Mercurial > repos > iuc > khmer_partition
annotate do-partition.xml @ 8:5a0fa29951ae draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7599ef16dc8b83ee49236ed5bb229260c969b0ab
author | iuc |
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date | Mon, 17 Jun 2024 11:46:46 +0000 |
parents | b7429b53be2a |
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b7429b53be2a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 14ea2dc5ef36219c908ed64b256794711ce7b902"
iuc
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1 <tool id="khmer_partition" name="khmer: Sequence partition all-in-one" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> |
6
e562293ee5ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"
iuc
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2 <description>Load, partition, and annotate sequences</description> |
8
5a0fa29951ae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7599ef16dc8b83ee49236ed5bb229260c969b0ab
iuc
parents:
7
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3 <expand macro="bio_tools"/> |
0
1413823dce99
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff
changeset
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4 <macros> |
1413823dce99
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
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5 <token name="@BINARY@">do-partition.py</token> |
1413823dce99
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff
changeset
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6 <import>macros.xml</import> |
1413823dce99
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff
changeset
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7 </macros> |
1413823dce99
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff
changeset
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8 <expand macro="requirements" /> |
1413823dce99
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff
changeset
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9 <expand macro="stdio" /> |
1413823dce99
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff
changeset
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10 <expand macro="version" /> |
1413823dce99
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
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11 <command><![CDATA[ |
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e562293ee5ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"
iuc
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12 set -u && |
e562293ee5ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"
iuc
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13 @LINK_SEQUENCES@ |
0
1413823dce99
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
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14 mkdir -p output && cd output && |
1413823dce99
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff
changeset
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15 @BINARY@ |
1413823dce99
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff
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16 @TABLEPARAMS@ |
1413823dce99
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff
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17 @THREADS@ |
1413823dce99
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
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18 output |
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e562293ee5ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"
iuc
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19 @USE_SEQUENCES@ |
0
1413823dce99
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff
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20 ]]> |
1413823dce99
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff
changeset
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21 </command> |
1413823dce99
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff
changeset
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22 <inputs> |
1413823dce99
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff
changeset
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23 <expand macro="input_sequences_filenames" /> |
1413823dce99
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff
changeset
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24 <expand macro="tableinputs" /> |
1413823dce99
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff
changeset
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25 </inputs> |
1413823dce99
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff
changeset
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26 <outputs> |
6
e562293ee5ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"
iuc
parents:
2
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27 <data name="information" format="txt" from_work_dir="output.info" label="${tool.name} on ${on_string}: summary." /> |
e562293ee5ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"
iuc
parents:
2
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28 <expand macro="output_sequences" extension="part"/> |
0
1413823dce99
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff
changeset
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29 </outputs> |
1413823dce99
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff
changeset
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30 <tests> |
1413823dce99
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff
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31 <test> |
1413823dce99
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff
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32 <param name="inputs" value="random-20-a.fa"/> |
6
e562293ee5ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"
iuc
parents:
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33 <output_collection name="sequences" type="list"> |
e562293ee5ec
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"
iuc
parents:
2
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34 <element name="random-20-a.fa" file="random-20-a.fa.part" /> |
0
1413823dce99
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff
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35 </output_collection> |
1413823dce99
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff
changeset
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36 </test> |
1413823dce99
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
diff
changeset
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37 </tests> |
1413823dce99
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
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38 <help><![CDATA[ |
1413823dce99
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
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changeset
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39 Load in a set of sequences, partition them, merge the partitions, and |
1413823dce99
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
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40 annotate the original sequences files with the partition information. |
1413823dce99
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
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41 |
1413823dce99
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
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42 This script combines the functionality of `load-graph.py`, |
1413823dce99
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
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43 `partition-graph.py`, `merge-partitions.py`, and |
1413823dce99
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
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44 `annotate-partitions.py` into one script. This is convenient |
1413823dce99
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
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45 but should probably not be used for large data sets, because |
1413823dce99
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
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46 `do-partition.py` doesn't provide save/resume functionality. |
2
09779cc94f94
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit bfa8bda732de882f6fa5f5375f8468ad229cceea
iuc
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0
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47 |
0
1413823dce99
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
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48 ]]> |
1413823dce99
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
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49 </help> |
1413823dce99
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
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50 <citations> |
1413823dce99
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
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51 <expand macro="software-citation" /> |
1413823dce99
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
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52 <expand macro="graph-citation" /> |
1413823dce99
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
parents:
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53 </citations> |
1413823dce99
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
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54 </tool> |