<?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="&lt;"/>
                    <add value="&gt;"/>
                </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>