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annotate jq.xml @ 0:2c232b51fffd draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jq commit 09e822fb844c9c724eb03dd12f352577ef404ea8
author iuc
date Tue, 04 Jul 2017 18:29:33 -0400
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2c232b51fffd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jq commit 09e822fb844c9c724eb03dd12f352577ef404ea8
iuc
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1 <?xml version="1.0"?>
2c232b51fffd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jq commit 09e822fb844c9c724eb03dd12f352577ef404ea8
iuc
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2 <tool id="jq" name="JQ" version="1.0">
2c232b51fffd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jq commit 09e822fb844c9c724eb03dd12f352577ef404ea8
iuc
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3 <description>process JSON</description>
2c232b51fffd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jq commit 09e822fb844c9c724eb03dd12f352577ef404ea8
iuc
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4 <requirements>
2c232b51fffd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jq commit 09e822fb844c9c724eb03dd12f352577ef404ea8
iuc
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5 <requirement type="package" version="1.5">jq</requirement>
2c232b51fffd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jq commit 09e822fb844c9c724eb03dd12f352577ef404ea8
iuc
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6 </requirements>
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iuc
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7 <command detect_errors="aggressive"><![CDATA[
2c232b51fffd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jq commit 09e822fb844c9c724eb03dd12f352577ef404ea8
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8 JQ_BIN=`which jq` &&
2c232b51fffd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jq commit 09e822fb844c9c724eb03dd12f352577ef404ea8
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9 cat '$input' | env -i JQ_BIN=\$JQ_BIN \$JQ_BIN -r -S '$filter $tsv' > '$output'
2c232b51fffd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jq commit 09e822fb844c9c724eb03dd12f352577ef404ea8
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10 ]]></command>
2c232b51fffd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jq commit 09e822fb844c9c724eb03dd12f352577ef404ea8
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11 <inputs>
2c232b51fffd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jq commit 09e822fb844c9c724eb03dd12f352577ef404ea8
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12 <param name="input" label="JSON Input" type="data" format="json" />
2c232b51fffd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jq commit 09e822fb844c9c724eb03dd12f352577ef404ea8
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13 <param name="filter" label="jq filter" type="text">
2c232b51fffd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jq commit 09e822fb844c9c724eb03dd12f352577ef404ea8
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14 <sanitizer>
2c232b51fffd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jq commit 09e822fb844c9c724eb03dd12f352577ef404ea8
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15 <valid>
2c232b51fffd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jq commit 09e822fb844c9c724eb03dd12f352577ef404ea8
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16 <add value='"'/>
2c232b51fffd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jq commit 09e822fb844c9c724eb03dd12f352577ef404ea8
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17 <add value="@"/>
2c232b51fffd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jq commit 09e822fb844c9c724eb03dd12f352577ef404ea8
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18 <add value="|"/>
2c232b51fffd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jq commit 09e822fb844c9c724eb03dd12f352577ef404ea8
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19 <add value="!"/>
2c232b51fffd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jq commit 09e822fb844c9c724eb03dd12f352577ef404ea8
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20 <add value="="/>
2c232b51fffd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jq commit 09e822fb844c9c724eb03dd12f352577ef404ea8
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21 <add value="$"/>
2c232b51fffd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jq commit 09e822fb844c9c724eb03dd12f352577ef404ea8
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22 <add value="["/>
2c232b51fffd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jq commit 09e822fb844c9c724eb03dd12f352577ef404ea8
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23 <add value="]"/>
2c232b51fffd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jq commit 09e822fb844c9c724eb03dd12f352577ef404ea8
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24 <add value="{"/>
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25 <add value="}"/>
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26 <add value="("/>
2c232b51fffd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jq commit 09e822fb844c9c724eb03dd12f352577ef404ea8
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27 <add value=")"/>
2c232b51fffd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jq commit 09e822fb844c9c724eb03dd12f352577ef404ea8
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28 <add value="&lt;"/>
2c232b51fffd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jq commit 09e822fb844c9c724eb03dd12f352577ef404ea8
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29 <add value="&gt;"/>
2c232b51fffd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jq commit 09e822fb844c9c724eb03dd12f352577ef404ea8
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30 </valid>
2c232b51fffd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jq commit 09e822fb844c9c724eb03dd12f352577ef404ea8
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31 </sanitizer>
2c232b51fffd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jq commit 09e822fb844c9c724eb03dd12f352577ef404ea8
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32 </param>
2c232b51fffd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jq commit 09e822fb844c9c724eb03dd12f352577ef404ea8
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33 <param name="tsv" label="Convert output to tabular" type="boolean" truevalue="| @tsv" falsevalue="" help="@tsv can be used normally, but this will automatically mark the output as tabular"/>
2c232b51fffd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jq commit 09e822fb844c9c724eb03dd12f352577ef404ea8
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34 </inputs>
2c232b51fffd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jq commit 09e822fb844c9c724eb03dd12f352577ef404ea8
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35 <outputs>
2c232b51fffd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jq commit 09e822fb844c9c724eb03dd12f352577ef404ea8
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36 <data format="json" name="output">
2c232b51fffd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jq commit 09e822fb844c9c724eb03dd12f352577ef404ea8
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37 <change_format>
2c232b51fffd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jq commit 09e822fb844c9c724eb03dd12f352577ef404ea8
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38 <when input="tsv" value="| @tsv" format="tabular" />
