Mercurial > repos > iuc > khmer_partition

annotate do-partition.xml @ 8:de6ba32d6021 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"
author iuc
date Wed, 18 Dec 2019 20:57:16 +0000
parents c72a41a26c7d
children 94e459e086bb
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de6ba32d6021 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"
iuc
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1 <tool id="khmer_partition" name="khmer: Sequence partition all-in-one" version="@WRAPPER_VERSION@@TOOL_VERSION@">
de6ba32d6021 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"
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2 <description>Load, partition, and annotate sequences</description>
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3 <macros>
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4 <token name="@BINARY@">do-partition.py</token>
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5 <import>macros.xml</import>
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
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6 </macros>
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
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7 <expand macro="requirements" />
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8 <expand macro="stdio" />
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
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9 <expand macro="version" />
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10 <command><![CDATA[
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de6ba32d6021 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"
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11 set -u &&
de6ba32d6021 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"
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12 @LINK_SEQUENCES@
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13 mkdir -p output && cd output &&
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
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14 @BINARY@
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15 @TABLEPARAMS@
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
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16 @THREADS@
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
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17 output
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18 @USE_SEQUENCES@
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19 ]]>
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20 </command>
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21 <inputs>
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22 <expand macro="input_sequences_filenames" />
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23 <expand macro="tableinputs" />
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24 </inputs>
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25 <outputs>
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26 <data name="information" format="txt" from_work_dir="output.info" label="${tool.name} on ${on_string}: summary." />
de6ba32d6021 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"
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27 <expand macro="output_sequences" extension="part"/>
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28 </outputs>
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29 <tests>
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30 <test>
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
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31 <param name="inputs" value="random-20-a.fa"/>
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de6ba32d6021 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"
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32 <output_collection name="sequences" type="list">
de6ba32d6021 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"
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33 <element name="random-20-a.fa" file="random-20-a.fa.part" />
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69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
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34 </output_collection>
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
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35 </test>
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36 </tests>
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
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37 <help><![CDATA[
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38 Load in a set of sequences, partition them, merge the partitions, and
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
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39 annotate the original sequences files with the partition information.
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40
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41 This script combines the functionality of `load-graph.py`,
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
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42 `partition-graph.py`, `merge-partitions.py`, and
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43 `annotate-partitions.py` into one script. This is convenient
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
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44 but should probably not be used for large data sets, because
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
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45 `do-partition.py` doesn't provide save/resume functionality.
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46
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47 ]]>
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48 </help>
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49 <citations>
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50 <expand macro="software-citation" />
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51 <expand macro="graph-citation" />
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52 </citations>
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53 </tool>