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annotate purge_gtf_from_multichrom_genes.xml @ 9:e00a79cf5f8c draft default tip

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"planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit fdb6ccd340e366ef386d69ff344036a83e479b2f"
author artbio
date Tue, 03 Mar 2020 07:28:39 -0500
parents 45a30e216fec
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45a30e216fec planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 4bc762d0932b87d4e91ce76bc3eeb52f0b8d3bc6
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1 <tool id="purgegtffrommultichromgenes" name="Purge GTF" version="@WRAPPER_VERSION@">
45a30e216fec planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 4bc762d0932b87d4e91ce76bc3eeb52f0b8d3bc6
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2 <description>from multi-chromosomes genes</description>
45a30e216fec planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 4bc762d0932b87d4e91ce76bc3eeb52f0b8d3bc6
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3 <macros>
45a30e216fec planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 4bc762d0932b87d4e91ce76bc3eeb52f0b8d3bc6
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4 <import>macros.xml</import>
45a30e216fec planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 4bc762d0932b87d4e91ce76bc3eeb52f0b8d3bc6
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5 </macros>
45a30e216fec planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 4bc762d0932b87d4e91ce76bc3eeb52f0b8d3bc6
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6 <requirements>
45a30e216fec planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 4bc762d0932b87d4e91ce76bc3eeb52f0b8d3bc6
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7 </requirements>
45a30e216fec planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 4bc762d0932b87d4e91ce76bc3eeb52f0b8d3bc6
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8 <stdio>
45a30e216fec planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 4bc762d0932b87d4e91ce76bc3eeb52f0b8d3bc6
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9 <exit_code range="1:" level="warning" description="Tool exception" />
45a30e216fec planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 4bc762d0932b87d4e91ce76bc3eeb52f0b8d3bc6
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10 </stdio>
45a30e216fec planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 4bc762d0932b87d4e91ce76bc3eeb52f0b8d3bc6
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11 <command detect_errors="exit_code"><![CDATA[
45a30e216fec planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 4bc762d0932b87d4e91ce76bc3eeb52f0b8d3bc6
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12 python '$__tool_directory__'/purge_gtf_from_multichrom_genes.py
45a30e216fec planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 4bc762d0932b87d4e91ce76bc3eeb52f0b8d3bc6
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13 --input '$input'
45a30e216fec planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 4bc762d0932b87d4e91ce76bc3eeb52f0b8d3bc6
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14 --output '$output'
45a30e216fec planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 4bc762d0932b87d4e91ce76bc3eeb52f0b8d3bc6
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15 --log '$log'
45a30e216fec planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 4bc762d0932b87d4e91ce76bc3eeb52f0b8d3bc6
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16
45a30e216fec planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 4bc762d0932b87d4e91ce76bc3eeb52f0b8d3bc6
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17 ]]></command>
45a30e216fec planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 4bc762d0932b87d4e91ce76bc3eeb52f0b8d3bc6
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18 <inputs>
45a30e216fec planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 4bc762d0932b87d4e91ce76bc3eeb52f0b8d3bc6
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19 <param name="input" type="data" format="gtf" label="GTF input file to be purged of multichromosome genes" />
45a30e216fec planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 4bc762d0932b87d4e91ce76bc3eeb52f0b8d3bc6
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20 </inputs>
45a30e216fec planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 4bc762d0932b87d4e91ce76bc3eeb52f0b8d3bc6
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45a30e216fec planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 4bc762d0932b87d4e91ce76bc3eeb52f0b8d3bc6
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22 <outputs>
45a30e216fec planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 4bc762d0932b87d4e91ce76bc3eeb52f0b8d3bc6
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23 <data format="tabular" name="log" label="gtf purge LOG" />
45a30e216fec planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 4bc762d0932b87d4e91ce76bc3eeb52f0b8d3bc6
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24 <data format="gtf" name="output" label="purged_${input.name}" />
45a30e216fec planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 4bc762d0932b87d4e91ce76bc3eeb52f0b8d3bc6
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25 </outputs>
45a30e216fec planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 4bc762d0932b87d4e91ce76bc3eeb52f0b8d3bc6
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45a30e216fec planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 4bc762d0932b87d4e91ce76bc3eeb52f0b8d3bc6
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27 <tests>
45a30e216fec planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 4bc762d0932b87d4e91ce76bc3eeb52f0b8d3bc6
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28 <test>
45a30e216fec planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 4bc762d0932b87d4e91ce76bc3eeb52f0b8d3bc6
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29 <param name="input" value="GTF_to_purge.gtf"/>
45a30e216fec planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 4bc762d0932b87d4e91ce76bc3eeb52f0b8d3bc6
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30 <output name="output" value="purged.gtf" ftype="gtf" />
45a30e216fec planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 4bc762d0932b87d4e91ce76bc3eeb52f0b8d3bc6
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31 <output name="log" value="purged.gtf.log" ftype="tabular" />
45a30e216fec planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 4bc762d0932b87d4e91ce76bc3eeb52f0b8d3bc6
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32 </test>
45a30e216fec planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 4bc762d0932b87d4e91ce76bc3eeb52f0b8d3bc6
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33 </tests>
45a30e216fec planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 4bc762d0932b87d4e91ce76bc3eeb52f0b8d3bc6
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45a30e216fec planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 4bc762d0932b87d4e91ce76bc3eeb52f0b8d3bc6
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35 <help>
45a30e216fec planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 4bc762d0932b87d4e91ce76bc3eeb52f0b8d3bc6
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36 .. class:: infomark
45a30e216fec planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 4bc762d0932b87d4e91ce76bc3eeb52f0b8d3bc6
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45a30e216fec planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 4bc762d0932b87d4e91ce76bc3eeb52f0b8d3bc6
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38 This script removes genes with multichromosome locations from gtf file. This avoid rsem error
45a30e216fec planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 4bc762d0932b87d4e91ce76bc3eeb52f0b8d3bc6
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39 due to ambiguous feature coordinates on multiple chromosomes.
45a30e216fec planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 4bc762d0932b87d4e91ce76bc3eeb52f0b8d3bc6
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45a30e216fec planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 4bc762d0932b87d4e91ce76bc3eeb52f0b8d3bc6
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45a30e216fec planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 4bc762d0932b87d4e91ce76bc3eeb52f0b8d3bc6
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42 </help>
45a30e216fec planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 4bc762d0932b87d4e91ce76bc3eeb52f0b8d3bc6
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43 <citations>
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44 <citation type="doi">10.1186/1471-2105-12-323</citation>
45a30e216fec planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 4bc762d0932b87d4e91ce76bc3eeb52f0b8d3bc6
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45 </citations>
45a30e216fec planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 4bc762d0932b87d4e91ce76bc3eeb52f0b8d3bc6
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45a30e216fec planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 4bc762d0932b87d4e91ce76bc3eeb52f0b8d3bc6
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47 </tool>