Mercurial > repos > malex > gait_gm

annotate split_wide_dataset.xml @ 2:2c218a253d56 draft default tip

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"planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b"
author malex
date Thu, 29 Jul 2021 20:48:10 +0000
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1 <tool id="secimtools_split_input_wide_dataset" name="Create: Design, Wide, and Annotation datasets" version="@WRAPPER_VERSION@">
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2 <description>from an input wide dataset</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 <stdio>
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8 <exit_code range="1" level="fatal" description="Repeated Unique IDs"/>
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9 </stdio>
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10 <command detect_errors="exit_code"><![CDATA[
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11 split_wide_dataset.py
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12 -i=$input
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13 #if $cond_UniqID.hasUniqID == "y":
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14 -id=$cond_UniqID.uniqID
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15 #if $cond_UniqID.only_numbers.hasOnlyNumbers == "y":
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16 -p2=$cond_UniqID.only_numbers.prefix2
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17 #end if
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18 #else:
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19 -p=$cond_UniqID.prefix
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20 #end if
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21 -s=$samples
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22 -w=$wide
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23 -d=$design
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24 -a=$annot
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25 ]]></command>
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26 <inputs>
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27 <param name="input" type="data" format="tabular" label="Input Wide Dataset" help="Input tab separated Wide Dataset. If input is not tab separated, see TIP below."/>
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28 <conditional name="cond_UniqID">
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29 <param name="hasUniqID" type="select" display="radio" label="Does your Wide Dataset have a unique FeatureID column?">
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30 <option value="y">Yes</option>
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31 <option value="n">No</option>
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32 </param>
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33 <when value="y">
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34 <param name="uniqID" type="text" size="30" value="" label="Unique FeatureID" help="Name of the column in your Wide Dataset that contains the unique FeatureIDs."/>
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35 <conditional name="only_numbers">
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36 <param name="hasOnlyNumbers" type="select" display="radio" label="Are your unique FeatureIDs ONLY Numbers?">
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37 <option value="y">Yes</option>
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38 <option value="n">No</option>
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39 </param>
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40 <when value="y">
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41 <param name="prefix2" type="text" size="30" value="" label="Prefix to use during generation of unique IDs" help="This prefix will be prepended to your NUMERIC unique FeatureID, with an underbar in between."/>
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42 </when>
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43 <when value="n" />
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44 </conditional>
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45 </when>
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46 <when value="n">
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47 <param name="prefix" type="text" size="30" value="" label="Prefix to use during generation of unique IDs" help="Unique IDs are required. You can input a prefix for the tool to use when creating a unique identifier (Optional). If you chose not to use a prefix, the tool-created uniqueID will be an underbar followed by a number."/>
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48 </when>
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49 </conditional>
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50 <param name="samples" label="Sample Columns" type="text" help="Enter the numbers (1-based) of the columns in your Wide Dataset that contain sample data. E.g. if your sample data is in columns 2-4 then enter '2,3,4' (no spaces). Columns that are not selected are treated as descriptor annotation columns. NOTE: annotation columns are expected to ALL be left of the data columns. "/>
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51 </inputs>
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52 <outputs>
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53 <data format="tabular" name="wide" label="${tool.name} on ${on_string}: Wide Dataset"/>
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54 <data format="tabular" name="design" label="${tool.name} on ${on_string}: Design Dataset"/>
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55 <data format="tabular" name="annot" label="${tool.name} on ${on_string}: Annotation Dataset"/>
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56 </outputs>
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57 <tests>
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58 <test>
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59 <param name="input" value="gene_input_dataset.tsv"/>
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60 <param name="prefix" value="Gene"/>
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61 <param name="hasUniqID" value="n"/>
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62 <param name="samples" value="2,3,4,5,6,7,8,9,10,11"/>
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63 <output name="wide" file="gene_wide_dataset.tsv"/>
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64 <output name="design" file="gene_design.tsv"/>
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65 <output name="annot" file="gene_annotation.tsv"/>
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66 </test>
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67 <test>
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68 <param name="input" value="metabolite_input_dataset.tsv"/>
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69 <param name="prefix" value="Met"/>
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70 <param name="hasUniqID" value="n"/>
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71 <param name="samples" value="2,3,4,5,6,7,8,9,10,11"/>
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72 <output name="wide" file="metabolite_wide_dataset.tsv"/>
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73 <output name="design" file="metabolite_design.tsv"/>
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74 <output name="annot" file="metabolite_annotation.tsv"/>
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75 </test>
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76 </tests>
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77 <help><![CDATA[
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78
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79 **Tool Description**
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80
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81 This tool takes a single file containing both feature data (e.g. gene or metabolite expression values) and annotation
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82 information (e.g. m/z ratio, compound name) and generates the following three files;
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83
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84 (1) a wide dataset containing a unique row identifier and the expression values,
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85 (2) a wide annotation file with the unique row identifier and any non-data descriptor columns, and
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86 (3) a design file with a single column called ‘sampleID’ with the name of the columns containing the expression data.
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87
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88 If the input dataset does not already contain a column with a unique identifier, the tool will create one.
