Mercurial > repos > crusoe > khmer
annotate macros.xml @ 60:fe697e0cb24a draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit d8e0950d53e504e02ee5db43c0804142b14d7fd2-dirty
| author | crusoe |
|---|---|
| date | Tue, 07 Jul 2015 11:59:39 -0400 |
| parents | 08a599cf71d0 |
| children |
| rev | line source |
|---|---|
| 10 | 1 <macros> |
| 2 <xml name="requirements"> | |
| 3 <requirements> | |
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fe697e0cb24a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit d8e0950d53e504e02ee5db43c0804142b14d7fd2-dirty
crusoe
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diff
changeset
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4 <requirement type="package" version="2.0rc1">khmer</requirement> |
| 10 | 5 </requirements> |
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60
fe697e0cb24a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit d8e0950d53e504e02ee5db43c0804142b14d7fd2-dirty
crusoe
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6 </xml> |
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fe697e0cb24a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit d8e0950d53e504e02ee5db43c0804142b14d7fd2-dirty
crusoe
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7 <xml name="version"> |
| 10 | 8 <version_command>@BINARY@ --version</version_command> |
| 9 </xml> | |
| 19 | 10 <token name="@TABLEPARAMS@">#if $parameters.type == "simple" |
| 21 | 11 --ksize=20 |
| 12 --n_tables=4 | |
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60
fe697e0cb24a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit d8e0950d53e504e02ee5db43c0804142b14d7fd2-dirty
crusoe
parents:
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diff
changeset
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13 --max-tablesize=$parameters.tablesize |
| 10 | 14 #else |
| 21 | 15 --ksize=$parameters.ksize |
| 16 --n_tables=$parameters.n_tables | |
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60
fe697e0cb24a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit d8e0950d53e504e02ee5db43c0804142b14d7fd2-dirty
crusoe
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diff
changeset
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17 --max-tablesize="$parameters.tablesize_specific" |
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18 #end if</token> |
| 59 | 19 <token name="@THREADS@">--threads \${GALAXY_SLOTS:-4}</token> |
| 10 | 20 <xml name="tableinputs"> |
| 21 <conditional name="parameters"> | |
| 22 <param name="type" | |
| 23 type="select" | |
| 24 label="Advanced Parameters" | |
| 13 | 25 help="ksize, n_tables, a specific tablesize" > |
| 10 | 26 <option value="simple" |
| 27 selected="true"> | |
| 28 Hide | |
| 29 </option> | |
| 30 <option value="specific"> | |
| 31 Show | |
| 32 </option> | |
| 33 </param> | |
| 34 <when value="simple"> | |
| 13 | 35 <param name="tablesize" |
| 10 | 36 type="select" |
| 37 label="Sample Type" | |
| 38 display="radio"> | |
| 39 <option value="1e9" | |
| 40 selected="true"> | |
| 41 Microbial Genome | |
| 42 </option> | |
| 43 <option value="2e9"> | |
| 44 Animal Transcriptome | |
| 45 </option> | |
| 46 <option value="4e9"> | |
| 59 | 47 Small Animal Genome or |
| 48 Low-Diversity Metagenome | |
| 10 | 49 </option> |
| 50 <option value="16e9"> | |
| 51 Large Animal Genome | |
| 52 </option> | |
| 53 </param> | |
| 54 </when> | |
| 55 <when value="specific"> | |
| 56 <param name="ksize" | |
| 57 type="integer" | |
| 58 value="20" | |
| 59 label="ksize" | |
| 60 help="k-mer size to use" /> | |
| 13 | 61 <param name="n_tables" |
| 10 | 62 type="integer" |
| 63 min="1" | |
| 64 value="4" | |
| 13 | 65 label="n_tables" |
| 66 help="number of tables to use" /> | |
| 16 | 67 <param name="tablesize_specific" |
| 10 | 68 type="text" |
| 13 | 69 label="tablesize" |
| 70 help="lower bound on the tablesize to use" /> | |
| 10 | 71 </when> |
| 72 </conditional> | |
| 73 </xml> | |
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74 <xml name="input_sequences_filenames"> |
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75 <param name="inputs" |
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76 multiple="true" |
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77 type="data" |
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78 format="fasta,fastq,fastqsanger,fastqsolexa,fastqillumina" |
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79 label="FAST[AQ] file(s)" |
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80 help="Put in order of precedence such as longest reads first." /> |
