Mercurial > repos > iuc > telescope_assign

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 3a6e7428a808860068e7cc07a101aa10a31697b8
author iuc
date Wed, 24 Aug 2022 22:30:35 +0000
parents 66ff74923224
children
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2d8c943f3e8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 3a6e7428a808860068e7cc07a101aa10a31697b8
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1 <tool id="telescope_assign" name="Reassign reads" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
0
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2 <description>with TELESCOPE using a statistical model</description>
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2d8c943f3e8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 3a6e7428a808860068e7cc07a101aa10a31697b8
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3 <xrefs>
2d8c943f3e8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 3a6e7428a808860068e7cc07a101aa10a31697b8
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4 <xref type="bio.tools">Telescope-expression</xref>
2d8c943f3e8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 3a6e7428a808860068e7cc07a101aa10a31697b8
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5 </xrefs>
0
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6 <macros>
1
2d8c943f3e8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 3a6e7428a808860068e7cc07a101aa10a31697b8
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7 <token name="@TOOL_VERSION@">1.0.3</token>
2d8c943f3e8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 3a6e7428a808860068e7cc07a101aa10a31697b8
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8 <token name="@VERSION_SUFFIX@">1</token>
0
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9 </macros>
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10 <requirements>
1
2d8c943f3e8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 3a6e7428a808860068e7cc07a101aa10a31697b8
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11 <requirement type="package" version="@TOOL_VERSION@">telescope</requirement>
0
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12 <requirement type="package" version="1.9">samtools</requirement>
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13 </requirements>
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14 <command detect_errors="exit_code"><![CDATA[
66ff74923224 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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15 mkdir tempdir &&
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16 mkdir outdir &&
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17
0
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18 telescope assign '$input_alignment' '$input_gtf'
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19 --tempdir tempdir
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20 --outdir outdir
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21 ## Not supported https://github.com/mlbendall/telescope/blob/6cd55256c6016feffdbfe10346bfecfcb1e30965/README.md?plain=1#L129
2d8c943f3e8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 3a6e7428a808860068e7cc07a101aa10a31697b8
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22 ## --ncpu \${GALAXY_SLOTS:-1}
0
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23 $updated_sam
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24 #if str($advanced.advanced_options) == 'select':
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25 --reassign_mode $advanced.reassign_mode
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26 --conf_prob $advanced.conf_prob
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27 --overlap_mode $advanced.overlap_mode
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28 --overlap_threshold $advanced.overlap_threshold
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29 --annotation_class $advanced.annotation_class
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30 --pi_prior $advanced.pi_prior
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31 --theta_prior $advanced.theta_prior
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32 --em_epsilon $advanced.em_epsilon
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33 --max_iter $advanced.max_iter
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34 $advanced.use_likelihood
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35 #end if
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36 #if $updated_sam
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37 &&
66ff74923224 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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38 if [ -f outdir/telescope-updated.bam ] ; then
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2d8c943f3e8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 3a6e7428a808860068e7cc07a101aa10a31697b8
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39 samtools sort -T "\${TMPDIR:-.}" outdir/telescope-updated.bam > '$updated_alignment' ;
0
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40 else
66ff74923224 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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41 echo 'Updated alignment file not found.' ;
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42 exit 1 ;
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43 fi
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44 #end if
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45 ]]></command>
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46 <inputs>
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47 <param name="input_alignment" type="data" format="sam,bam" label="Input SAM or BAM file" />
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48 <param name="input_gtf" type="data" format="gtf" label="Input annotation" />
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49 <param argument="--updated_sam" type="boolean" truevalue="--updated_sam" falsevalue="" label="Also output an updated BAM file with reassigned reads" />
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50 <conditional name="advanced">
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51 <param name="advanced_options" type="select" label="Advanced options">
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52 <option value="defaults">Use defaults</option>
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53 <option value="select">Select values</option>
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54 </param>
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55 <when value="defaults" />
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56 <when value="select">
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57 <param argument="--reassign_mode" type="select" label="Reassignment mode"
