Mercurial > repos > iuc > chromeister

annotate chromeister.xml @ 2:23f7b4075f4d draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chromeister commit 732d2f1bd7944e0ad8f6660eb10b33acc635ff3d"
author iuc
date Mon, 14 Dec 2020 14:09:39 +0000
parents 9f884d6a5779
children 4d428c882301
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468aa591d03d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chromeister commit 5405b8a0f1ee81d66cc271578829ef013925e80c"
iuc
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1 <tool id="chromeister" name="Chromeister" version="@TOOL_VERSION@">
468aa591d03d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chromeister commit 5405b8a0f1ee81d66cc271578829ef013925e80c"
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2 <description>ultra-fast pairwise genome comparisons</description>
468aa591d03d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chromeister commit 5405b8a0f1ee81d66cc271578829ef013925e80c"
iuc
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3 <macros>
2
23f7b4075f4d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chromeister commit 732d2f1bd7944e0ad8f6660eb10b33acc635ff3d"
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4 <token name="@TOOL_VERSION@">1.3.c</token>
0
468aa591d03d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chromeister commit 5405b8a0f1ee81d66cc271578829ef013925e80c"
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5 </macros>
468aa591d03d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chromeister commit 5405b8a0f1ee81d66cc271578829ef013925e80c"
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6 <requirements>
468aa591d03d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chromeister commit 5405b8a0f1ee81d66cc271578829ef013925e80c"
iuc
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7 <requirement type="package" version="@TOOL_VERSION@">chromeister</requirement>
468aa591d03d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chromeister commit 5405b8a0f1ee81d66cc271578829ef013925e80c"
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8 </requirements>
468aa591d03d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chromeister commit 5405b8a0f1ee81d66cc271578829ef013925e80c"
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9 <command><![CDATA[
468aa591d03d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chromeister commit 5405b8a0f1ee81d66cc271578829ef013925e80c"
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10 #import re
468aa591d03d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chromeister commit 5405b8a0f1ee81d66cc271578829ef013925e80c"
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11
468aa591d03d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chromeister commit 5405b8a0f1ee81d66cc271578829ef013925e80c"
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12 #set $queryName=re.sub('[^\w\-_.]', '_', str($query.name))
468aa591d03d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chromeister commit 5405b8a0f1ee81d66cc271578829ef013925e80c"
iuc
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13 #set $dbName=re.sub('[^\w\-_.]', '_', str($db.name))
468aa591d03d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chromeister commit 5405b8a0f1ee81d66cc271578829ef013925e80c"
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14
468aa591d03d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chromeister commit 5405b8a0f1ee81d66cc271578829ef013925e80c"
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15 ln -s $query '$queryName' &&
468aa591d03d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chromeister commit 5405b8a0f1ee81d66cc271578829ef013925e80c"
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16 ln -s $db '$dbName' &&
468aa591d03d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chromeister commit 5405b8a0f1ee81d66cc271578829ef013925e80c"
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17 CHROMEISTER
468aa591d03d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chromeister commit 5405b8a0f1ee81d66cc271578829ef013925e80c"
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18 -query '$queryName'
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19 -db '$dbName'
468aa591d03d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chromeister commit 5405b8a0f1ee81d66cc271578829ef013925e80c"
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20 -dimension $dimension
468aa591d03d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chromeister commit 5405b8a0f1ee81d66cc271578829ef013925e80c"
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21 -kmer $kmer
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22 -diffuse $diffuse
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23 -out '$queryName'-'$dbName'.mat &&
468aa591d03d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chromeister commit 5405b8a0f1ee81d66cc271578829ef013925e80c"
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24
468aa591d03d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chromeister commit 5405b8a0f1ee81d66cc271578829ef013925e80c"
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25 #if str($grid) == "grid":
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26 compute_score.R
468aa591d03d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chromeister commit 5405b8a0f1ee81d66cc271578829ef013925e80c"
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27 #else:
468aa591d03d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chromeister commit 5405b8a0f1ee81d66cc271578829ef013925e80c"
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28 compute_score-nogrid.R
468aa591d03d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chromeister commit 5405b8a0f1ee81d66cc271578829ef013925e80c"
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29 #end if
468aa591d03d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chromeister commit 5405b8a0f1ee81d66cc271578829ef013925e80c"
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30 '$queryName'-'$dbName'.mat $dimension > '$output_score' &&
468aa591d03d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chromeister commit 5405b8a0f1ee81d66cc271578829ef013925e80c"
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31
2
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32
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33 detect_events.py '$queryName'-'$dbName'.mat.raw.txt
23f7b4075f4d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chromeister commit 732d2f1bd7944e0ad8f6660eb10b33acc635ff3d"
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34 #if str($pngevents) == "pngevents":
