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"planemo upload commit 5c6a5c0f9aacbc7def652b33cc35ee37aa543d05-dirty"
author csbl
date Tue, 24 Nov 2020 03:55:18 +0000
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1 <tool id="repeatmodeler" name="RepeatModeler - Model repetitive DNA" version="0.1.0" python_template_version="3.5">
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2 <requirements>
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3 <requirement type="package" version="2.0.1">repeatmodeler</requirement>
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4 </requirements>
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5 <command detect_errors="exit_code"><![CDATA[
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6 BuildDatabase -name '$name' '$input_file' && RepeatModeler -database '$name' -pa '$pa' && cp '$name'-families.fa '$output'
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7 ]]></command>
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8 <inputs>
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9 <param type="data" name="input_file" format="fasta" label="Input genome fasta"/>
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10 <param argument="-name" type="text" value="" label="Title for building database" />
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11 <param argument="-pa" type="text" value="" label="Numer of paralleled job: # of nodes" />
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12 </inputs>
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13 <outputs>
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14 <!-- <data format="fasta" name="RepeatModels" from_work_dir="*-families.fa" label="${tool.name} on ${on_string}: RepeatModels::FASTA" /> -->
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15 <!-- <data format="txt" name="StockholmFormat" from_work_dir="*-families.stk" label="${tool.name} on ${on_string}: RepeatModels::StockholmFormat" /> -->
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16 <data format="fasta" name="output" label="${tool.name} on ${on_string}: RepeatModels::FASTA" />
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17 </outputs>
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18 <tests>
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19 <test>
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20 <param name="input_file" value="eco.fasta" ftype="fasta"/>
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21 <param name="name" value="eco" />
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22 <param name="pa" value="4" />
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23 <output name="output" file="consensi.fa.classified" compare="sim_size" delta_frac="0.1" />
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24 </test>
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25 </tests>
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26 <help><![CDATA[
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27 RepeatModeler - 2.0.1
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28
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29 NAME
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30 RepeatModeler - Model repetitive DNA
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31
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32 SYNOPSIS
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33 RepeatModeler [-options] -database <XDF Database>
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34
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35 DESCRIPTION
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36 The options are:
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37
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38 -h(elp)
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39 Detailed help
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40
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41 -database <DBNAME>
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42 The name of the sequence database to run an analysis on. This is the
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43 name that was provided to the BuildDatabase script using the "-name"
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44 option.
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45
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46 -pa #
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47 Specify the number of parallel search jobs to run. RMBlast jobs will
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48 use 4 cores each and ABBlast jobs will use a single core each. i.e.
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49 on a machine with 12 cores and running with RMBlast you would use
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50 -pa 3 to fully utilize the machine.
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51
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52 -recoverDir <Previous Output Directory>
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53 If a run fails in the middle of processing, it may be possible
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54 recover some results and continue where the previous run left off.
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55 Simply supply the output directory where the results of the failed
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56 run were saved and the program will attempt to recover and continue
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57 the run.
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58
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59 -srand #
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60 Optionally set the seed of the random number generator to a known
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61 value before the batches are randomly selected ( using Fisher Yates
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62 Shuffling ). This is only useful if you need to reproduce the sample
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63 choice between runs. This should be an integer number.
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64
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65 -LTRStruct [optional]
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66 Run the LTR structural discovery pipeline ( LTR_Harvest and
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67 LTR_retreiver ) and combine results with the RepeatScout/RECON
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68 pipeline. [optional]
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69
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70 -genomeSampleSizeMax #
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71 Optionally change the maximum bp of the genome to sample in all
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72 rounds of RECON (default=243000000).
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73
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74 CONFIGURATION OVERRIDES
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75 -ltr_retriever_dir <string>
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76 The path to the installation of the LTR_Retriever structural LTR
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77 analysis package.
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78
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79 -rmblast_dir <string>
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80 The path to the installation of the RMBLAST sequence alignment
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81 program.
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82
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83 -repeatmasker_dir <string>
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84 The path to the installation of RepeatMasker.
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85
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86 -trf_prgm <string>
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87 The full path including the name for the TRF program ( 4.0.9 or
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88 higher )
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89
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90 -ninja_dir <string>
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91 The path to the installation of the Ninja phylogenetic analysis
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92 package.
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93
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94 -recon_dir <string>
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95 The path to the installation of the RECON de-novo repeatfinding
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96 program.
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97
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98 -genometools_dir <string>
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99 The path to the installation of the GenomeTools package.
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100
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101 -abblast_dir <string>
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102 The path to the installation of the ABBLAST sequence alignment
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103 program.
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104
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105 -rscout_dir <string>
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106 The path to the installation of the RepeatScout ( 1.0.6 or higher )
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107 de-novo repeatfinding program.
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108
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109 -mafft_dir <string>
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110 The path to the installation of the MAFFT multiple alignment
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111 program.
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112
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113 -cdhit_dir <string>
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114 The path to the installation of the CD-Hit sequence clustering
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115 package.
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116
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117 SEE ALSO
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118 RepeatMasker, RMBlast
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119
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120 COPYRIGHT
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121 Copyright 2005-2019 Institute for Systems Biology
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122
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123 AUTHOR
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124 RepeatModeler:
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125 Robert Hubley <rhubley@systemsbiology.org>
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126 Arian Smit <asmit@systemsbiology.org>
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127
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128 LTR Pipeline Extensions:
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129 Jullien Michelle Flynn <jmf422@cornell.edu>
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130 ]]></help>
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131 <citations>
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132 <citation type="doi">10.1073/pnas.1921046117</citation>
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133 <citation type="doi">10.1186/s13059-018-1577-z</citation>
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134 </citations>
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135 </tool>