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58 help="After EM is complete, each fragment is reassigned according to the expected value of its membership weights. The reassignment method is the method for resolving the &quot;best&quot; reassignment for fragments that have multiple possible reassignments. Available modes are: &quot;exclude&quot; - fragments with multiple best assignments are excluded from the final counts; &quot;choose&quot; - the best assignment is randomly chosen from among the set of best assignments; &quot;average&quot; - the fragment is divided evenly among the best assignments; &quot;conf&quot; - only assignments that exceed a certain threshold (see --conf_prob) are accepted; &quot;unique&quot; - only uniquely aligned reads are included. NOTE: Results using all assignment modes are included in the Telescope report by default. This argument determines what mode will be used for the &quot;final counts&quot; column. (default: exclude)">
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59 <option value="exclude">Exclude</option>
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60 <option value="choose">Choose</option>
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61 <option value="average">Average</option>
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62 <option value="conf">Conf</option>
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63 <option value="unique">Unique</option>
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64 </param>
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65 <param argument="--conf_prob" type="float" value="0.9" min="0" max="1" label="Minimum probability for high confidence assignment" />
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66 <param argument="--overlap_mode" type="select" label="Overlap mode" help="The method used to determine whether a fragment overlaps feature">
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67 <option value="threshold">Threshold</option>
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68 <option value="intersection-strict">Strict intersection</option>
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69 <option value="union">Union</option>
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70 </param>
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71 <param argument="--overlap_threshold" type="float" value="0.2" min="0" max="1" label="Fraction of fragment that must be contained within a feature to be assigned to that locus" help="Ignored unless overlap mode is 'threshold'" />
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72 <param argument="--annotation_class" type="select" label="Annotation class" help="Both htseq and intervaltree appear to yield identical results. Performance differences are TBD.">
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73 <option value="intervaltree">Interval tree</option>
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74 <option value="htseq">HTSeq</option>
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75 </param>
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76 <param argument="--pi_prior" type="integer" value="0" label="Prior on &#960;" help="Equivalent to adding n unique reads." />
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77 <param argument="--theta_prior" type="integer" value="0" label="Prior on &#952;" help="Equivalent to adding n non-unique reads." />
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78 <param argument="--em_epsilon" type="float" value="0.0000001" label="EM Algorithm &#965; cutoff" help="Default: 1e-7" />
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79 <param argument="--max_iter" type="integer" value="100" label="EM Algorithm maximum iterations" help="Default: 100" />
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80 <param argument="--use_likelihood" type="boolean" truevalue="--use_likelihood" falsevalue="" label="Use difference in log-likelihood as convergence criteria" />
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81 </when>
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82 </conditional>
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83 </inputs>
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84 <outputs>
66ff74923224 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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85 <data name="output" format="tabular" from_work_dir="outdir/telescope-telescope_report.tsv" />
66ff74923224 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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86 <data name="updated_alignment" format="bam">
66ff74923224 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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87 <filter>updated_sam</filter>
66ff74923224 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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88 </data>
66ff74923224 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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89 </outputs>
66ff74923224 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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90 <tests>
66ff74923224 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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91 <test>
66ff74923224 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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92 <param name="input_alignment" value="telescope-in1.bam" />
66ff74923224 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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93 <param name="input_gtf" value="telescope-in1.gtf" />
66ff74923224 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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94 <param name="updated_sam" value="true" />
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95 <output name="output" file="telescope-out1.tabular" />
66ff74923224 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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96 <output name="updated_alignment" file="telescope-out1.bam" />
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97 </test>
66ff74923224 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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98 </tests>
66ff74923224 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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99 <help><![CDATA[
66ff74923224 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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100 Output
66ff74923224 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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101 ------
66ff74923224 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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102
66ff74923224 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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103 Telescope has two main output files: the telescope report and an updated
66ff74923224 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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104 SAM file (optional). The report file is most important for downstream
66ff74923224 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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105 differential expression analysis since it contains the fragment count
66ff74923224 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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106 estimates. The updated SAM file is useful for downstream locus-specific
66ff74923224 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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107 analyses.