23f7b4075f4d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chromeister commit 732d2f1bd7944e0ad8f6660eb10b33acc635ff3d"
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35 png &&
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36 mv '$queryName'-'$dbName'.mat.events.png '$output_events_png'
23f7b4075f4d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chromeister commit 732d2f1bd7944e0ad8f6660eb10b33acc635ff3d"
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37 #end if
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38
23f7b4075f4d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chromeister commit 732d2f1bd7944e0ad8f6660eb10b33acc635ff3d"
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39 &&
23f7b4075f4d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chromeister commit 732d2f1bd7944e0ad8f6660eb10b33acc635ff3d"
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40
0
468aa591d03d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chromeister commit 5405b8a0f1ee81d66cc271578829ef013925e80c"
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41 mv '$queryName'-'$dbName'.mat '$output' &&
468aa591d03d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chromeister commit 5405b8a0f1ee81d66cc271578829ef013925e80c"
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42 mv '$queryName'-'$dbName'.mat.filt.png '$output_imagen' &&
468aa591d03d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chromeister commit 5405b8a0f1ee81d66cc271578829ef013925e80c"
iuc
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43 mv '$queryName'-'$dbName'.mat.events.txt '$output_events' &&
468aa591d03d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chromeister commit 5405b8a0f1ee81d66cc271578829ef013925e80c"
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44 mv '$queryName'-'$dbName'.mat.csv '$output_csv'
468aa591d03d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chromeister commit 5405b8a0f1ee81d66cc271578829ef013925e80c"
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45 ]]></command>
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46 <inputs>
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47 <param name="query" type="data" format="fasta" label="Query sequence" help="Query sequence file in fasta format"/>
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48 <param name="db" type="data" format="fasta" label="Reference sequence" help="Reference sequence file in fasta format"/>
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49 <param name="dimension" type="integer" value="1000" min="500" max="2000" label="Output dotplot size" help="Use around 1000 for chromosome-sized sequences and around 2000 for complete genomes"/>
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50 <param name="kmer" type="select" label="K-mer seed size" help="Use 32 as default, and 16 in case no similarities are found">
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51 <option value="32" selected="true">32</option>
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52 <option value="16">16</option>
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53 </param>
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54 <param name="diffuse" type="integer" value="4" min="1" max="4" label="Diffuse value" help="Level of the heuristic subsampling employed. Change to 1 or 2 if no similarity is found"/>
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55 <param name="grid" type="boolean" truevalue="grid" falsevalue="" checked="true" label="Add grid to plot for multi-fasta data sets" help="Do not use grid if your multi-fasta contains more than a hundred sequences (approximately)"/>
2
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56 <param name="pngevents" type="boolean" truevalue="pngevents" falsevalue="" checked="true" label="Generate image of detected events" help="If enabled, a png image will be generated showing the detected blocks and classified by color"/>
0
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57 </inputs>
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58 <outputs>
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59 <data name="output" format="txt" label="${tool.name} on ${on_string}: Comparison matrix"/>
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60 <data name="output_imagen" format="png" label="${tool.name} on ${on_string}: Comparison dotplot"/>
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61 <data name="output_csv" format="csv" label="${tool.name} on ${on_string}: Comparison metainformation"/>
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62 <data name="output_events" format="txt" label="${tool.name} on ${on_string}: Detected events"/>
2
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63 <data name="output_events_png" format="png" label="${tool.name} on ${on_string}: Detected events plot">
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64 <filter>pngevents</filter>
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65 </data>
0
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66 <data name="output_score" format="txt" label="${tool.name} on ${on_string}: Comparison score"/>
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67 </outputs>
2
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68
0
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69 <tests>
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70 <!-- test run w defaults (and non default for dimension) -->
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71 <test expect_num_outputs="5">
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72 <param name="query" value="mycoplasma-232.fasta"/>
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73 <param name="db" value="mycoplasma-7422.fasta"/>
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74 <param name="dimension" value="500"/>
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75 <output name="output" file="mycoplasma-232.fasta-mycoplasma-7422.fasta.mat"/>
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76 <output name="output_imagen" file="mycoplasma-232.fasta-mycoplasma-7422.fasta.mat.filt.png" compare="sim_size"/>
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77 <output name="output_csv" file="mycoplasma-232.fasta-mycoplasma-7422.fasta.mat.csv"/>
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78 <output name="output_events" file="mycoplasma-232.fasta-mycoplasma-7422.fasta.mat.events.txt"/>
468aa591d03d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chromeister commit 5405b8a0f1ee81d66cc271578829ef013925e80c"
