Mercurial > repos > iuc > jq
changeset 0:5ff75eb1a893 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jq commit 09e822fb844c9c724eb03dd12f352577ef404ea8
| author | iuc |
|---|---|
| date | Tue, 04 Jul 2017 18:29:48 -0400 |
| parents | |
| children | |
| files | jq.xml test-data/list.json test-data/out-1.json |
| diffstat | 3 files changed, 124 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/jq.xml Tue Jul 04 18:29:48 2017 -0400 @@ -0,0 +1,120 @@ +<?xml version="1.0"?> +<tool id="jq" name="JQ" version="1.0"> + <description>process JSON</description> + <requirements> + <requirement type="package" version="1.5">jq</requirement> + </requirements> + <command detect_errors="aggressive"><![CDATA[ +JQ_BIN=`which jq` && +cat '$input' | env -i JQ_BIN=\$JQ_BIN \$JQ_BIN -r -S '$filter $tsv' > '$output' + ]]></command> + <inputs> + <param name="input" label="JSON Input" type="data" format="json" /> + <param name="filter" label="jq filter" type="text"> + <sanitizer> + <valid> + <add value='"'/> + <add value="@"/> + <add value="|"/> + <add value="!"/> + <add value="="/> + <add value="$"/> + <add value="["/> + <add value="]"/> + <add value="{"/> + <add value="}"/> + <add value="("/> + <add value=")"/> + <add value="<"/> + <add value=">"/> + </valid> + </sanitizer> + </param> + <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"/> + </inputs> + <outputs> + <data format="json" name="output"> + <change_format> + <when input="tsv" value="| @tsv" format="tabular" /> + </change_format> + </data> + </outputs> + <tests> + <test> + <param name="input" value="list.json"/> + <param name="filter" value=".[] | [.foo, .bar]"/> + <param name="tsv" value="| @tsv"/> + <output name="output" file="out-1.json" /> + </test> + <test> + <param name="input" value="list.json"/> + <param name="filter" value='{"a": env}'/> + <param name="tsv" value=""/> + <output name="output"> + <assert_contents> + <has_text text="JQ_BIN"/> + <not_has_text text="GALAXY_CONFIG"/> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ +JQ +== + + jq is a lightweight and flexible JSON processor. + +Brief Examples +-------------- + +See `the manual <https://stedolan.github.io/jq/manual/>`__ for a much +more detailed guide on using JQ. + +Select an Attribute +~~~~~~~~~~~~~~~~~~~ + +Given an input like the following + +:: + + {"foo": 42, "bar": "less interesting data"} + +To select just the value of ``foo``, supply the filter ``.foo`` + +Loop over an Array +~~~~~~~~~~~~~~~~~~ + +Given an input like the following + +:: + + [{"foo": 1123}, {"foo": 6536}, {"foo": 5321}] + +To select the values of ``foo``, supply the filter ``.[].foo`` or +``.[] | .foo``. This will produce a file with one number per line. + +If you wish to select multiple things: + +:: + + [{"foo": 1123, "bar": "a"}, {"foo": 6536, "bar": "b"}, {"foo": 5321, "bar": "c"}] + +To select the values of ``foo`` AND ``bar``, supply the filter +``.[] | [.foo, .bar]``. This will produce and output array like: + +:: + + [ + [1123, "a"] + [6536, "b"] + [5321, "c"] + ] + +A common next step is to turn this into a tabular output which more +Galaxy tools can work with. This can be done by checking the box for +tabular. This will invoke the JQ filter of ``@tsv`` at the end of the +processing chain, and produce a tabular file. + + ]]></help> + <citations/> +</tool>