annotate macros.xml @ 1:724dcbb35c9a draft default tip

planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/blob/main/tools/saqc/ commit b674325a07b6e964e25cd65967149018dc2671fe
author ufz
date Sat, 16 Aug 2025 11:43:23 +0000
parents 55bbea0cdc60
children
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1 <macros>
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2 <xml name="requirements">
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3 <requirements>
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4 <requirement type="package" version="@TOOL_VERSION@">saqc</requirement>
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5 </requirements>
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6 </xml>
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7
1
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8 <token name="@TOOL_VERSION@">2.6.0</token>
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9 <token name="@VERSION_SUFFIX@">0</token>
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11 <xml name="citations">
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12 <citations>
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13 <citation type="doi">https://doi.org/10.1016/j.envsoft.2023.105809</citation>
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14 </citations>
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15 </xml>
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16
1
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17 <xml name="field">
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18 <param argument="field"
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19 label="Field"
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20 optional="false"
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21 value=""
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22 type="text"
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23 help="Variable to process"/>
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24 </xml>
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25
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26 <xml name="field_multiple">
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27 <repeat name="field_repeat" title="field(s)" min="1">
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28 <param argument="field"
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29 label="Field"
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30 optional="false"
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31 value=""
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32 type="text"
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33 help="Variable to process"/>
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34 </repeat>
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35 </xml>
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36
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37 <xml name="flag">
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38 <param argument="flag"
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39 label="Flag"
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40 optional="true"
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41 value="255.0"
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42 type="float"
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43 help="The flag value the function uses to mark observations"/>
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44 </xml>
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45
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46 <xml name="saqc_tests">
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47 <tests>
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48 <expand macro="config_tests"/>
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49 <test>
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50 <param name="data" value="test1/data.csv" ftype="csv"/>
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51 <repeat name="methods_repeat">
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52 <conditional name="module_cond">
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53 <param name="module_select" value="outliers"/>
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54 <conditional name="method_cond">
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55 <param name="method_select" value="flagRange"/>
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56 <param name="field" value="SM2"/>
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57 <param name="max" value="60.0"/>
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58 <param name="min" value="10.0"/>
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59
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60 <param name="flag" value="255.0"/>
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61 </conditional>
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62 </conditional>
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63 </repeat>
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64 <repeat name="methods_repeat">
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65 <conditional name="module_cond">
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66 <param name="module_select" value="outliers"/>
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67 <conditional name="method_cond">
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68
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69 <param name="method_select" value="flagZScore"/>
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70
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71 <repeat name="field_repeat">
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72 <param name="field" value="SM2"/>
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73 </repeat>
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74 <param name="center" value="false"/>
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75 <conditional name="window_cond">
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76 <param name="window_select_type" value="timedelta"/>
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77 <param name="window" value="30d"/>
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78 </conditional>
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79 <param name="thresh" value="3.5"/>
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80 <param name="method" value="modified"/>
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81
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82 <param name="flag" value="255.0"/>
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83 </conditional>
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84 </conditional>
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85 </repeat>
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86 <repeat name="methods_repeat">
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87 <conditional name="module_cond">
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88 <param name="module_select" value="tools"/>
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89 <conditional name="method_cond">
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90 <param name="method_select" value="plot"/>
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91 <param name="field" value="SM2"/>
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92 <param name="path" value="test"/>
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93 <conditional name="history_cond">
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94 <param name="history_select_type" value="valid" />
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95 <param name="history" value="valid" />
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96 </conditional>
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97 <param name="mode" value="oneplot"/>
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98 <param name="max_gap" value="" />
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99 <param name="xscope" value="" />
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100 <param name="yscope" value="" />
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101 <param name="dfilter" value="inf" />
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102 </conditional>
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103 </conditional>
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104 </repeat>
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105
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106 <output name="output" value="test1/out.csv" ftype="csv"/>
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107 <output name="config_out" ftype="txt">
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108 <assert_contents>
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109 <has_n_lines n="4"/>
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110 <has_n_columns n="2" sep=";"/>
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111 <has_text_matching expression="flagRange.*max=60.0.*min=10.0"/>
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112 <has_text_matching expression='flagZScore.*method="modified".*thresh=3.5.*window="30d"'/>
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113 <has_text_matching expression='plot.*dfilter=float\(&apos;inf&apos;\).*history="valid".*path="test"'/>
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114 </assert_contents>
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115 </output>
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116
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117 <output_collection name="plots" type="list">
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118 <element name="test" ftype="png">
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119 <assert_contents>
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120 <has_text text="PNG"/>
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121 <has_size value="120k" delta="10k"/>
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122 </assert_contents>
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123 </element>
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124 </output_collection>
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125 </test>
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126 </tests>
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127 </xml>
0
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128 </macros>