Mercurial > repos > devteam > column_maker

annotate column_maker.xml @ 3:35937a6b04fb draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit f6e96ffa420035051ea4632596dfd171074aa66d
author devteam
date Thu, 25 Oct 2018 17:31:05 -0400
parents 292c605c2dc7
children 3335c0d583d8
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3
35937a6b04fb planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit f6e96ffa420035051ea4632596dfd171074aa66d
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1 <tool id="Add_a_column1" name="Compute" version="1.2.0">
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2 <description>an expression on every row</description>
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3 <requirements>
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4 <requirement type="package" version="2.7.13">python</requirement>
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5 <requirement type="package" version="4.4">sed</requirement>
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6 </requirements>
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7 <command detect_errors="aggressive"><![CDATA[
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8 #if $header_lines_conditional.header_lines_select == "yes":
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9 (sed -n '1,1p' '$input' | sed "s|$|%${header_lines_conditional.header_new_column_name}|" | tr "%" "\t") > header &&
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10 sed '1,1d' '$input' > data &&
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11 #else:
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12 touch header &&
35937a6b04fb planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit f6e96ffa420035051ea4632596dfd171074aa66d
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13 ln -s '$input' data &&
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14 #end if
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15
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16 python '$__tool_directory__/column_maker.py'
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17 data column_maker_output
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18 "$cond"
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19 $round
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20 ${input.metadata.columns}
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21 "${input.metadata.column_types}" &&
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22 cat header column_maker_output > '$out_file1'
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23 ]]></command>
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24 <inputs>
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25 <param name="cond" type="text" value="c3-c2" label="Add expression"/>
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26 <param format="tabular" name="input" type="data" label="as a new column to" help="Dataset missing? See TIP below"/>
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27 <param name="round" type="select" label="Round result?">
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28 <option value="no">NO</option>
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29 <option value="yes">YES</option>
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30 </param>
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31 <conditional name="header_lines_conditional">
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32 <param name="header_lines_select" type="select" label="Skip a header line" help="# characters are already considered as comments and kept" >
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33 <option value="no" >no</option>
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34 <option value="yes" >yes</option>
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35 </param>
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36 <when value="no">
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37 </when>
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38 <when value="yes">
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39 <param name="header_new_column_name" type="text" value="New Column" label="The new column name" />
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40 </when>
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41 </conditional>
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42 </inputs>
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43 <outputs>
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44 <data format_source="input" name="out_file1" metadata_source="input"/>
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45 </outputs>
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46 <tests>
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47 <test>
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48 <param name="cond" value="c3-c2"/>
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49 <param name="input" value="1.bed"/>
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50 <param name="round" value="no"/>
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51 <output name="out_file1" file="column_maker_out1.interval"/>
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52 </test>
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53 <test>
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54 <param name="cond" value="c4*1"/>
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55 <param name="input" value="1.interval"/>
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56 <param name="round" value="no"/>
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57 <output name="out_file1" file="column_maker_out2.interval"/>
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58 </test>
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59 <test>
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60 <param name="cond" value="c4*1"/>
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61 <param name="input" value="1.header.tsv"/>
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62 <param name="round" value="no"/>
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63 <conditional name="header_lines_conditional">
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64 <param name="header_lines_select" value="yes" />
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65 <param name="header_new_column_name" value="value1_again" />
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66 </conditional>
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67 <output name="out_file1" file="column_maker_out2.header.tsv"/>
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68 </test>
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69 <test>
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70 <param name="cond" value="c4*1"/>
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71 <param name="input" value="1.interval"/>
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72 <param name="round" value="yes"/>
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73 <output name="out_file1" file="column_maker_out3.interval"/>
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74 </test>
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75 </tests>
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76 <help>
0
4dadd821722f Imported from capsule None
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77
4dadd821722f Imported from capsule None
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78 .. class:: infomark
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79
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80 **TIP:** If your data is not TAB delimited, use *Text Manipulation-&gt;Convert*
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81
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82 -----
4dadd821722f Imported from capsule None
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83
4dadd821722f Imported from capsule None
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84 **What it does**
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85
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86 This tool computes an expression for every row of a dataset and appends the result as a new column (field).
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87
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88 - Columns are referenced with **c** and a **number**. For example, **c1** refers to the first column of a tab-delimited file
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89
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90 - **c3-c2** will add a length column to the dataset if **c2** and **c3** are start and end position
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91
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92 -----
4dadd821722f Imported from capsule None
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93
4dadd821722f Imported from capsule None
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94 **Example**
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95
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96 If this is your input::
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97
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98 chr1 151077881 151077918 2 200 -
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99 chr1 151081985 151082078 3 500 +
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100
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101 computing "c4*c5" will produce::
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102
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103 chr1 151077881 151077918 2 200 - 400.0
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104 chr1 151081985 151082078 3 500 + 1500.0
3
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105
0
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106 if, at the same time, "Round result?" is set to **YES** results will look like this::
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107
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108 chr1 151077881 151077918 2 200 - 400
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109 chr1 151081985 151082078 3 500 + 1500
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110
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111 You can also use this tool to evaluate expressions. For example, computing "c3>=c2" for Input will result in the following::
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112
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113 chr1 151077881 151077918 2 200 - True
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114 chr1 151081985 151082078 3 500 + True
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115
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116 or computing "type(c2)==type('') for Input will return::
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117
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118 chr1 151077881 151077918 2 200 - False
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119 chr1 151081985 151082078 3 500 + False
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120
2
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121
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122 The following build-in functions are available::
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123
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124 abs | all | any | bin | bool | chr | ceil | cmp | complex
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125
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126 divmod | exp | float | log | floor | hex | int | len | long
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127
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128 max | min | oct | ord | pow | range | reversed
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129
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130 round | sorted | sqrt | str | sum | type | unichr | unicode |
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131
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132 </help>
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133 <citations />
0
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134 </tool>