Mercurial > repos > crusoe > khmer
annotate normalize-by-median.xml @ 10:d00e18a0a3f2
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| author | Michael R. Crusoe <mcrusoe@msu.edu> |
|---|---|
| date | Sun, 29 Jun 2014 09:22:32 -0400 |
| parents | 50e354731c85 |
| children | cec78b574760 |
| rev | line source |
|---|---|
| 0 | 1 <tool id="gedlab-khmer-normalize-by-median" |
| 2 name="Normalize By Median" | |
| 7 | 3 version="1.1-4" |
| 0 | 4 force_history_refresh="true"> |
| 5 | |
| 6 <description> | |
| 7 Filters a fastq/fasta file using digital normalization via | |
| 8 median k-mer abundances. | |
| 9 </description> | |
| 10 | |
| 11 <requirements> | |
| 12 <requirement | |
| 3 | 13 type="package" |
| 0 | 14 version="1.1"> |
| 15 khmer | |
| 16 </requirement> | |
| 17 </requirements> | |
| 18 | |
| 19 <version_command> | |
| 20 normalize-by-median.py --version | |
| 21 </version_command> | |
| 22 | |
| 23 <command> | |
| 24 mkdir output; | |
| 25 cd output; | |
| 26 normalize-by-median.py | |
| 27 $paired_switch | |
| 28 #if $parameters.type == "simple" | |
| 29 --ksize=20 | |
| 30 --n_tables=4 | |
|
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--tablesize -> --min-tablesize
Michael R. Crusoe <mcrusoe@msu.edu>
parents:
3
diff
changeset
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31 --min-tablesize=$parameters.tablesize |
| 0 | 32 --cutoff=20 |
| 33 #else | |
| 34 --ksize=$parameters.ksize | |
| 35 --n_tables=$parameters.n_tables | |
|
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0ce1807835d0
--tablesize -> --min-tablesize
Michael R. Crusoe <mcrusoe@msu.edu>
parents:
3
diff
changeset
|
36 --min-tablesize=$parameters.tablesize_specific |
| 0 | 37 --cutoff=$parameters.cutoff |
| 38 #end if | |
| 39 #if $save_countingtable | |
| 40 --savetable=$countingtable | |
| 41 #end if | |
| 42 #if $countingtable_to_load | |
| 43 --loadtable=$countingtable_to_load | |
| 44 #end if | |
| 45 #for input in $inputs | |
| 46 $input | |
| 47 #end for | |
| 48 </command> | |
| 49 | |
| 50 <inputs> | |
| 51 <param name="inputs" | |
| 52 multiple="true" | |
| 53 type="data" | |
| 54 format="fasta,fastq,fastqsanger,fastqsolexa,fastqillumina" | |
| 55 label="FAST[AQ] file(s)" | |
| 56 help="Put in order of precedence such as longest reads first." /> | |
| 57 | |
| 58 <param name="paired_switch" | |
| 59 type="boolean" | |
| 60 checked="false" | |
| 61 truevalue="--paired" | |
| 62 falsevalue="" | |
| 63 label="Are the inputs interleaved paired ends?" | |
| 64 help="If so, then selecting this option will process the paired ends together." /> | |
| 65 | |
| 66 <param name="countingtable_to_load" | |
| 67 type="data" | |
| 68 optional="true" | |
| 69 label="an optional k-mer counting table to load" | |
| 70 help="The inputs file(s) will be processed using the kmer counts in the specified k-mer counting table file as a starting point." /> | |
| 71 | |
| 72 <param name="save_countingtable" | |
| 73 type="boolean" | |
| 74 label="Save the k-mer counting table(s) in a file" | |
| 75 help="" /> | |
| 76 | |
| 77 <conditional name="parameters"> | |
| 78 <param name="type" | |
| 79 type="select" | |
| 80 label="Advanced Parameters" | |
| 81 help="ksize, n_tabless, a specific tablesize, cutoff" > | |
