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1 <tool id="MaREA RAS Generator" name="RAS Generator" version="1.0.0">
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2 <description></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" version="0.23.0">pandas</requirement>
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8 <requirement type="package" version="1.1.0">scipy</requirement>
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9 <requirement type="package" version="0.10.1">cobra</requirement>
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10 <requirement type="package" version="4.2.1">lxml</requirement>
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11 <requirement type="package" version="0.8.1">svglib</requirement>
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12 <requirement type="package" version="3.4.0">reportlab</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.py
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17 --rules_selector $cond_rule.rules_selector
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18 --tool_dir $__tool_directory__
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19 --option $cond.type_selector
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20 --out_log $log
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21 --input_datas ${input_Datasets}
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22 --single_ras_file $ras_single
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23 --none ${cond.None}
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24 #end if
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25 ]]>
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26 </command>
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27
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28 <inputs>
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29 <conditional name="cond_rule">
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30 <expand macro="options"/>
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31 <when value="HMRcore">
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32 </when>
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33 <when value="Recon">
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34 </when>
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35 <when value="Custom">
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36 <param name="Custom_rules" type="data" format="tabular, csv, tsv, xml" label="Custom rules" />
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37 <conditional name="cond_map">
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38 <param name="yes_no" type="select" label="Custom map? (optional)">
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39 <option value="no" selected="true">no</option>
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40 <option value="yes">yes</option>
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41 </param>
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42 <when value="yes">
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43 <param name="Custom_map" argument="--custom_map" type="data" format="xml, svg" label="custom-map.svg"/>
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44 </when>
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45 <when value="no">
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46 </when>
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47 </conditional>
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48 </when>
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49 </conditional>
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50 <conditional name="cond">
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51
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52 <param name="input_Datasets" argument="--input_datas" type="data" format="tabular, csv, tsv" label="add dataset" />
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53 <param name="input_name" argument="--names" type="text" label="Dataset's name:" value="Dataset" help="Default: Dataset" />
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54 <param name="None" argument="--none" type="boolean" truevalue="true" falsevalue="false" checked="true" label="(A and NaN) solved as (A)?" />
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55
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56
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57 </when>
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58 </conditional>
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59 </inputs>
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60
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61 <outputs>
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62 <data format="txt" name="log" label="MaREA - Log" />
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63 <data format="tabular" name="ras_single" label="MaREA - RAS - ${cond.input_name}">
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64 <filter>cond['type_selector'] == "datasets_rasonly"</filter>
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65 </data>
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66 <collection name="results" type="list" label="MaREA - Results">
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67 <filter>cond['type_selector'] == "datasets" or cond['type_selector'] == "dataset_class"</filter>
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68 <discover_datasets pattern="__name_and_ext__" directory="result"/>
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69 </collection>
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70 <collection name="ras" type="list" label="MaREA - RAS list" format_source="tabular">
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71 <filter>cond['type_selector'] != "datasets_rasonly" and cond['advanced']['choice'] and cond['advanced']['generateRas']</filter>
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72 <discover_datasets pattern="__name_and_ext__" directory="ras" format="tabular"/>
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73 </collection>
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74
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75 </outputs>
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76 <tests>
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77 <test>
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78 <param name="pValue" value="0.56"/>
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79 <output name="log" file="log.txt"/>
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80 </test>
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81 </tests>
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82 <help>
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83 <![CDATA[
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84
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85 What it does
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86 -------------
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87
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88 This tool analyzes RNA-seq dataset(s) as described in Graudenzi et al."`MaREA`_: Metabolic feature extraction, enrichment and visualization of RNAseq data" bioRxiv (2018): 248724.
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89
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90 Accepted files are:
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91 - option 1) two or more RNA-seq datasets, each referring to samples in a given condition/class. The user can specify a label for each class (as e.g. "*classA*" and "*classB*");
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92 - option 2) one RNA dataset and one class-file specifying the class/condition each sample belongs to.
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93
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94 Optional files:
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95 - custom GPR (Gene-Protein-Reaction) rules. Two accepted formats:
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96
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97 * (Cobra Toolbox and CobraPy compliant) xml of metabolic model;
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98 * .csv file specifyig for each reaction ID (column 1) the corresponding GPR rule (column 2).
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99 - custom svg map. Graphical elements must have the same IDs of reactions. See HmrCore svg map for an example.
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100
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101 The tool generates:
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102 1) a tab-separated file: reporting fold-change and p-values of reaction activity scores (RASs) between a pair of conditions/classes;
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103 2) a metabolic map file (downlodable as .svg): visualizing up- and down-regulated reactions between a pair of conditions/classes;
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104 3) a log file (.txt).
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105
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106 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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107
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108 Class-file format: each row of the class-file reports the sample ID (column1) and the label of the class/condition the sample belongs to (column 2).
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109
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110 To calculate P-Values and Fold-Changes and to generate maps, comparisons are performed for each possible pair of classes.
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111
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112 Output files will be named as classA_vs_classB. Reactions will conventionally be reported as up-regulated (down-regulated) if they are significantly more (less) active in class having label "classA".
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113
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114
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115 Example input
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116 -------------
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117
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118 **"Custom Rules"** option:
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119
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120 Custom Rules Dastaset:
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121
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122 @CUSTOM_RULES_EXEMPLE@
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123
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124 **"RNAseq of group 1 + RNAseq of group 2 + ... + RNAseq of group N"** option:
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125
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126 RNA-seq Dataset 1:
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127
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128 @DATASET_EXEMPLE1@
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129
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130 RNA-seq Dataset 2:
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131
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132 @DATASET_EXEMPLE2@
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133
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134 **"RNAseq of all samples + sample group specification"** option:
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135
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136 RNA-seq Dataset:
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137
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138 @DATASET_EXEMPLE1@
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139
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140 Class-file:
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141
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142 +------------+------------+
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143 | Patient_ID | class |
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144 +============+============+
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145 | TCGAAA3529 | MSI |
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146 +------------+------------+
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147 | TCGAA62671 | MSS |
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148 +------------+------------+
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149 | TCGAA62672 | MSI |
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150 +------------+------------+
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151
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152 |
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153
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154 .. class:: infomark
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155
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156 **TIP**: If your data is not TAB delimited, use `Convert delimiters to TAB`_.
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157
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158 .. class:: infomark
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159
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160 **TIP**: If your dataset is not split into classes, use `MaREA cluster analysis`_.
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161
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162 @REFERENCE@
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163
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164 .. _MaREA: https://www.biorxiv.org/content/early/2018/01/16/248724
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165 .. _Convert delimiters to TAB: https://usegalaxy.org/?tool_id=Convert+characters1&version=1.0.0&__identifer=6t22teyofhj
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166 .. _MaREA cluster analysis: http://link del tool di cluster.org
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167
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168 ]]>
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169 </help>
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170 <expand macro="citations" />
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171 </tool>
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172
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