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annotate coverage_sampler.xml @ 19:246302afd481 draft

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planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit f71cd1e6bbc1e28942506b3face7284245827520-dirty
author chrisd
date Wed, 29 Jun 2016 03:01:25 -0400
parents 9dd9da093f21
children 2268b850b57a
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1 <tool id="gene_fraction" name="Coverage Sampler" version="0.1.0">
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2 <description>A simple tool for calculating the amount of a gene that is covered by a sample of alignments</description>
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3 <requirements>
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4 <requirement type="package" version="0.1">coverage_sampler</requirement>
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5 </requirements>
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6 <stdio>
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7 <exit_code range="1:" />
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8 </stdio>
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9 <command><![CDATA[
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10 csa
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11 -ref_fp $reference
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12 -sam_fp $sam
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13 -min $min
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14 -max $max
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15 -t $threshold
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16 -skip $skip
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17 -samples $samples
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18 -out_fp $output
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19 ]]></command>
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20 <inputs>
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21 <param type="data" name="reference" format="fasta" label="Reference sequence" />
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22 <param type="data" name="sam" format="sam" label="SAM file" />
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23 <param name="min" type="integer" label="Starting sample level"
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24 value="1" min="1" max="100" help="(-min)" />
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25 <param name="max" type="integer" label="Ending sample level"
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26 value="1" min="1" max="100" help="(-max)" />
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27 <param name="threshold" type="integer" label="Gene fraction threshold"
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28 value="0" min="0" max="100" help="(-t)" />
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29 <param name="skip" type="integer" label="Amount of sample levels to skip"
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30 value="1" min="1" max="100" help="(-skip)" />
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31 <param name="samples" type="integer" label="Iterations per sample level"
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32 value="1" min="1" max="100" help="(-samples)" />
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33 </inputs>
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34 <outputs>
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35 <data name="output" format="tabular" />
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36 </outputs>
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37 <tests>
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38 <test>
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39 <param name="reference" value="ref.fa"/>
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40 <param name="sam" value="sampe.sam"/>
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41 <param name="min" value="100"/>
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42 <param name="max" value="100"/>
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43 <param name="threshold" value="50"/>
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44 <param name="skip" value="5"/>
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45 <param name="samples" value="1"/>
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46 <output name="output" file="csa_result" ftype="tabular"/>
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47 </test>
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48 <test>
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49 <param name="reference" value="ref.fa"/>
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50 <param name="sam" value="sampe.sam"/>
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51 <param name="min" value="100"/>
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52 <param name="max" value="100"/>
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53 <param name="threshold" value="80"/>
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54 <param name="skip" value="5"/>
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55 <param name="samples" value="1"/>
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56 <output name="output" file="csa_no_result" ftype="tabular"/>
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57 </test>
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58 </tests>
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59 <help>
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60 <![CDATA[
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62 **Coverage sampler**
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63
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64 Coverage sampler is a simple tool for calculating the amount of a gene that is covered by a sample of alignments. The tool takes
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65 in as input a fasta and alignment file. The output of this program is a tab delimited text file describing the fraction of each gene
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66 that was covered from a random sampling of alignments.
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67
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68 ------
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69
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70 **Options**
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71
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72 - min This parameter specifies the starting sample level for the program. For example, a min value
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73 of five tells the program to begin by taking five percent of alignments from the alignment file.
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74
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75 - max This parameter specifies the ending sample level for the program.
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76
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77 - skip This parameter specifies the amount of levels to skip between min and max. For example,
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78 if you specify a min value of five, a max value of 100, and a skip value of five, then
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79 you would be sampling alignments in intervals of five.
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80
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81 - t This parameter specifies a threshold value. Only genes having a gene fraction greater than
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82 this value are provided as output.
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83
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84 - samples This parameter specifies the amount of iterations you would like to sample at. For example,
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85 a sample value of five would sample each level five times.
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87 ------
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89 **Output**
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90
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91 Output of this program is a tab delimited text file with following:
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92
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93 Level The sampling level alignments were taken at
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94
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95 Iteration The ith iteration of the current sampling level
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96
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97 Gene Id The reference sequence having a gene fraction greater than threshold
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98
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99 Gene Fraction The overall fraction of the gene that was covered from the sample of alignments
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100
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101 Hits The amount of times that the reference sequence was seen from the sample of alignments
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102
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103 ------
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104
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105 **Development**
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107 Development is being done on github_
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108
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109 .. _github: https://github.com/cdeanj/coverage_sampler
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110
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111 ]]>
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112 </help>
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113 <citations>
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114 </citations>
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115 </tool>