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1 <tool id="secimtools_add_pval_flags" name="Add Binary (0/1) -value Flags" version="@WRAPPER_VERSION@">
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2 <description>using custom thresholds</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <command detect_errors="exit_code"><![CDATA[
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8 add_pval_flags.py
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9 -de=$DE_Dataset
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10 -id=$uniqID
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11 -p=$pvalue
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12 -t=$thresholds
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13 -o=$output
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14 -fl=$flags
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15 ]]></command>
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16 <inputs>
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17 <param name="DE_Dataset" type="data" format="tabular" label="Select Dataset containing p-values from your history"/>
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18 <param name="uniqID" type="text" size="30" value="" label="Unique FeatureID" help="Name of the column in your Dataset that contains unique FeatureIDs."/>
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19 <param name="pvalue" type="text" size="30" value="" label="P-Value" help="Name of the column containing your p-values."/>
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20 <param name="thresholds" type="text" size="30" value="0.1,0.05,0.01" label="P-Value Thresholds" help="Enter the threshold(s). P-values less than the given threshold(s) will be flagged with a 1. Separate more than 1 threshold value with a comma, no spaces allowed."/>
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21 </inputs>
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22 <outputs>
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23 <data format="tabular" name="output" label="${tool.name} on ${on_string}: Output File"/>
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24 <data format="tabular" name="flags" label="${tool.name} on ${on_string}: Flags File"/>
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25 </outputs>
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26 <tests>
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27 <test>
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28 <param name="DE_Dataset" value="limma_voom_gene_file_01fhl.tsv"/>
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29 <param name="uniqID" value="UniqueID"/>
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30 <param name="pvalue" value="P.Value"/>
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31 <param name="thresholds" value="0.1,0.05,0.01"/>
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32 <output name="output" file="add_flags_gene_output_file_01fhl.tsv"/>
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33 <output name="flags" file="add_flags_gene_flags_file_01fhl.tsv"/>
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34 </test>
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35 <test>
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36 <param name="DE_Dataset" value="limma_voom_metabolite_file_01fhl.tsv"/>
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37 <param name="uniqID" value="UniqueID"/>
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38 <param name="pvalue" value="P.Value"/>
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39 <param name="thresholds" value="0.1,0.05,0.01"/>
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40 <output name="output" file="add_flags_metabolite_output_file_01fhl.tsv"/>
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41 <output name="flags" file="add_flags_metabolite_flags_file_01fhl.tsv"/>
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42 </test>
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43 </tests>
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44 <help><![CDATA[
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45
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46
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47 **Tool Description**
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48
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49 This tool generates an indicator variable (0 or 1) to identify p-values below a user-specified threshold. A “1” is used to indicate (flag)
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50 p-values less than the indicated threshold p-value. The user can flag nominal p-values or p-values after correction for multiple testing.
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51
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52 --------------------------------------------------------------------------------
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53
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54 **INPUT**
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55
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56 **Example of a dataset containing p-values**
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57
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58 +-----------+---------+---------+-----+
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59 | FeatureID | P-value | FDR | ... |
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60 +===========+=========+=========+=====+
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61 | one | 2.02e-6 | 1.83e-6 | ... |
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62 +-----------+---------+---------+-----+
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63 | two | 2.87e-5 | 0.0063 | ... |
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64 +-----------+---------+---------+-----+
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65 | three | 0.001 | 0.19 | ... |
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66 +-----------+---------+---------+-----+
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67 | four | 0.22 | 0.99 | ... |
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68 +-----------+---------+---------+-----+
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69 | ... | ... | ... | ... |
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70 +-----------+---------+---------+-----+
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71
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72 **P-value**
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73
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74 Name of the column in your Dataset that contains p-values.
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75
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76 **P-value Threshold**
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77
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78 P-values less than the threshold will be flagged with a 1. P-values greater than the threshold will be flagged with a 0.
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79
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80 **NOTE:** More than one threshold value is allowed. Separate flags will be generated for each threshold value.
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81
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82 --------------------------------------------------------------------------------
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83
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84 **OUTPUT**
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85
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86 Two output files are generated from the Add Binary (0/1) P-value Flags tool:
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87
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88 **Output File.** A TSV file containing the same columns as the Input Dataset plus an additional column(s) containing 0/1 binary indicators for whether the P-value was less that the user-specified threshold. The indicator columns are named by appending the user-specified threshold to 'Flag_' prefix (e.g. Flag_user-specified threshold, Flag_0.10).
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89
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90 +-----------+---------+---------+--------+-------------+-----+
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91 | FeatureID | p-value | FDR | Flag_0.2 | Flag_0.05 | ... |
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92 +===========+=========+=========+==========+===========+=====+
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93 | one | 2.02e-6 | 1.83e-6 | 1 | 1 | ... |
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94 +-----------+---------+---------+----------+-----------+-----+
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95 | two | 2.87e-5 | 0.0063 | 1 | 1 | ... |
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96 +-----------+---------+---------+----------+-----------+-----+
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97 | three | 0.001 | 0.19 | 1 | 0 | ... |
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98 +-----------+---------+---------+----------+-----------+-----+
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99 | four | 0.22 | 0.99 | 0 | 0 | ... |
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100 +-----------+---------+---------+----------+-----------+-----+
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101 | ... | ... | ... | ... | ... | ... |
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102 +-----------+---------+---------+----------+-----------+-----+
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103
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104 **Flag Table.** A TSV file containing only the FeatureID column from the input dataset and the tool-generated binary indicator flags.
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105
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106 +-----------+----------+-----------+-----+
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107 | FeatureID | Flag_0.2 | Flag_0.05 | ... |
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108 +===========+==========+===========+=====+
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109 | one | 1 | 1 | ... |
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110 +-----------+----------+-----------+-----+
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111 | two | 1 | 1 | ... |
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112 +-----------+----------+-----------+-----+
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113 | three | 1 | 0 | ... |
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114 +-----------+----------+-----------+-----+
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115 | four | 0 | 0 | ... |
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116 +-----------+----------+-----------+-----+
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117 | ... | ... | ... | ... |
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118 +-----------+----------+-----------+-----+
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119
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120 ]]>
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121 </help>
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122 <citations>
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123 <citation type="bibtex">@ARTICLE{Kirpich17secimtools,
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124 author = {Alexander S. Kirpich, Miguel Ibarra, Oleksandr Moskalenko, Justin M. Fear, Joseph Gerken, Xinlei Mi, Ali Ashrafi, Alison M. Morse, Lauren M. McIntyre},
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125 title = {SECIMTools: A suite of Metabolomics Data Analysis Tools},
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126 journal = {BMC Bioinformatics},
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127 year = {in press}
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128 }</citation>
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129 <citation type="bibtex">@article{garcia2010paintomics,
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130 title={Paintomics: a web based tool for the joint visualization of transcriptomics and metabolomics data},
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131 author={Garc{\'\i}a-Alcalde, Fernando and Garc{\'\i}a-L{\'o}pez, Federico and Dopazo, Joaqu{\'\i}n and Conesa, Ana},
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132 journal={Bioinformatics},
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133 volume={27},
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134 number={1},
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135 pages={137--139},
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136 year={2010},
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137 publisher={Oxford University Press}
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138 }</citation>
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139 </citations>
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140 </tool>
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