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79 <output name="output_score" file="mycoplasma-232.fasta-mycoplasma-7422.fasta.scr.txt"/>
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80 <assert_command>
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81 <has_text text="-dimension 500"/>
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82 <has_text text="-kmer 32"/>
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83 <has_text text="-diffuse 4"/>
468aa591d03d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chromeister commit 5405b8a0f1ee81d66cc271578829ef013925e80c"
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84 <has_text text="compute_score.R"/>
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85 </assert_command>
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86 </test>
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87 <!-- test run w non defaults (and default for dimension) -->
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88 <test expect_num_outputs="5">
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89 <param name="query" value="mycoplasma-232.fasta"/>
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90 <param name="db" value="mycoplasma-7422.fasta"/>
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91 <param name="kmer" value="16"/>
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92 <param name="diffuse" value="3"/>
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93 <param name="grid" value=""/>
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94 <output name="output">
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95 <assert_contents>
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96 <has_text text="892758"/>
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97 <has_text text="898495"/>
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98 <has_n_lines n="1002"/>
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99 </assert_contents>
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100 </output>
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101 <output name="output_imagen">
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102 <assert_contents>
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103 <has_text text="PNG"/>
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104 </assert_contents>
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105 </output>
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106 <output name="output_csv" file="mycoplasma-232.fasta-mycoplasma-7422.fasta.mat.csv"/>
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107 <output name="output_events">
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108 <assert_contents>
2
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109 <has_text text="xStart,yStart,xEnd,yEnd,strand,approximate length,description"/>
0
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110 <has_text text="inverted transposition"/>
2
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111 <has_text text="conserved block"/>
0
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112 </assert_contents>
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113 </output>
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114 <output name="output_score">
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115 <assert_contents>
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116 <has_text text="0.057"/>
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117 </assert_contents>
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118 </output>
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119 <assert_command>
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120 <has_text text="-dimension 1000"/>
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121 <has_text text="-kmer 16"/>
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122 <has_text text="-diffuse 3"/>
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123 <has_text text="compute_score-nogrid.R"/>
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124 </assert_command>
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125 </test>
2
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126 <test expect_num_outputs="6">
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127 <param name="query" value="mycoplasma-232.fasta"/>
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128 <param name="db" value="mycoplasma-7422.fasta"/>
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129 <param name="kmer" value="32"/>
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130 <param name="diffuse" value="4"/>
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131 <param name="dimension" value="1000"/>
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132 <param name="grid" value=""/>
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133 <param name="pngevents" value="pngevents"/>
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134 <output name="output"/>
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135 <output name="output_imagen"/>
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136 <output name="output_csv"/>
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137 <output name="output_events"/>
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138 <output name="output_score"/>
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139 <output name="output_events_png">
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140 <assert_contents>
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141 <has_text text="PNG"/>
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142 </assert_contents>
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143 </output>
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144 </test>
0
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145 </tests>
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146 <help>
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147 *CHROMEISTER*
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148
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149 CHROMEISTER is a heuristic approach for the ultra fast previsualization of pairwise genome comparisons. It is able to compare enormous genomes (up to 30 thousand million base pairs, or 10 times the size of the human genome) much faster than other methods while yielding significant, reusable and exploitable information such as synteny blocks, evolutionary events or pairwise genome similarity metrics.
