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annotate carpet-src-1/tools/CARPET/calcolo_p_v4_norm.xml @ 0:cdd489d98766

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Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
author matces
date Tue, 07 Jun 2011 16:50:41 -0400
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cdd489d98766 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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1 <tool id="expressions" name="TEA" version="1.0.0">
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2 <description>Tiling Expression Analizer</description>
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3 <command interpreter="perl">calcolo_p_v4_norm_intron.pl -opt ${ann_choice.type1} -log ${ann_choice.type_data} -ann ${ann_choice.ann} -wt ${ann_choice.wt} -treat ${ann_choice.treat} -out $output -fdr ${ann_choice.fdr} -pv ${ann_choice.pv} -norm ${ann_choice.norm} -rc ${ann_choice.rc} -fc ${ann_choice.summary_choice.fc} -exon ${ann_choice.type} -sum_met ${ann_choice.summary_choice.fc_output}</command>
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4 <inputs>
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5 <conditional name="ann_choice">
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6 <param name="type1" type="select" label="Analysis type">
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7 <option value="comp">comparison</option>
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8 <option value="expr">expression</option>
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9 </param>
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10
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11 <when value="comp">
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12 <param format="tabular" name="ann" type="data" label="annotation file"/>
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13 <param format="tabular" name="wt" type="data" label="expression chip condition A"/>
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14 <param format="tabular" name="treat" type="data" label="expression chip condition B"/>
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15 <param name="type_data" type="select" label="Data type">
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16 <option value="log">log2 value</option>
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17 <option value="no_log">raw value</option>
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18 </param>
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19 <param name="norm" type="select" label="Normalization">
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20 <option value="yes">quantile-normalization</option>
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21 <option value="no">no normalization</option>
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22 </param>
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23 <param name="type" type="select" label="probes selection">
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24 <option value="internal_exon">internal exon</option>
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25 <option value="all_exon">all exon</option>
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26 <option value="last_exon">last exon</option>
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27 </param>
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28 <conditional name="summary_choice">
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29 <param name="fc_output" type="select" label="summary method">
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30 <option value="mean">mean</option>
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31 <option value="median">median</option>
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32 <option value="both">both</option>
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33 </param>
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34 <when value="mean">
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35 <param name="fc" size="3" type="text" value="1.5" label="Fold change cutoff"/>
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36 </when>
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37 <when value="median">
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38 <param name="fc" size="3" type="text" value="1.5" label="Fold change cutoff"/>
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39 </when>
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40 <when value="both">
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41 <param name="fc" size="12" type="text" value="NOT-NEEDED" label="Fold change cutoff"/>
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42 </when>
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43 </conditional>
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44 <param name="rc" size="2" type="text" value="7" label="raw value cutoff (log2)"/>
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45 <param name="fdr" type="select" label="FDR correction">
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46 <option value="yes">yes</option>
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47 <option value="no">no</option>
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48 </param>
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49 <param name="pv" size="4" type="text" value="0.05" label="p-value cutoff"/>
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50
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51
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52
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53 </when>
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54 <when value="expr">
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55 <param format="tabular" name="ann" type="data" label="annotation file"/>
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56 <param format="tabular" name="wt" type="data" label="expression chip"/>
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57 <param format="tabular" name="treat" type="data" label="NOT NEEDED"/>
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58 <param name="type_data" type="select" label="Data type">
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59 <option value="log">log2 value</option>
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60 <option value="no_log">raw value</option>
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61 </param>
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62 <param name="type" type="select" label="probes selection">
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63 <option value="internal_exon">internal exon</option>
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64 <option value="all_exon">all exon</option>
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65 <option value="last_exon">last exon</option>
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66 </param>
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67 <conditional name="summary_choice">
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68 <param name="fc_output" type="select" label="summary method">
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69 <option value="mean">mean</option>
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70 <option value="median">median</option>
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71 <option value="both">both</option>
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72 </param>
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73 <when value="mean">
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74 <param name="fc" size="12" type="text" value="NOT-NEEDED" label="Fold change cutoff"/>
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75 </when>
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76 <when value="median">
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77 <param name="fc" size="12" type="text" value="NOT-NEEDED" label="Fold change cutoff"/>
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78 </when>
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79 <when value="both">
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80 <param name="fc" size="12" type="text" value="NOT-NEEDED" label="Fold change cutoff"/>
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81 </when>
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82 </conditional>
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83 <param name="norm" size="12" type="text" value="NOT-NEEDED" label="Normalization"/>
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84 <param name="pv" size="12" type="text" value="NOT-NEEDED" label="p-value cutoff"/>
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85 <param name="fdr" size="12" type="text" value="NOT-NEEDED" label="FDR correction"/>
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86 <param name="rc" size="12" type="text" value="NOT-NEEDED" label="raw value cutoff (log2)"/>
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87 </when>
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88 </conditional>
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89
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90
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91 </inputs>
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92 <outputs>
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93 <data format="tabular" name="output" />
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94 </outputs>
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95
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96 <help>
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97 .. class:: infomark
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98
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99 **What it does**
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100
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101 TEA utilizes NimbleGen expression files in gff format and annotated table by ENO as INPUT FILES and generates a table with the expression value. When comparing two different conditions a Fold Change and a p-value are calculated.
