Mercurial > repos > iuc > meryl_print

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
author iuc
date Tue, 08 Oct 2024 16:44:16 +0000
parents 08b34a6c34ec
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08b34a6c34ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
iuc
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1 <tool id="meryl_print" name="Meryl" version="@TOOL_VERSION@+@GALAXY_TOOL_VERSION@@SUFFIX_VERSION@" profile="@PROFILE@">
08b34a6c34ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
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2 <description>get k-mer counts</description>
08b34a6c34ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
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3 <macros>
08b34a6c34ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
iuc
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4 <import>macros.xml</import>
08b34a6c34ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
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5 </macros>
08b34a6c34ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
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6 <expand macro="edam_ontology"/>
08b34a6c34ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
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7 <xrefs>
08b34a6c34ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
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8 <xref type="bio.tools">meryl</xref>
08b34a6c34ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
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9 </xrefs>
08b34a6c34ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
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10 <expand macro="requirements"/>
08b34a6c34ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
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11 <version_command>meryl --version</version_command>
08b34a6c34ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
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12 <command detect_errors="exit_code"><![CDATA[
08b34a6c34ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
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13 export GALAXY_MEMORY_GB=\$((\${GALAXY_MEMORY_MB:-8192}/1024)) &&
08b34a6c34ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
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14 mkdir -p ./temp_db/ &&
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4ffdd07cc5b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
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15 tar -xmf $input_meryldb_02 --use-compress-program="pigz -p \${GALAXY_SLOTS:-1}" -C ./temp_db/ &&
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08b34a6c34ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
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16 mv ./temp_db/* tmp.meryl &&
08b34a6c34ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
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17 meryl print tmp.meryl > read-db.tabular
08b34a6c34ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
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18 ]]></command>
08b34a6c34ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
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19 <inputs>
08b34a6c34ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
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20 <param name="input_meryldb_02" type="data" format="meryldb" label="Input meryldb"/>
08b34a6c34ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
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21 </inputs>
08b34a6c34ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
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22 <outputs>
08b34a6c34ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
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23 <data name="read_db_print" format="tabular" from_work_dir="read-db.tabular"/>
08b34a6c34ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
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24 </outputs>
08b34a6c34ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
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25 <tests>
08b34a6c34ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
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26 <test expect_num_outputs="1">
08b34a6c34ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
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27 <param name="input_meryldb_02" value="maternal.meryldb" ftype="meryldb"/>
08b34a6c34ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
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28 <output name="read_db_print" file="output_25.read-db.tabular" sort="true"/>
08b34a6c34ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
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29 </test>
08b34a6c34ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
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30 </tests>
08b34a6c34ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
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31 <help>
08b34a6c34ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
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32
08b34a6c34ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
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33 .. class:: infomark
08b34a6c34ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
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34
08b34a6c34ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
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35 **Purpose**
08b34a6c34ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
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36
08b34a6c34ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
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37 Meryl is the k-mer counter. This tool gets the k-mer counts as a table.
08b34a6c34ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
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38
08b34a6c34ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
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39 </help>
08b34a6c34ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
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40 <expand macro="citations"/>
08b34a6c34ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a95f5b04b1219489a327a622184633a561fe5ac0
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41 </tool>