2c232b51fffd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jq commit 09e822fb844c9c724eb03dd12f352577ef404ea8
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39 </change_format>
2c232b51fffd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jq commit 09e822fb844c9c724eb03dd12f352577ef404ea8
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40 </data>
2c232b51fffd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jq commit 09e822fb844c9c724eb03dd12f352577ef404ea8
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41 </outputs>
2c232b51fffd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jq commit 09e822fb844c9c724eb03dd12f352577ef404ea8
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42 <tests>
2c232b51fffd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jq commit 09e822fb844c9c724eb03dd12f352577ef404ea8
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43 <test>
2c232b51fffd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jq commit 09e822fb844c9c724eb03dd12f352577ef404ea8
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44 <param name="input" value="list.json"/>
2c232b51fffd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jq commit 09e822fb844c9c724eb03dd12f352577ef404ea8
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45 <param name="filter" value=".[] | [.foo, .bar]"/>
2c232b51fffd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jq commit 09e822fb844c9c724eb03dd12f352577ef404ea8
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46 <param name="tsv" value="| @tsv"/>
2c232b51fffd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jq commit 09e822fb844c9c724eb03dd12f352577ef404ea8
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47 <output name="output" file="out-1.json" />
2c232b51fffd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jq commit 09e822fb844c9c724eb03dd12f352577ef404ea8
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48 </test>
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49 <test>
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50 <param name="input" value="list.json"/>
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51 <param name="filter" value='{"a": env}'/>
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52 <param name="tsv" value=""/>
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53 <output name="output">
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54 <assert_contents>
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55 <has_text text="JQ_BIN"/>
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56 <not_has_text text="GALAXY_CONFIG"/>
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57 </assert_contents>
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58 </output>
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59 </test>
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60 </tests>
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61 <help><![CDATA[
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62 JQ
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63 ==
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64
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65 jq is a lightweight and flexible JSON processor.
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66
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67 Brief Examples
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68 --------------
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69
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70 See `the manual <https://stedolan.github.io/jq/manual/>`__ for a much
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71 more detailed guide on using JQ.
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72
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73 Select an Attribute
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74 ~~~~~~~~~~~~~~~~~~~
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75
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76 Given an input like the following
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77
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78 ::
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79
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80 {"foo": 42, "bar": "less interesting data"}
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81
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82 To select just the value of ``foo``, supply the filter ``.foo``
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83
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84 Loop over an Array
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85 ~~~~~~~~~~~~~~~~~~
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86
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87 Given an input like the following
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88
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89 ::
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90
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91 [{"foo": 1123}, {"foo": 6536}, {"foo": 5321}]
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92
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93 To select the values of ``foo``, supply the filter ``.[].foo`` or
2c232b51fffd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jq commit 09e822fb844c9c724eb03dd12f352577ef404ea8
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94 ``.[] | .foo``. This will produce a file with one number per line.
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95
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96 If you wish to select multiple things:
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97
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98 ::
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99
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100 [{"foo": 1123, "bar": "a"}, {"foo": 6536, "bar": "b"}, {"foo": 5321, "bar": "c"}]
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101
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102 To select the values of ``foo`` AND ``bar``, supply the filter
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103 ``.[] | [.foo, .bar]``. This will produce and output array like:
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104
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105 ::
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106
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107 [
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108 [1123, "a"]
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109 [6536, "b"]
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110 [5321, "c"]
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111 ]
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112
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113 A common next step is to turn this into a tabular output which more
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114 Galaxy tools can work with. This can be done by checking the box for
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115 tabular. This will invoke the JQ filter of ``@tsv`` at the end of the
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116 processing chain, and produce a tabular file.
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117
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118 ]]></help>
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119 <citations/>
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120 </tool>