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150
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151 What is CHROMEISTER good for?
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152 It is specially suitable to obtain a fast visualization of a pairwise genome comparison. Due to its unique-seeds filtering, it is particularly useful to inspect noisy, full-of-repeats genome comparisons. Additionally, since it outputs a scoring metric for each comparison, it can be used for massive all vs all comparisons that get automatically processed based on such metric.
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153
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154 What is CHROMEISTER NOT good for?
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155 It should NOT be used to obtain alignments. CHROMEISTER, as it is, does not produce a set of alignments (although it can be done using the GECKO pipeline, see github repository). It should also NOT be used to perform studies on DNA repeats, since CHROMEISTER filters these as part of its main signal detection process.
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156
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157 *How to use*
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158
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159 To use Chromeister, upload two .fasta data sets and select these as "Query sequence" and as "Reference sequence". Once so, choose the parameters that best suite your comparison:
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160
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161 **Input parameters**
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162
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163 - Output dotplot size (dimension): This parameter corresponds to the resolution of the comparison. That is, higher resolution is recommended for large genomes (e.g. use 2000 for more than 3 GBps) and lower resolutions (e.g. use 1000 for everything else) should be used for comparisons involving chromosomes or partial genomes. A value of 1000 will produce a 1,000 x 1,000 output dotplot png image.
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164 - K-mer seed size: This parameter is the seed size used to find unique hits. The recommended value is 32 for all sequences except for small experiments such as bacterial, where 16 is recommended.
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165 - Diffuse value: This parameter determines the level of heuristic subsampling employed. A level of 1 will use perfect indexing (no subsampling). The recommended level is 4, which represents a good trade-off between exact and inexact hits. Only use 1 if no similarity is found.
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166
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167 **Output data sets**
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168
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169 - Comparison matrix (plain text), i.e. a scaled matrix containing the number of unique and inexact hits per resolution cell.
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170 - A .png dotplot of the comparison with an automatic scoring distance (useful for classifying) and a grid (if enabled) separating the different sequences (chromosomes for instance) compared.
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171 - A .csv file including the coordinates of each sequence/chromosome contained within the query and reference sequences (useful for multi-fasta inputs).
2
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172 - Events file. A text file where each row is a "Computational Synteny Block". This means that these events are Large-Scale Genome Rearrangements heuristically determined and classified as conserved, transposed or inverted blocks. But this is only an informative labelling that only considers coordinates and does not employ genes nor other external information. A plot will be also available if enabled with option `Generate image of events` featuring the events that have been detected automatically. There is a color legend for each block, namely:
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173 - Red: conserved blocks (close to the diagonal)
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174 - Green: inverted blocks (reverse strand)
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175 - Blue: transposed blocks (not reverted and not on the diagonal)
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176 </help>
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177
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178 <citations>
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179 <citation type="doi">10.1038/s41598-019-46773-w</citation>
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180 </citations>
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181 </tool>