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102
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103 PLEASE, for more detailed information refer to the CARPET user Manual:
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104 click to download_ it.
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105
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106 .. _download: /static/example_file/CARPET_userManual.zip
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107
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108 --------
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109
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110 **Parameters:**
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111
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112 - **Analysis type:**
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113 - **expression** analysis calculates an expression value for each transcript coming from the mean or the median of all matching probes
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114 - **comparison** analysis calculate an expression value for each transcript in both conditions, then calculates a Fold Change for each transcript and a p-value based on t-Test distribution.
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115 - **Data type:**
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116 - **log2 value:** the data is not converted in log2
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117 - **raw value:** the data is converted in log2
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118 - **Normalization:** quantile normalization between the two chips (not necessary if analysis type is "expression")
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119 - **probe selection:**
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120 - **internal exon:** only probes annotated as exons are used to calculate expression value.
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121 - **all exon:** also probes annotated at the boundaries of introns/exons are used to calculate the expression value. (probes in intronexon position usually have lower signal)
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122 - **last exon:** only probes in the last exon are used to calculate expression value. This analysis can be preferred for cDNA generated by oligo-dT RT, since 3' of transcripts are generally better represented.
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123 - **summary method:**
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124 - **mean:** fold change for each gene is calculated based on the mean value
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125 - **median:** fold change for each gene is calculated based on the median value
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126 - **both:** both are used
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127 - **Fold change cutoff:** only transcripts with FC higher than cutoff are kept
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128 - **FDR:**
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129 - **yes:** False Discovery Rate correction is applied (as described in Storie et al. 2002)
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130 - **no:** No correction --> raw p-value
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131 - **p-value cutoff:** only transcripts with p-value less than cutoff are kept
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132 - **raw value cutoff (log2):** only transcripts with raw value higher than cutoff at least in one experiment are kept
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133
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134 --------
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135
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136
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137 **INPUT FILE**
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138
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139 Nimblegen gives you back a GFF file with the coordinates of each probe and the signal raw value.
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140
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141 Click here_ to download a GFF file example.
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142
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143 .. _here: /static/example_file/Expression_analysis_files.zip
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144
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145
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146 Example of Nimblegen Expression GFF format::
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147
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148 chr19 Nimblegen tiling_array 100000 1000051 20459 + . probe_name
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149 chr19 Nimblegen tiling_array 100100 1000151 1394 + . probe_name
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150
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151 .. class:: warningmark
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152
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153 The sixth column **must** contain the raw signal (**NOT** log2) that Nimblegen gives you back after the experiment
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154
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155 The annotation table **MUST** be created usign ENO tool, before running TEA.
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156
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157 ---------
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158
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159 .. class:: infomark
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160
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161 **How does it work?**
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162
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163 For each gene is built the signal distibution of the probes matching Exon.
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164
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165 -In an expression experiment, the mean or the median of the distribution represents the result of Tea.
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166
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167 -In a comparison experiment the distibution of the gene exon signal is compared between the two conditions (1 and 2) and a t-test is performed with the possibility to introduce FDR correction.
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168
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169 .. image:: static/images/CARPET/Tea.png
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170
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171
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172
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173
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174 **OUTPUT**
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175
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176 - **expresion**
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177
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178 .. image:: static/images/CARPET/expression.png
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179
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180 - **comparison**
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181
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182 .. image:: static/images/CARPET/comparison.png
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183
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184 </help>
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185
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186
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187 </tool>