annotate value_from_yaml_or_json.xml @ 0:47839d77a281 draft default tip

"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/value_from_yaml_or_json commit 28fa7f14add96533ed9538b675a5fb58438566d5-dirty"

<tool id="value_from_yaml_or_json" name="Value from YAML or JSON" version="0.1.0" python_template_version="3.5">
    <requirements>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
#def getValue(contents, path)
  #set $rslt = $contents
  #set $keys = path.split(':')
  #for k in $keys:
      #if isinstance($rslt,dict)
          #if k in $rslt.keys()
              #set $rslt = $rslt[k]
          #else
              #for dk in $rslt.keys():
                  #if str(dk) == k
                      #set $rslt = $rslt[dk]
                  #end if
              #end for
          #end if
      #elif isinstance($rslt,list)
          #set $rslt = $rslt[int(k)]
      #end if
  #end for
  #return $rslt
#end def
#set $fh = open(str($input),'r')
#if $input.is_of_type('yaml')
#import yaml
#set $data = $yaml.safe_load(fh.read())
#else
#import json
#set $data =  $json.load($fh)
#end if
#silent $fh.close()
#set $value = $getValue($data,  $path)
echo "$value" > '$output'
    ]]></command>
    <inputs>
        <param name="input" type="data" format="yaml,json" label="YAML or JSON from which to extract value"/>
        <param name="path" type="text" value="" label="path to value via dict keys or list indices" 
               help="separate keys/indexes with the colon char : ">
            <sanitizer>
                <valid initial="string.printable">
                </valid>
            </sanitizer>
        </param>
    </inputs>
    <outputs>
        <data name="output" format="txt" />
    </outputs>
    <tests>
        <!-- Test-1 json dict -->
        <test>
            <param name="input" ftype="json" value="input.json"/> 
            <param name="path" value="beam:energy"/> 
            <output name="output">
                <assert_contents>
                    <has_line line="41.9906" />
                </assert_contents>
            </output>
        </test>
        <!-- Test-2 json list -->
        <test>
            <param name="input" ftype="json" value="input.json"/> 
            <param name="path" value="calibration_crystal:0:orientation:1"/> 
            <output name="output">
                <assert_contents>
                    <has_line line="0.6945507909200794" />
                </assert_contents>
            </output>
        </test>
        <!-- Test-3 yaml dict -->
        <test>
            <param name="input" ftype="yaml" value="input.yaml"/> 
            <param name="path" value="beam:energy"/> 
            <output name="output">
                <assert_contents>
                    <has_line line="41.9906" />
                </assert_contents>
            </output>
        </test>
        <!-- Test-4 yaml list -->
        <test>
            <param name="input" ftype="yaml" value="input.yaml"/> 
            <param name="path" value="calibration_crystal:0:orientation:1"/> 
            <output name="output">
                <assert_contents>
                    <has_line line="0.6945507909200794" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
Extract a value from a YAML or JSON dataset and save to the output dataset.  
It is expected that this will be most useful in workflows for extracting values that can be linked to parameters.

*If more elaborate filtering of JSON datasets is required, the* `JQ tool`_ *is available.*

.. _JQ tool: https://toolshed.g2.bx.psu.edu/view/iuc/jq/5ff75eb1a893 

-----

With a JSON or YAML input dataset, specify the path for the value you wish to output by listing the key/index of the elements separated by the colon character.

**Example Input YAML File** ::

    beam:
      energy: 41.9906
      vector:
        azimuth: 90.0
        polar_angle: 90.0
    calibration_crystal:
      0:
        orientation:
        - 1.2148784044413221
        - 0.6945507909200794
        - 0.765702046701113
        position:
        - 0.06060121926310595
        - 0.1312120981443553
        - -0.06694059935413639
      1:
        orientation:
        - 1.4105172207115466
        - -0.14336674130145605
        - -0.37238882282338215
        position:
        - 0.016940740257706914
        - -0.1183857552099456
        - 0.34767784259162654

*Specifying path:*  **beam:energy** 
    *outputs:* **41.9906**

*Specifying path:*  **calibration_crystal:1:position:2**
    *outputs:* **0.34767784259162654**

*Specifying path:*  **calibration_crystal:1:position**
    *outputs:* **[0.016940740257706914, -0.1183857552099456, 0.34767784259162654]**

    ]]></help>
</tool>