzi et al."`MaREA`_: Metabolic feature extraction, enrichment and visualization of RNAseq data" bioRxiv (2018): 248724.
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92
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93 Accepted files are:
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94 1) For "Recon 2.2 rules" or "HMRcore rules" options: RNA-seq dataset. The user can specify a label of output prefix (as e.g. "K=3 *dataset*" and "K=4 *MyDataset*");
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95 2) For "Custom rules" option: custom rules dataset, custom map (.svg) and RNA-seq dataset. The user can specify a label of output prefix (as e.g. "K=3 *dataset*" and "K=4 *MyDataset*").
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96
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97 Optional files:
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98 - custom GPR (Gene-Protein-Reaction) rules. Two accepted formats:
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99
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100 * (Cobra Toolbox and CobraPy compliant) xml of metabolic model;
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101 * .csv file specifyig for each reaction ID (column 1) the corresponding GPR rule (column 2).
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102 - custom svg map. Graphical elements must have the same IDs of reactions. See HmrCore svg map for an example.
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103
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104 The tool generates:
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105 1) Clusters n1 - n2 (n1 and n2 refer to min and max number of clusters): class-files (as many files as the chosen different number of clusters k to be tested) specifying the class/condition each sample belongs to;
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106 2) Log: a log file (.txt);
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107 3) *dataset* elbow evaluation method: diagram (.pdf) of elbow evaluation method;
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108 4) *dataset* dendrogram (optional): dendrogram (.pdf) if the user chooses to produce a dendrogram (hierachical clustering).
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109
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110 RNA-seq datasets format: tab-separated text files, reporting the expression level (e.g., TPM, RPKM, ...) of each gene (row) for a given sample (column). Header: sample ID.
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111
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112
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113 Example input
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114 -------------
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115
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116 **RNA-seq dataset**:
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117
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118 @DATASET_EXEMPLE@
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119
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120 **Custom Rules Dataset**:
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121
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122 @CUSTOM_RULES_EXEMPLE@
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123
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124 **Custom Map**:
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125
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126 *see the generated HMRcore .svg map for example*
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127
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128
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129
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130 .. class:: infomark
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131
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132 **TIP**: If your data is not TAB delimited, use `Convert delimiters to TAB`_.
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133
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134 .. class:: warningmark
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135
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136 If dendrogram it's too populated, each path and label can be not clear.
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137
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138 @REFERENCE@
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139
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140 .. _MaREA: https://www.biorxiv.org/content/early/2018/01/16/248724
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141 .. _Convert delimiters to TAB: https://usegalaxy.org/?tool_id=Convert+characters1&version=1.0.0&__identifer=6t22teyofhj
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142
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143
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144 ]]>
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145 </help>
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146 <expand macro="citations" />
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147 </tool>
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148
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149
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