| 82 <option value="simple" | |
| 83 selected="true"> | |
| 84 Hide | |
| 85 </option> | |
| 86 <option value="specific"> | |
| 87 Show | |
| 88 </option> | |
| 89 </param> | |
| 90 <when value="simple"> | |
| 91 <param name="tablesize" | |
| 92 type="select" | |
| 93 label="Sample Type" | |
| 94 display="radio"> | |
| 95 <option value="1e9" | |
| 96 selected="true"> | |
| 97 Microbial Genome | |
| 98 </option> | |
| 99 <option value="2e9"> | |
| 100 Animal Transcriptome | |
| 101 </option> | |
| 102 <option value="4e9"> | |
| 103 Small Animal Genome or Low-Diversity Metagenome | |
| 104 </option> | |
| 105 <option value="16e9"> | |
| 106 Large Animal Genome | |
| 107 </option> | |
| 108 </param> | |
| 109 </when> | |
| 110 <when value="specific"> | |
| 111 <param name="ksize" | |
| 112 type="integer" | |
| 113 value="20" | |
| 114 label="ksize" | |
| 115 help="k-mer size to use" /> | |
| 6 | 116 <param name="n_tables" |
| 0 | 117 type="integer" |
| 118 min="1" | |
| 119 value="4" | |
| 120 label="n_tables" | |
| 121 help="number of k-mer counting tables to use" /> | |
| 8 | 122 <param name="tablesize_specific" |
| 0 | 123 type="text" |
| 124 label="tablesize" | |
| 125 help="lower bound on the tablesize to use" /> | |
| 126 <param name="cutoff" | |
| 127 type="integer" | |
| 128 min="1" | |
| 129 value="20" | |
| 130 label="cutoff" /> | |
| 131 </when> | |
| 132 </conditional> | |
| 133 </inputs> | |
| 134 <outputs> | |
|
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50e354731c85
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Michael R. Crusoe <mcrusoe@msu.edu>
parents:
8
diff
changeset
|
135 <data name="countingtable" |
| 0 | 136 format="data" |
| 137 label="${tool.name} k-mer counting table from #echo ', '.join(map(str, $inputs ))#"> | |
|
9
50e354731c85
default to visible outputs
Michael R. Crusoe <mcrusoe@msu.edu>
parents:
8
diff
changeset
|
138 <filter>save_countingtable == True</filter> |
| 0 | 139 </data> |
| 140 <data name="outputs" | |
| 141 format="input" | |
| 142 label="${tool.name} processed nucleotide sequence file"> | |
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9
50e354731c85
default to visible outputs
Michael R. Crusoe <mcrusoe@msu.edu>
parents:
8
diff
changeset
|
143 <discover_datasets pattern="__name__" directory="output" visible="true"/> |
| 0 | 144 </data> |
| 145 | |
| 146 </outputs> | |
| 147 <stdio> | |
| 148 <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR --> | |
| 149 <exit_code range="1:" | |
| 150 level="fatal" /> | |
| 151 </stdio> | |
| 152 | |
| 153 <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin --> | |
| 154 <tests> | |
| 155 <!-- [HELP] Test files have to be in the ~/test-data directory | |
| 156 <test> | |
| 157 <param name="input" value="input_test.tab" /> | |
| 158 <param name="int" value="10" /> | |
| 159 <output name="output" file="output_test.txt" /> | |
| 160 </test> --> | |
| 161 <!-- [HELP] Multiple tests can be defined with different parameters --> | |
| 162 <!-- | |
| 163 <test> | |
| 164 </test> | |
| 165 --> | |
| 166 </tests> | |
| 167 | |
| 168 <!-- [OPTIONAL] Help displayed in Galaxy --> | |
| 169 <!-- | |
| 170 <help> | |
| 171 </help> | |
| 172 --> | |
| 173 </tool> |