Mercurial > repos > crusoe > khmer
annotate do-partition.xml @ 59:08a599cf71d0
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| author | Michael R. Crusoe <mcrusoe@msu.edu> |
|---|---|
| date | Mon, 18 Aug 2014 07:02:05 -0400 |
| parents | 2c03c19808c5 |
| children | fe697e0cb24a |
| rev | line source |
|---|---|
| 45 | 1 <tool id="gedlab-khmer-do-partition" |
| 2 name="Sequence partition all-in-one" | |
| 3 version="1.1-1" | |
| 4 force_history_refresh="true"> | |
| 5 | |
| 6 <description> | |
| 7 Load, partition, and annotate FAST[AQ] sequences | |
| 8 </description> | |
| 9 <macros> | |
| 10 <token name="@BINARY@">do-parition.py</token> | |
| 11 <import>macros.xml</import> | |
| 12 </macros> | |
| 13 <expand macro="requirements" /> | |
| 14 <command> | |
| 15 mkdir -p output; | |
| 16 @BINARY@ | |
| 17 @TABLEPARAMS@ | |
| 18 @THREADS@ | |
| 19 output | |
| 20 #for input in $inputs | |
| 21 $input | |
| 22 #end for ; | |
| 23 mv output.info $infomation ; | |
| 24 mv *.part output/ | |
| 25 </command> | |
| 26 | |
| 27 <inputs> | |
| 28 <expand macro="input_sequences_filenames" /> | |
|
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3d65329a491d
PEP8 & params for do-partition
Michael R. Crusoe <mcrusoe@msu.edu>
parents:
45
diff
changeset
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29 <param name="ksize" |
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3d65329a491d
PEP8 & params for do-partition
Michael R. Crusoe <mcrusoe@msu.edu>
parents:
45
diff
changeset
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30 type="integer" |
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3d65329a491d
PEP8 & params for do-partition
Michael R. Crusoe <mcrusoe@msu.edu>
parents:
45
diff
changeset
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31 value="20" |
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3d65329a491d
PEP8 & params for do-partition
Michael R. Crusoe <mcrusoe@msu.edu>
parents:
45
diff
changeset
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32 label="ksize" |
| 59 | 33 help="k-mer size to use (--ksize/-k)" /> |
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3d65329a491d
PEP8 & params for do-partition
Michael R. Crusoe <mcrusoe@msu.edu>
parents:
45
diff
changeset
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34 <param name="n_tables" |
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3d65329a491d
PEP8 & params for do-partition
Michael R. Crusoe <mcrusoe@msu.edu>
parents:
45
diff
changeset
|
35 type="integer" |
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3d65329a491d
PEP8 & params for do-partition
Michael R. Crusoe <mcrusoe@msu.edu>
parents:
45
diff
changeset
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36 min="1" |
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3d65329a491d
PEP8 & params for do-partition
Michael R. Crusoe <mcrusoe@msu.edu>
parents:
45
diff
changeset
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37 value="4" |
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3d65329a491d
PEP8 & params for do-partition
Michael R. Crusoe <mcrusoe@msu.edu>
parents:
45
diff
changeset
|
38 label="n_tables" |
| 59 | 39 help="number of tables to use (--n_tables/-N)" /> |
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3d65329a491d
PEP8 & params for do-partition
Michael R. Crusoe <mcrusoe@msu.edu>
parents:
45
diff
changeset
|
40 <param name="tablesize_specific" |
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3d65329a491d
PEP8 & params for do-partition
Michael R. Crusoe <mcrusoe@msu.edu>
parents:
45
diff
changeset
|
41 type="text" |
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3d65329a491d
PEP8 & params for do-partition
Michael R. Crusoe <mcrusoe@msu.edu>
parents:
45
diff
changeset
|
42 label="tablesize" |
| 59 | 43 help="lower bound on the tablesize to use (--min-tablesize/-x)" /> |
| 45 | 44 </inputs> |
| 45 <outputs> | |
| 46 <data name="information" | |
| 47 format="text" | |
| 48 label="${tool.name} summary for #echo ','.join(map(str, $inputs ))#" /> | |
| 49 <expand macro="output_sequences" /> | |
| 50 </outputs> | |
| 59 | 51 <expand macro="stdio" /> |
| 45 | 52 <!-- <tests> |
| 53 <test interactor="api"> | |
| 54 <conditional name="parameters"> | |
| 55 <param name="type" value="specific" /> | |
| 56 <param name="inputs" value="test-abund-read-2.fa"/> | |
| 57 <param name="cutoff" value="1" /> | |
| 58 <param name="ksize" value="17" /> | |
| 59 </conditional> | |
| 60 <output name="output"> | |
| 61 <discover_dataset name="test-abund-read-2.fa.keep"> | |
| 62 <assert_contents> | |
| 63 <has_line_matching expression="GGTTGACGGGGCTCAGGGGG" /> | |
| 64 </assert_contents> | |
| 65 </discover_dataset> | |
| 66 </output> | |
| 67 </test> | |
| 68 <test interactor="api"> | |
| 69 <param name="inputs" value="test-abund-read-2.fa" /> | |
| 70 <param name="cutoff" value="2" /> | |
| 71 <param name="ksize" value="17" /> | |
| 72 <output name="output"> | |
| 73 <discover_dataset name="test-abund-read-2.fa.keep"> | |
| 74 <assert_contents> | |
| 75 <has_line_matching expression="GGTTGACGGGGCTCAGGGGG" /> | |
| 76 <has_line_matching expression="GGTTGACGGGGCTCAGGG" /> | |
| 77 </assert_contents> | |
| 78 </discover_dataset> | |
| 79 </output> | |
| 80 </test> | |
| 81 <test interactor="api"> | |
| 82 <param name="inputs" value="test-abund-read-paired.fa" /> | |
| 83 <param name="cutoff" value="1" /> | |
| 84 <param name="ksize" value="17" /> | |
| 85 <param name="paired" value="true" /> | |
| 86 <output name="output"> | |
| 87 <discover_dataset name="test-abund-read-paired.fa.keep"> | |
| 88 <assert_contents> | |
| 89 <has_line_matching expression="GGTTGACGGGGCTCAGGGGG" /> | |
| 90 <has_line_matching expression="GGTTGACGGGGCTCAGGG" /> | |
| 91 </assert_contents> | |
| 92 </discover_dataset> | |
| 93 </output> | |
| 94 </test> | |
| 95 | |
| 96 </tests> | |
| 97 --> | |
| 53 | 98 <citations> |
| 99 <expand macro="software-citation" /> | |
| 100 <expand macro="graph-citation" /> | |
| 101 </citations> | |
| 45 | 102 <!-- [OPTIONAL] Help displayed in Galaxy --> |
| 103 <!-- | |
| 104 <help> | |
| 105 </help> | |
| 106 --> | |
| 107 </tool> |