Mercurial > repos > iuc > khmer_partition

annotate do-partition.xml @ 10:02bc1ef43ef7 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
author iuc
date Tue, 31 Aug 2021 09:12:27 +0000
parents 94e459e086bb
children bd185cf6bd34
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94e459e086bb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 14ea2dc5ef36219c908ed64b256794711ce7b902"
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1 <tool id="khmer_partition" name="khmer: Sequence partition all-in-one" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>Load, partition, and annotate sequences</description>
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3 <expand macro="bio_tools"/>
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4 <macros>
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5 <token name="@BINARY@">do-partition.py</token>
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
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6 <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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7 </macros>
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
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8 <expand macro="requirements" />
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
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9 <expand macro="stdio" />
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
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10 <expand macro="version" />
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11 <command><![CDATA[
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12 set -u &&
de6ba32d6021 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"
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13 @LINK_SEQUENCES@
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14 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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15 @BINARY@
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16 @TABLEPARAMS@
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17 @THREADS@
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18 output
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19 @USE_SEQUENCES@
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20 ]]>
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21 </command>
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
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22 <inputs>
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23 <expand macro="input_sequences_filenames" />
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24 <expand macro="tableinputs" />
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25 </inputs>
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
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26 <outputs>
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27 <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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28 <expand macro="output_sequences" extension="part"/>
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29 </outputs>
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30 <tests>
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31 <test>
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
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32 <param name="inputs" value="random-20-a.fa"/>
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33 <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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34 <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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35 </output_collection>
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36 </test>
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37 </tests>
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
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38 <help><![CDATA[
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39 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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40 annotate the original sequences files with the partition information.
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
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41
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42 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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43 `partition-graph.py`, `merge-partitions.py`, and
69180013f797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
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44 `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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45 but should probably not be used for large data sets, because
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46 `do-partition.py` doesn't provide save/resume functionality.
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47
0
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48 ]]>
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49 </help>
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50 <citations>
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51 <expand macro="software-citation" />
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52 <expand macro="graph-citation" />
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53 </citations>
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54 </tool>