Mercurial > repos > scottx611x > data_manager_fetch_gene_annotation

annotate data_manager/gene_annotation_fetcher.xml @ 39:2ab076cf69df draft

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planemo upload for repository https://scottx611x@toolshed.g2.bx.psu.edu/repos/scottx611x/data_manager_fetch_gene_annotation
author scottx611x
date Fri, 08 Jul 2016 11:17:50 -0400
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39
2ab076cf69df planemo upload for repository https://scottx611x@toolshed.g2.bx.psu.edu/repos/scottx611x/data_manager_fetch_gene_annotation
scottx611x
parents:
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1 <?xml version="1.0"?>
2ab076cf69df planemo upload for repository https://scottx611x@toolshed.g2.bx.psu.edu/repos/scottx611x/data_manager_fetch_gene_annotation
scottx611x
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2 <tool id="gene_annotation_fetcher_data_manager" name="Gene Annotation Fetch" tool_type="manage_data" version="1.0.0">
2ab076cf69df planemo upload for repository https://scottx611x@toolshed.g2.bx.psu.edu/repos/scottx611x/data_manager_fetch_gene_annotation
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3 <description>gene annotation fetcher</description>
2ab076cf69df planemo upload for repository https://scottx611x@toolshed.g2.bx.psu.edu/repos/scottx611x/data_manager_fetch_gene_annotation
scottx611x
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4 <stdio>
2ab076cf69df planemo upload for repository https://scottx611x@toolshed.g2.bx.psu.edu/repos/scottx611x/data_manager_fetch_gene_annotation
scottx611x
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5 <exit_code description="Error" level="fatal" range="1:" />
2ab076cf69df planemo upload for repository https://scottx611x@toolshed.g2.bx.psu.edu/repos/scottx611x/data_manager_fetch_gene_annotation
scottx611x
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6 </stdio>
2ab076cf69df planemo upload for repository https://scottx611x@toolshed.g2.bx.psu.edu/repos/scottx611x/data_manager_fetch_gene_annotation
scottx611x
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7 <command interpreter="python">
2ab076cf69df planemo upload for repository https://scottx611x@toolshed.g2.bx.psu.edu/repos/scottx611x/data_manager_fetch_gene_annotation
scottx611x
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8 <![CDATA[
2ab076cf69df planemo upload for repository https://scottx611x@toolshed.g2.bx.psu.edu/repos/scottx611x/data_manager_fetch_gene_annotation
scottx611x
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9 data_manager.py --out "${out_file}"
2ab076cf69df planemo upload for repository https://scottx611x@toolshed.g2.bx.psu.edu/repos/scottx611x/data_manager_fetch_gene_annotation
scottx611x
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10 #if $gene_annotation_url:
2ab076cf69df planemo upload for repository https://scottx611x@toolshed.g2.bx.psu.edu/repos/scottx611x/data_manager_fetch_gene_annotation
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11 --url "${gene_annotation_url}"
2ab076cf69df planemo upload for repository https://scottx611x@toolshed.g2.bx.psu.edu/repos/scottx611x/data_manager_fetch_gene_annotation
scottx611x
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12 #end if
2ab076cf69df planemo upload for repository https://scottx611x@toolshed.g2.bx.psu.edu/repos/scottx611x/data_manager_fetch_gene_annotation
scottx611x
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13 #if $database_name:
2ab076cf69df planemo upload for repository https://scottx611x@toolshed.g2.bx.psu.edu/repos/scottx611x/data_manager_fetch_gene_annotation
scottx611x
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14 --dbkey "${database_name}"
2ab076cf69df planemo upload for repository https://scottx611x@toolshed.g2.bx.psu.edu/repos/scottx611x/data_manager_fetch_gene_annotation
scottx611x
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15 #end if
2ab076cf69df planemo upload for repository https://scottx611x@toolshed.g2.bx.psu.edu/repos/scottx611x/data_manager_fetch_gene_annotation
scottx611x
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16 ]]>
2ab076cf69df planemo upload for repository https://scottx611x@toolshed.g2.bx.psu.edu/repos/scottx611x/data_manager_fetch_gene_annotation
scottx611x
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17 </command>
