Mercurial > repos > crusoe > khmer
annotate macros.xml @ 59:08a599cf71d0
Bjoern's suggestions
| author | Michael R. Crusoe <mcrusoe@msu.edu> |
|---|---|
| date | Mon, 18 Aug 2014 07:02:05 -0400 |
| parents | be2f355d6841 |
| children | fe697e0cb24a |
| rev | line source |
|---|---|
| 10 | 1 <macros> |
| 2 <xml name="requirements"> | |
| 3 <requirements> | |
| 4 <!-- <requirement type="binary">@BINARY@</requirement> --> | |
| 5 <requirement type="package" version="1.1">khmer</requirement> | |
| 6 </requirements> | |
| 7 <version_command>@BINARY@ --version</version_command> | |
| 8 </xml> | |
| 19 | 9 <token name="@TABLEPARAMS@">#if $parameters.type == "simple" |
| 21 | 10 --ksize=20 |
| 11 --n_tables=4 | |
| 12 --min-tablesize=$parameters.tablesize | |
| 10 | 13 #else |
| 21 | 14 --ksize=$parameters.ksize |
| 15 --n_tables=$parameters.n_tables | |
| 16 --min-tablesize=$parameters.tablesize_specific | |
|
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Include countingtable output for a-d-s
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17 #end if</token> |
| 59 | 18 <token name="@THREADS@">--threads \${GALAXY_SLOTS:-4}</token> |
| 10 | 19 <xml name="tableinputs"> |
| 20 <conditional name="parameters"> | |
| 21 <param name="type" | |
| 22 type="select" | |
| 23 label="Advanced Parameters" | |
| 13 | 24 help="ksize, n_tables, a specific tablesize" > |
| 10 | 25 <option value="simple" |
| 26 selected="true"> | |
| 27 Hide | |
| 28 </option> | |
| 29 <option value="specific"> | |
| 30 Show | |
| 31 </option> | |
| 32 </param> | |
| 33 <when value="simple"> | |
| 13 | 34 <param name="tablesize" |
| 10 | 35 type="select" |
| 36 label="Sample Type" | |
| 37 display="radio"> | |
| 38 <option value="1e9" | |
| 39 selected="true"> | |
| 40 Microbial Genome | |
| 41 </option> | |
| 42 <option value="2e9"> | |
| 43 Animal Transcriptome | |
| 44 </option> | |
| 45 <option value="4e9"> | |
| 59 | 46 Small Animal Genome or |
| 47 Low-Diversity Metagenome | |
| 10 | 48 </option> |
| 49 <option value="16e9"> | |
| 50 Large Animal Genome | |
| 51 </option> | |
| 52 </param> | |
| 53 </when> | |
| 54 <when value="specific"> | |
| 55 <param name="ksize" | |
| 56 type="integer" | |
| 57 value="20" | |
| 58 label="ksize" | |
| 59 help="k-mer size to use" /> | |
| 13 | 60 <param name="n_tables" |
| 10 | 61 type="integer" |
| 62 min="1" | |
| 63 value="4" | |
| 13 | 64 label="n_tables" |
| 65 help="number of tables to use" /> | |
| 16 | 66 <param name="tablesize_specific" |
| 10 | 67 type="text" |
| 13 | 68 label="tablesize" |
| 69 help="lower bound on the tablesize to use" /> | |
| 10 | 70 </when> |
| 71 </conditional> | |
| 72 </xml> | |
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cec78b574760
Actually import the macros
Michael R. Crusoe <mcrusoe@msu.edu>
parents:
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changeset
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73 <xml name="input_sequences_filenames"> |
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cec78b574760
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Michael R. Crusoe <mcrusoe@msu.edu>
parents:
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74 <param name="inputs" |
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cec78b574760
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Michael R. Crusoe <mcrusoe@msu.edu>
parents:
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75 multiple="true" |
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cec78b574760
Actually import the macros
Michael R. Crusoe <mcrusoe@msu.edu>
parents:
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76 type="data" |
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cec78b574760
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Michael R. Crusoe <mcrusoe@msu.edu>
parents:
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77 format="fasta,fastq,fastqsanger,fastqsolexa,fastqillumina" |
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cec78b574760
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Michael R. Crusoe <mcrusoe@msu.edu>
parents:
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78 label="FAST[AQ] file(s)" |
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cec78b574760
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parents:
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79 help="Put in order of precedence such as longest reads first." /> |
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cec78b574760
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Michael R. Crusoe <mcrusoe@msu.edu>
parents:
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changeset
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80 </xml> |
| 10 | 81 <xml name="input_sequence_filename"> |
| 82 <param name="input_sequence_filename" | |
| 83 type="data" | |
| 84 format="fasta,fastq,fastqsanger,fastqsolexa,fastqillumina" | |
| 85 label="FAST[AQ] file(s)" /> | |
| 86 </xml> | |
| 87 <xml name="input_counting_table_filename"> | |
| 88 <param name="input_counting_table_filename" | |
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Set filetype for countingtable input
Michael R. Crusoe <mcrusoe@msu.edu>
parents:
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diff
changeset
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89 type="data" |
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46d13bbb21f2
Set filetype for countingtable input
