Mercurial > repos > iuc > beacon2_pxf2bff

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
author iuc
date Sun, 01 Oct 2023 16:29:48 +0000
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738410e73fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
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1 <tool id="beacon2_pxf2bff" name="Beacon2 PXF2BFF" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
738410e73fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
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2 <description>converts Phenopacket PXF (JSON) to BFF (JSON)</description>
738410e73fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
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3 <macros>
738410e73fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
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4 <import>macros.xml</import>
738410e73fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
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5 </macros>
738410e73fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
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6 <expand macro="xrefs"/>
738410e73fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
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7 <expand macro="requirements"/>
738410e73fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
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8 <expand macro="creators"/>
738410e73fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
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9 <command detect_errors="exit_code"><![CDATA[
738410e73fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
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10 #import re
738410e73fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
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11 #set $names = []
738410e73fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
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12 #set $x=1
738410e73fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
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13 #for $x, $i in enumerate($input):
738410e73fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
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14 #set $name_base = re.sub('[^\w\-_\.]', '_', $i.element_identifier)
738410e73fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
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15 #set $name = $name_base
738410e73fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
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16 #silent $names.append( $name )
738410e73fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
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17 ln -s '$i' ${name} &&
738410e73fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
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18 #end for
738410e73fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
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19 pxf2bff
738410e73fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
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20 #for $name in $names:
738410e73fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
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21 -i ${name}
738410e73fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
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22 #end for
738410e73fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
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23 -o ./
738410e73fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
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24 ]]></command>
738410e73fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
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25 <inputs>
738410e73fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
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26 <param argument="--input" type="data" multiple="true" format="json" label="Phenopacket JSON files" help="" />
738410e73fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
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27 </inputs>
738410e73fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
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28 <outputs>
738410e73fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
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29 <data name="BFF_JSON_File" format="json" label="${tool.name} on ${on_string}: BFF_JSON_File" from_work_dir="individuals.json" />
738410e73fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
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30 </outputs>
738410e73fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
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31 <tests>
738410e73fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
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32 <test expect_num_outputs="1">
738410e73fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
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33 <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" />
738410e73fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
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34 <output name="BFF_JSON_File" file="individuals.json" />
738410e73fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
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35 </test>
738410e73fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
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36 </tests>
738410e73fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
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37 <help><![CDATA[
738410e73fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
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38 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
738410e73fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
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39 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.
738410e73fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
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40 ]]></help>
738410e73fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
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41 <expand macro="citations" />
738410e73fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
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42 </tool>