2ab076cf69df planemo upload for repository https://scottx611x@toolshed.g2.bx.psu.edu/repos/scottx611x/data_manager_fetch_gene_annotation
scottx611x
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18 <inputs>
2ab076cf69df planemo upload for repository https://scottx611x@toolshed.g2.bx.psu.edu/repos/scottx611x/data_manager_fetch_gene_annotation
scottx611x
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19 <param
2ab076cf69df planemo upload for repository https://scottx611x@toolshed.g2.bx.psu.edu/repos/scottx611x/data_manager_fetch_gene_annotation
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20 help="Enter a unique identifier for the Data Table column to be created, or leave blank for an auto-generated uuid" label="Identifier for this DataTable entry" name="database_name" type="text" optional="True" />
2ab076cf69df planemo upload for repository https://scottx611x@toolshed.g2.bx.psu.edu/repos/scottx611x/data_manager_fetch_gene_annotation
scottx611x
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21 <param
2ab076cf69df planemo upload for repository https://scottx611x@toolshed.g2.bx.psu.edu/repos/scottx611x/data_manager_fetch_gene_annotation
scottx611x
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22 label="Enter URL pointing to a remote .gtf file" name="gene_annotation_url" type="text" optional="False"/>
2ab076cf69df planemo upload for repository https://scottx611x@toolshed.g2.bx.psu.edu/repos/scottx611x/data_manager_fetch_gene_annotation
scottx611x
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23 </inputs>
2ab076cf69df planemo upload for repository https://scottx611x@toolshed.g2.bx.psu.edu/repos/scottx611x/data_manager_fetch_gene_annotation
scottx611x
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24 <outputs>
2ab076cf69df planemo upload for repository https://scottx611x@toolshed.g2.bx.psu.edu/repos/scottx611x/data_manager_fetch_gene_annotation
scottx611x
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25 <data format="data_manager_json" name="out_file" />
2ab076cf69df planemo upload for repository https://scottx611x@toolshed.g2.bx.psu.edu/repos/scottx611x/data_manager_fetch_gene_annotation
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26 </outputs>
2ab076cf69df planemo upload for repository https://scottx611x@toolshed.g2.bx.psu.edu/repos/scottx611x/data_manager_fetch_gene_annotation
scottx611x
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27 <tests>
2ab076cf69df planemo upload for repository https://scottx611x@toolshed.g2.bx.psu.edu/repos/scottx611x/data_manager_fetch_gene_annotation
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28 <test>
2ab076cf69df planemo upload for repository https://scottx611x@toolshed.g2.bx.psu.edu/repos/scottx611x/data_manager_fetch_gene_annotation
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29 <param name="database_name" value="cool_name"/>
2ab076cf69df planemo upload for repository https://scottx611x@toolshed.g2.bx.psu.edu/repos/scottx611x/data_manager_fetch_gene_annotation
scottx611x
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30 <param name="gene_annotation_url" value="http://www.scott-ouellette.com/gene_annotations/chr1-hg19_genes.gtf"/>
2ab076cf69df planemo upload for repository https://scottx611x@toolshed.g2.bx.psu.edu/repos/scottx611x/data_manager_fetch_gene_annotation
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31 <output name="out_file" file="gene_annotation_out.json" compare="contains"/>
2ab076cf69df planemo upload for repository https://scottx611x@toolshed.g2.bx.psu.edu/repos/scottx611x/data_manager_fetch_gene_annotation
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32 <!--<extra_files type="file" name="chr1-hg19_genes.gtf" value="chr1-hg19_genes.gtf"/>-->
2ab076cf69df planemo upload for repository https://scottx611x@toolshed.g2.bx.psu.edu/repos/scottx611x/data_manager_fetch_gene_annotation
scottx611x
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33 </test>
2ab076cf69df planemo upload for repository https://scottx611x@toolshed.g2.bx.psu.edu/repos/scottx611x/data_manager_fetch_gene_annotation
scottx611x
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34 </tests>
2ab076cf69df planemo upload for repository https://scottx611x@toolshed.g2.bx.psu.edu/repos/scottx611x/data_manager_fetch_gene_annotation
scottx611x
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35 </tool>