66ff74923224 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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108
66ff74923224 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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109 Telescope report
66ff74923224 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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110 ~~~~~~~~~~~~~~~~
66ff74923224 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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111
66ff74923224 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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112 The first line in the telescope report is a comment (starting with a
66ff74923224 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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113 “#”) that contains information about the run such as the number of
66ff74923224 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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114 fragments processed, number of mapped fragments, number of uniquely and
66ff74923224 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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115 ambiguously mapped fragments, and number of fragments mapping to the
66ff74923224 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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116 annotation. The total number of mapped fragments may be useful for
66ff74923224 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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117 normalization.
66ff74923224 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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118
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119 The rest of the report is a table with calculated expression values for
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120 individual transposable element locations. The columns of the table are:
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121
66ff74923224 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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122 - ``transcript`` - Transcript ID, by default from "locus" field. See
66ff74923224 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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123 --attribute argument to use a different attribute.
66ff74923224 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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124 - ``transcript_length`` - Approximate length of transcript. This is
66ff74923224 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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125 calculated from the annotation, not the data, and is equal to the
66ff74923224 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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diff changeset
126 spanning length of the annotation minus any non-model regions.
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127 - ``final_count`` - Total number of fragments assigned to transcript
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128 after fitting the Telescope model. This is the column to use for
66ff74923224 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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129 downstream analysis that models data as negative binomial, i.e.
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130 DESeq2.
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131 - ``final_conf`` - Final confident fragments. The number of fragments
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132 assigned to transcript whose posterior probability exceeds a cutoff,
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133 0.9 by default. Set this using the --conf_prob argument.
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134 - ``final_prop`` - Final proportion of fragments represented by
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diff changeset
135 transcript. This is the final estimate of the π parameter.
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136 - ``init_aligned`` - Initial number of fragments aligned to transcript.
66ff74923224 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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137 A given fragment will contribute +1 to each transcript that it is
66ff74923224 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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138 aligned to, thus the sum of this will be greater than the number of
66ff74923224 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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diff changeset
139 fragments if there are multimapped reads.
66ff74923224 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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140 - ``unique_count`` - Unique count. Number of fragments aligning
66ff74923224 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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141 uniquely to this transcript.
66ff74923224 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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142 - ``init_best`` - Initial number of fragments aligned to transcript
66ff74923224 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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143 that have the "best" alignment score for that fragment. Fragments
66ff74923224 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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144 that have the same best alignment score to multiple transcripts will
66ff74923224 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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145 contribute +1 to each transcript.
66ff74923224 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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146 - ``init_best_random`` - Initial number of fragments aligned to
66ff74923224 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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diff changeset
147 transcript that have the "best" alignment score for that fragment.
66ff74923224 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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148 Fragments that have the same best alignment score to multiple
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149 transcripts will be randomly assigned to one transcript.
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150
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151 Updated BAM file
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152 ~~~~~~~~~~~~~~~~
66ff74923224 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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153
66ff74923224 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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154 The updated BAM file contains those fragments that has at least 1
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155 initial alignment to a transposable element. The final assignment and
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156 probabilities are encoded in the SAM tags:
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157
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158 - ``ZF:Z`` Assigned Feature - The name of the feature that alignment is
66ff74923224 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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159 assigned to.
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160 - ``ZT:Z`` Telescope tag - A value of ``PRI`` indicates that this
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161 alignment is the best hit for the feature and is used in the
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162 likelihood calculations. Otherwise the value will be ``SEC``, meaning
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163 that another alignment to the same feature has a higher score.
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164 - ``ZB:Z`` Best Feature = The name(s) of the highest scoring feature(s)
66ff74923224 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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165 for the fragment.
66ff74923224 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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166 - ``YC:Z`` Specifies color for alignment as R,G,B. UCSC sanctioned tag,
66ff74923224 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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diff changeset
167 see documentation `here.`_
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168 - ``XP:Z`` Alignment probability - estimated posterior probability for
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169 this alignment.
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170
66ff74923224 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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171 .. _here.: http://genome.ucsc.edu/goldenpath/help/hgBamTrackHelp.html
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172
66ff74923224 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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173 ]]>
66ff74923224 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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174 </help>
66ff74923224 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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175 <citations>
66ff74923224 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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176 <citation type="doi">10.1101/398172</citation>
66ff74923224 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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177 </citations>
1
2d8c943f3e8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 3a6e7428a808860068e7cc07a101aa10a31697b8
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178 </tool>