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2
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1 <tool id="khmer_load_into_counting" name="Load Into Counting" version="1.0.6">
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0
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2 <description>Creates k-mer countgraph using reads</description>
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3 <requirements>
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4 <requirement type="package" version="2.1.2">khmer</requirement>
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5 </requirements>
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6 <command detect_errors="exit_code"><![CDATA[
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7 load-into-counting.py
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8 $advanced.b
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9 $advanced.small
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1
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10 -k $kmer
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11 -U $advanced.ukmer
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12 #if str( $advanced.max_mem ) != "0"
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13 -M $advanced.max_mem
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14 #end if
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15 #if str( $advanced.fp_rate ) != "0"
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16 --fp-rate $advanced.fp_rate
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17 #end if
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1
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18 -N $advanced.num_table
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19 -x $advanced.table_size
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0
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20 hash.ct.gz
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21 #if str( $data_input.data_selector ) == "paired"
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22 $data_input.input1.forward $data_input.input1.reverse
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23 #end if
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24 #if str( $data_input.data_selector ) == "single"
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25 $data_input.input2
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26 #end if
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27 ]]></command>
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28 <inputs>
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29 <conditional name="data_input">
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30 <param name="data_selector" type="select" label="Single or Paired-end Data" help="Select between paired and single end data to add name to dataset">
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31 <option value="paired">Paired</option>
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32 <option value="single">Single</option>
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33 </param>
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34 <when value="paired">
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35 <param name="input1" format="data" type="data_collection" collection_type="paired" label="Select a paired collection" help="a paired data"/>
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36 </when>
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37 <when value="single">
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38 <param name="input2" format="data" type="data" label="input" help="Specify dataset with single reads"/>
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39 </when>
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40 </conditional>
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1
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41 <param name="kmer" type="integer" value="32" label="K-mer" help="K-mer size to use (default: 32)" />
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0
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42 <section name="advanced" title="Advanced options" expanded="false">
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43 <param type="boolean" argument="--small" label="Small count" checked="false" truevalue="--small-count" falsevalue="" help="Reduce memory usage by using a smaller counter for individual kmers. (default: False)"/>
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44 <param type="boolean" argument="-b" label="big count" checked="True" truevalue="-b" falsevalue="--no-bigcount" help="Reduce memory usage by using a smaller counter for individual kmers. (default: True)"/>
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45 <param name="thread" type="integer" value="1" label="Threads" help="Number of simultaneous threads to execute (default: 1)" />
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1
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46
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0
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47 <param name="ukmer" type="integer" value="0" label="Unique K-mer" help="approximate number of unique kmers in the input set (default: 0)" />
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1
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48 <param name="num_table" type="integer" value="1" label="Number of tables" help="number of tables to use (default: False)" />
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49 <param name="table_size" type="integer" value="1000000000" label="Maximum size of table" help="maximum size of tables to use (default: False)" />
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0
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50 <param name="max_mem" type="integer" value="0" label="Maximum Memory" help="number of tables to use (default: False)" />
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51 <param name="fp_rate" type="integer" value="0" label="FP rate override" help="Override the automatic FP rate setting for the current script" />
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52 </section>
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53 </inputs>
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54 <outputs>
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2
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55 <data name="hash_output" label="Hash output" format="data" type="data_collection" from_work_dir="hash.ct.gz"/>
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0
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56 </outputs>
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57 <help><![CDATA[
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58 || This is the script load-into-counting.py in khmer.
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59 || You are running khmer version 2.1.2
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60 || You are also using screed version 1.0
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61 ||
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62 || If you use this script in a publication, please cite EACH of the following:
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63 ||
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64 || * MR Crusoe et al., 2015. http://dx.doi.org/10.12688/f1000research.6924.1
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65 || * Q Zhang et al., http://dx.doi.org/10.1371/journal.pone.0101271
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66 || * A. Döring et al. http://dx.doi.org:80/10.1186/1471-2105-9-11
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67 ||
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68 || Please see http://khmer.readthedocs.io/en/latest/citations.html for details.
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69
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70 usage: load-into-counting.py [--version] [--info] [-h] [-k KSIZE]
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71 [-U UNIQUE_KMERS] [--fp-rate FP_RATE]
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72 [-M MAX_MEMORY_USAGE] [--small-count]
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73 [-T THREADS] [-b] [-s FORMAT] [-f] [-q]
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74 output_countgraph_filename
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75 input_sequence_filename
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76 [input_sequence_filename ...]
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77
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78 Build a k-mer countgraph from the given sequences.
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79
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80 positional arguments:
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81 output_countgraph_filename
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82 The name of the file to write the k-mer countgraph to.
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83 input_sequence_filename
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84 The names of one or more FAST[AQ] input sequence
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85 files.
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86
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87 optional arguments:
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88 --version show program's version number and exit
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89 --info print citation information
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90 -h, --help show this help message and exit
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91 -k KSIZE, --ksize KSIZE
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92 k-mer size to use (default: 32)
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93 -U UNIQUE_KMERS, --unique-kmers UNIQUE_KMERS
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94 approximate number of unique kmers in the input set
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95 (default: 0)
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96 --fp-rate FP_RATE Override the automatic FP rate setting for the current
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97 script (default: None)
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98 -M MAX_MEMORY_USAGE, --max-memory-usage MAX_MEMORY_USAGE
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99 maximum amount of memory to use for data structure
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100 (default: None)
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101 --small-count Reduce memory usage by using a smaller counter for
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102 individual kmers. (default: False)
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103 -T THREADS, --threads THREADS
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104 Number of simultaneous threads to execute (default: 1)
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105 -b, --no-bigcount The default behaviour is to count past 255 using
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106 bigcount. This flag turns bigcount off, limiting
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107 counts to 255. (default: True)
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108 -s FORMAT, --summary-info FORMAT
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109 What format should the machine readable run summary be
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110 in? (`json` or `tsv`, disabled by default) (default:
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111 None)
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112 -f, --force Overwrite output file if it exists (default: False)
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113 -q, --quiet
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114
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115 Note: with `-b`/`--no-bigcount` the output will be the exact size of the k-mer
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116 countgraph and this script will use a constant amount of memory. In exchange
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117 k-mer counts will stop at 255. The memory usage of this script with `-b` will
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118 be about 1.15x the product of the `-x` and `-N` numbers.
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119
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120 Example:
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121
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122 load-into-counting.py -k 20 -x 5e7 out data/100k-filtered.fa
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123
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124 Multiple threads can be used to accelerate the process, if you have extra cores
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125 to spare.
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126
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127 Example:
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128
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129 load-into-counting.py -k 20 -x 5e7 -T 4 out data/100k-filtered.fa
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130
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131
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132 ]]></help>
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133 <citations>
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134 <citation type="bibtex">
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135 @misc{githubkhmer,
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136 author = {Crusoe, Michael},
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137 year = {2015},
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138 title = {khmer},
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139 publisher = {GitHub},
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140 journal = {GitHub repository},
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141 url = {https://github.com/dib-lab/khmer},
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142 }</citation>
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143 </citations>
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144 </tool>
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