annotate pxf2bff.xml @ 1:23449c685168 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit eecd43b81a8c9f2175c50a71ae85ce9185a9d3a7

<tool id="beacon2_pxf2bff" name="Beacon2 PXF2BFF" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
    <description>converts Phenopacket PXF (JSON) to BFF (JSON)</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="xrefs"/>
    <expand macro="requirements"/>
    <expand macro="creators"/>
    <command detect_errors="exit_code"><![CDATA[   
        #import re
        #set $names = []
        #set $x=1
        #for $x, $i in enumerate($input):
            #set $name_base = re.sub('[^\w\-_\.]', '_', $i.element_identifier)
            #set $name = $name_base
            #silent $names.append( $name )
            ln -s '$i' ${name}  &&
        #end for
        pxf2bff
            #for $name in $names:
                -i ${name}
            #end for
            -o ./
    ]]></command>
    <inputs>
        <param argument="--input" type="data" multiple="true" format="json" label="Phenopacket JSON files" help="" />
    </inputs>
    <outputs>
        <data name="BFF_JSON_File" format="json" label="${tool.name} on ${on_string}: BFF_JSON_File" from_work_dir="individuals.json" />
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="input" ftype="json" value="EGAF00005572750.json,EGAF00005572753.json,EGAF00005572884.json,EGAF00005572893.json,EGAF00005572727.json,EGAF00005572756.json,EGAF00005572721.json,EGAF00005572902.json,EGAF00005572759.json,EGAF00005572881.json,EGAF00005572896.json,EGAF00005572890.json,EGAF00005572861.json,EGAF00005572899.json,EGAF00005572762.json,EGAF00005572887.json,EGAF00005572724.json,EGAF00005572747.json" />
            <output name="BFF_JSON_File" file="individuals.json" />
        </test>
    </tests>
    <help><![CDATA[
      The tool combines different Phenopacket JSON files into one JSON file. The Phenopacket Schema represents an open standard for sharing disease and phenotype information to
      improve our ability to understand, diagnose, and treat both rare and common diseases. The generated file will be ready to be stored on the MongoDB instance as MongoDB works directly with JSON files.
    ]]></help>
    <expand macro="citations" />
</tool>