Michael R. Crusoe <mcrusoe@msu.edu>
parents:
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diff
changeset
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90 format="ct" |
| 10 | 91 label="the k-mer counting table to query" |
| 92 help="The abundances of the k-mers in the input nucleotide sequence file will be calculated using the kmer counts in this k-mer counting table." /> | |
| 93 </xml> | |
| 94 <xml name="abundance-histogram-output"> | |
| 95 <data name="output_histogram_filename" | |
| 96 format="text" | |
| 97 label="${tool.name} k-mer abundance histogram. The | |
| 98 columns are: (1) k-mer abundance, (2) k-mer count, (3) | |
| 99 cumulative count, (4) fraction of total distinct | |
| 100 k-mers."> | |
| 101 </data> | |
| 102 </xml> | |
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cec78b574760
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Michael R. Crusoe <mcrusoe@msu.edu>
parents:
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diff
changeset
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103 <xml name="output_sequences"> |
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cec78b574760
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Michael R. Crusoe <mcrusoe@msu.edu>
parents:
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104 <data name="output" |
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cec78b574760
Actually import the macros
Michael R. Crusoe <mcrusoe@msu.edu>
parents:
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changeset
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105 format="input" |
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cec78b574760
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Michael R. Crusoe <mcrusoe@msu.edu>
parents:
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changeset
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106 label="${tool.name} processed nucleotide sequence file"> |
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cec78b574760
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Michael R. Crusoe <mcrusoe@msu.edu>
parents:
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changeset
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107 <discover_datasets pattern="__name__" directory="output" visible="true"/> |
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cec78b574760
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Michael R. Crusoe <mcrusoe@msu.edu>
parents:
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changeset
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108 </data> |
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cec78b574760
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Michael R. Crusoe <mcrusoe@msu.edu>
parents:
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109 </xml> |
| 45 | 110 <xml name="output_sequences_single"> |
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47
96da0e8a98e4
Fix diginorm output; filter-abund cheetah error
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parents:
45
diff
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111 <data name="output" |
| 45 | 112 format="input" |
| 113 label="${tool.name} processed nucleotide sequence file" /> | |
| 114 </xml> | |
| 26 | 115 <xml name="input_zero"> |
| 116 <param name="zero" | |
| 117 type="boolean" | |
| 118 truevalue="" | |
| 119 falsevalue="--no-zero" | |
| 120 checked="true" | |
| 59 | 121 help="Output zero count bins (--no-zero)" /> |
| 26 | 122 </xml> |
| 55 | 123 <xml name="software-citation"> |
| 58 | 124 <citation type="bibtex">@article{khmer2014, |
| 125 author = "Crusoe, Michael and Edvenson, Greg and Fish, Jordan and Howe, | |
| 126 Adina and McDonald, Eric and Nahum, Joshua and Nanlohy, Kaben and | |
| 127 Ortiz-Zuazaga, Humberto and Pell, Jason and Simpson, Jared and Scott, Camille | |
| 128 and Srinivasan, Ramakrishnan Rajaram and Zhang, Qingpeng and Brown, C. Titus", | |
| 129 title = "The khmer software package: enabling efficient sequence | |
| 130 analysis", | |
| 131 year = "2014", | |
| 132 month = "04", | |
| 133 publisher = "Figshare", | |
| 134 url = "http://dx.doi.org/10.6084/m9.figshare.979190" | |
| 135 }</citation> | |
| 55 | 136 </xml> |
| 137 <xml name="diginorm-citation"> | |
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Add citation for count-median; change diginorm to @unpublished
Michael R. Crusoe <mcrusoe@msu.edu>
parents:
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138 <citation type="bibtex">@unpublished{diginorm, |
| 58 | 139 author = "Brown, C Titus and Howe, Adina and Zhang, Qingpeng and Pyrkosz, |
| 140 Alexis B and Brom, Timothy H", | |
| 141 title = "A Reference-Free Algorithm for Computational Normalization of | |
| 142 Shotgun Sequencing Data", | |
| 143 year = "2012", | |
| 144 eprint = "arXiv:1203.4802", | |
| 145 url = "http://arxiv.org/abs/1203.4802", | |
| 55 | 146 }</citation></xml> |
| 147 <xml name="graph-citation"> | |
| 148 <citation type="doi">10.1073/pnas.1121464109</citation> | |
| 149 </xml> | |
| 150 <xml name="counting-citation"> | |
| 151 <citation type="doi">10.1371/journal.pone.0101271</citation> | |
| 152 </xml> | |
| 59 | 153 <xml name="stdio"> |
| 154 <stdio> | |
| 155 <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR --> | |
| 156 <exit_code range="1:" | |
| 157 level="fatal" /> | |
| 158 </stdio> | |
| 159 </xml> | |
| 53 | 160 </macros> |