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81 </xml> |
| 10 | 82 <xml name="input_sequence_filename"> |
| 83 <param name="input_sequence_filename" | |
| 84 type="data" | |
| 85 format="fasta,fastq,fastqsanger,fastqsolexa,fastqillumina" | |
| 86 label="FAST[AQ] file(s)" /> | |
| 87 </xml> | |
| 88 <xml name="input_counting_table_filename"> | |
| 89 <param name="input_counting_table_filename" | |
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90 type="data" |
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91 format="ct" |
| 10 | 92 label="the k-mer counting table to query" |
| 93 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." /> | |
| 94 </xml> | |
| 95 <xml name="abundance-histogram-output"> | |
| 96 <data name="output_histogram_filename" | |
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fe697e0cb24a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit d8e0950d53e504e02ee5db43c0804142b14d7fd2-dirty
crusoe
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97 format="txt" |
| 10 | 98 label="${tool.name} k-mer abundance histogram. The |
| 99 columns are: (1) k-mer abundance, (2) k-mer count, (3) | |
| 100 cumulative count, (4) fraction of total distinct | |
| 101 k-mers."> | |
| 102 </data> | |
| 103 </xml> | |
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104 <xml name="output_sequences"> |
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105 <data name="output" |
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60
fe697e0cb24a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit d8e0950d53e504e02ee5db43c0804142b14d7fd2-dirty
crusoe
parents:
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diff
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106 format_source="inputs" |
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107 label="${tool.name} processed nucleotide sequence file"> |
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108 <discover_datasets pattern="__name__" directory="output" visible="true"/> |
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109 </data> |
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110 </xml> |
| 45 | 111 <xml name="output_sequences_single"> |
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112 <data name="output" |
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60
fe697e0cb24a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit d8e0950d53e504e02ee5db43c0804142b14d7fd2-dirty
crusoe
parents:
59
diff
changeset
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113 format_source="input_sequence_filename" |
| 45 | 114 label="${tool.name} processed nucleotide sequence file" /> |
| 115 </xml> | |
| 26 | 116 <xml name="input_zero"> |
| 117 <param name="zero" | |
| 118 type="boolean" | |
| 119 truevalue="" | |
| 120 falsevalue="--no-zero" | |
| 121 checked="true" | |
| 59 | 122 help="Output zero count bins (--no-zero)" /> |
| 26 | 123 </xml> |
| 55 | 124 <xml name="software-citation"> |
| 58 | 125 <citation type="bibtex">@article{khmer2014, |
| 126 author = "Crusoe, Michael and Edvenson, Greg and Fish, Jordan and Howe, | |
| 127 Adina and McDonald, Eric and Nahum, Joshua and Nanlohy, Kaben and | |
| 128 Ortiz-Zuazaga, Humberto and Pell, Jason and Simpson, Jared and Scott, Camille | |
| 129 and Srinivasan, Ramakrishnan Rajaram and Zhang, Qingpeng and Brown, C. Titus", | |
| 130 title = "The khmer software package: enabling efficient sequence | |
| 131 analysis", | |
| 132 year = "2014", | |
| 133 month = "04", | |
| 134 publisher = "Figshare", | |
| 135 url = "http://dx.doi.org/10.6084/m9.figshare.979190" | |
| 136 }</citation> | |
| 55 | 137 </xml> |
| 138 <xml name="diginorm-citation"> | |
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139 <citation type="bibtex">@unpublished{diginorm, |
| 58 | 140 author = "Brown, C Titus and Howe, Adina and Zhang, Qingpeng and Pyrkosz, |
| 141 Alexis B and Brom, Timothy H", | |
| 142 title = "A Reference-Free Algorithm for Computational Normalization of | |
| 143 Shotgun Sequencing Data", | |
| 144 year = "2012", | |
| 145 eprint = "arXiv:1203.4802", | |
| 146 url = "http://arxiv.org/abs/1203.4802", | |
| 55 | 147 }</citation></xml> |
| 148 <xml name="graph-citation"> | |
| 149 <citation type="doi">10.1073/pnas.1121464109</citation> | |
| 150 </xml> | |
| 151 <xml name="counting-citation"> | |
| 152 <citation type="doi">10.1371/journal.pone.0101271</citation> | |
| 153 </xml> | |
| 59 | 154 <xml name="stdio"> |
| 155 <stdio> | |
| 156 <exit_code range="1:" | |
| 157 level="fatal" /> | |
| 158 </stdio> | |
| 159 </xml> | |
| 53 | 160 </macros> |