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planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
author iuc
date Sat, 17 Oct 2015 04:02:33 -0400
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0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
iuc
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1 <tool id="gedlab-khmer-filter-below-abund" name="Filter below abundance cutoff of 50" version="@WRAPPER_VERSION@-3">
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
iuc
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2 <description>
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
iuc
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3 Trims fastq/fasta sequences at k-mers with abundance below 50
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
iuc
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4 based on a provided k-mer countgraph
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
iuc
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5 </description>
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
iuc
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6 <macros>
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
iuc
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7 <token name="@BINARY@">filter-below-abund.py</token>
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
iuc
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8 <import>macros.xml</import>
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
iuc
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9 </macros>
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
iuc
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10 <expand macro="requirements" />
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
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11 <expand macro="stdio" />
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
iuc
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12 <expand macro="version" />
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
iuc
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13 <command><![CDATA[
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
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14 set -xu &&
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
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15 #for $num, $input in enumerate($inputs)
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
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16 ln -s ${input} sequence-${num} &&
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
iuc
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17 mkdir output && cd output &&
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
iuc
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18 @BINARY@
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
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19 ${input_countgraph_filename}
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
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20 ../sequence*
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
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21 ]]>
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
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22 </command>
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
iuc
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23 <inputs>
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
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24 <expand macro="input_sequences_filenames" />
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
iuc
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25 <expand macro="input_countgraph_filename" />
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
iuc
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26 </inputs>
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
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27 <outputs>
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
iuc
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28 <collection name="sequence_files" type="list">
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
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29 <discover_datasets pattern="__name__" directory="output" />
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
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30 </collection>
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
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31 </outputs>
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
iuc
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32 <tests>
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
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33 <test>
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
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34 <param name="inputs" value="test-abund-read-2.fa" />
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
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35 <param name="input_countgraph_filename" value="test-abund-read-2.large.oxlicg" ftype="oxlicg" />
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
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36 <output_collection name="sequence_files">
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
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37 <element name="sequence-0.below" file="test-abund-read-2.fa.below" />
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
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38 </output_collection>
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
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39 </test>
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
iuc
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40 </tests>
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
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41 <help><![CDATA[
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
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42 Trims sequences at the first kmer with abundance above 50.
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
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43
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
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44 @HELP_FOOTER@
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
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45 ]]></help>
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
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46 <citations>
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
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47 <expand macro="software-citation" />
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
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48 <expand macro="counting-citation" />
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
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49 </citations>
0187f18785a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 37727831a2630b7a7d4fb033366cbd772c3086c8
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50 </tool>