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annotate biom_from_uc.xml @ 5:e4c56e1361d9 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 1ec368e960b856bfa1c62af80faa579087cef9ae
author iuc
date Tue, 20 Dec 2022 19:39:32 +0000
parents c82e077989ee
children bd2d2d53d5dd
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2cdeed709bf4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 4ca0a67fd4126f8b2a135b6cb7894042e980b39a"
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1 <tool id="biom_from_uc" name="Create a BIOM table" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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26c9cf427dcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
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2 <description>from a vsearch/uclust/usearch BIOM file</description>
26c9cf427dcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
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3 <macros>
26c9cf427dcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
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4 <import>macros.xml</import>
26c9cf427dcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
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5 </macros>
26c9cf427dcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
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6 <expand macro="requirements" />
26c9cf427dcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
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7 <expand macro="version_command" />
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8 <command detect_errors="exit_code">
26c9cf427dcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
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9 <![CDATA[
26c9cf427dcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
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10 biom from-uc
26c9cf427dcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
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11 --input-fp '$input_fp'
26c9cf427dcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
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12 --output-fp '$output_fp'
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c82e077989ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit ddde8018cc6ff30dbb448e66be5433ce36e56b55
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13 #if $rep_set_fp
c82e077989ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit ddde8018cc6ff30dbb448e66be5433ce36e56b55
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14 --rep-set-fp '$rep_set_fp'
c82e077989ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit ddde8018cc6ff30dbb448e66be5433ce36e56b55
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15 #end if
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26c9cf427dcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
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16 ]]>
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17 </command>
26c9cf427dcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
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18 <inputs>
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19 <param name="input_fp" argument="--input-fp" type="data" format="txt" label="UC File" />
26c9cf427dcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
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20 <param name="rep_set_fp" argument="--rep-set-fp" type="data" format="fasta" optional="true" label="Fasta file containing representative sequences with where sequences are labeled with OTU identifiers, and description fields contain original sequence identifiers" help="This output is created, for example, by vsearch with the --relabel_sha1 --relabel_keep options."/>
26c9cf427dcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
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21 </inputs>
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22 <outputs>
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23 <data format="biom1" name="output_fp"/>
26c9cf427dcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
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24 </outputs>
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25 <tests>
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26 <test>
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27 <param name="input_fp" value="uc_table.uc" />
26c9cf427dcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
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28 <output name="output_fp" file="biom_from_uc.biom" compare="sim_size"/>
26c9cf427dcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
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29 </test>
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30 </tests>
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31 <help><![CDATA[
26c9cf427dcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
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32 Create a BIOM table from a vsearch/uclust/usearch BIOM file.
26c9cf427dcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
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33 ]]></help>
26c9cf427dcd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
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34 <expand macro="citations" />
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35 </tool>