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89 The user can specify a prefix for the unique identifier column (e.g. 'met' for metabolite data). In cases where the input
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90 dataset contains a numeric identifier, the tool will append a user-specified prefix or, if no prefix is specified, an underbar.
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91 Since the user specifies which columns contain expression values, the resulting wide dataset contains only these data columns
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92 and the unique row identifier column. Columns not specified as containing expression values are output into the annotation dataset.
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93 The resulting design file template contains a single column called ‘sampleID’ that contains the names of the user-specified samples
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94 in the input data file. The design file can be modified by the user to include additional metadata columns.
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95
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96 --------------------------------------------------------------------------------
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97
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98 **INPUT**
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99
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100 **Example - Wide Format Input Dataset**
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101
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102 +---------+-----------+---------+---------+-----+
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103 | rowID | m/z ratio | sample1 | sample2 | ... |
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104 +=========+===========+=========+=========+=====+
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105 | 1 | 8.845 | 20 | 10 | ... |
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106 +---------+-----------+---------+---------+-----+
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107 | 2 | 0.258 | 22 | 30 | ... |
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108 +---------+-----------+---------+---------+-----+
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109 | 3 | 10.54 | 27 | 2 | ... |
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110 +---------+-----------+---------+---------+-----+
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111 | 4 | 8.594 | 17 | 8 | ... |
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112 +---------+-----------+---------+---------+-----+
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113 | ... | ... | ... | ... | ... |
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114 +---------+-----------+---------+---------+-----+
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115
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116 **NOTE:** The input dataset has features in rows and samples in columns. Any descriptor columns that are present will be used to populate the Annotation File.
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117
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118 **Unique FeatureID**
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119
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120 If the Input Dataset has a column with unique FeatureIDs, the user can specify the name of this column. If the Input Dataset does not have a column with unique FeatureIDs, the tool will create a numeric one.
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121
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122 **Prefix**
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123
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124 The user can add a prefix to the tool-generated unique FeatureID, if desired. Example: If met is input then the unique FeatureID column will consist of met\_ followed by a number.
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125
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126 **Sample Columns**
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127
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128 Name of the columns in the Input Dataset that contain sample information. All columns not specified as samples will be used to populate the Annotation File.
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129
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130 --------------------------------------------------------------------------------
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131
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132 **OUTPUT**
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133
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134
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135 **A Wide Dataset containing the FeatureID column and all columns selected as samples**
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136
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137 +------------+---------+---------+---------+-----+
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138 | FeatureID | sample1 | sample2 | sample3 | ... |
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139 +============+=========+=========+=========+=====+
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140 | met_1 | 10 | 20 | 10 | ... |
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141 +------------+---------+---------+---------+-----+
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142 | met_2 | 5 | 22 | 30 | ... |
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143 +------------+---------+---------+---------+-----+
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144 | met_3 | 30 | 27 | 2 | ... |
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145 +------------+---------+---------+---------+-----+
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146 | met_4 | 32 | 17 | 8 | ... |
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147 +------------+---------+---------+---------+-----+
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148 | ... | ... | ... | ... | ... |
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149 +------------+---------+---------+---------+-----+
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150
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151 In the above example, *met* was input for Prefix
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152
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153
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154 **A Design Dataset template containing a column called sampleID with the column headers from the input dataset that were chosen as samples**
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155
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156 +----------+---------+
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157 | SampleID | |
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158 +==========+=========+
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159 | sample1 | |
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160 +----------+---------+
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161 | sample2 | |
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162 +----------+---------+
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163 | sample3 | |
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164 +----------+---------+
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165 | sample4 | |
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166 +----------+---------+
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167 | ... | |
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168 +----------+---------+
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169
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170
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171 **An Annotation Dataset containing the unique FeatureID column and any non-sample descriptor columns**
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172
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173 +-------------+------------+-----+
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174 | FeatureID | m/z ratio | ... |
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175 +=============+============+=====+
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176 | FeatureID_1 | 8.845 | ... |
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177 +-------------+------------+-----+
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178 | FeatureID_2 | 0.258 | ... |
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179 +-------------+------------+-----+
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180 | FeatureID_3 | 10.54 | ... |
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181 +-------------+------------+-----+
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182 | FeatureID_4 | 8.594 | ... |
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183 +-------------+------------+-----+
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184 | ... | ... | ... |
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185 +-------------+------------+-----+
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186
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187
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188 ]]>
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189 </help>
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190 <citations>
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191 <citation type="bibtex">@ARTICLE{Kirpich17secimtools,
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192 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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193 title = {SECIMTools: A suite of Metabolomics Data Analysis Tools},
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194 journal = {BMC Bioinformatics},
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195 year = {in press}
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196 }</citation>
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197 <citation type="bibtex">@article{garcia2010paintomics,
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198 title={Paintomics: a web based tool for the joint visualization of transcriptomics and metabolomics data},
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199 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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200 journal={Bioinformatics},
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201 volume={27},
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202 number={1},
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203 pages={137--139},
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204 year={2010},
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205 publisher={Oxford University Press}
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206 }</citation>
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207 </citations>
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208 </tool>