Mercurial > repos > iuc > telescope_assign

annotate telescope_assign.xml @ 0:71fcee7f54df draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
author iuc
date Tue, 03 Sep 2019 18:11:46 -0400
parents
children 54144e379f6d
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71fcee7f54df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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1 <?xml version="1.0"?>
71fcee7f54df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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2 <tool id="telescope_assign" name="Reassign reads" version="@VERSION@">
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3 <description>with TELESCOPE using a statistical model</description>
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4 <macros>
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5 <token name="@VERSION@">1.0.3</token>
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6 </macros>
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7 <requirements>
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8 <requirement type="package" version="@VERSION@">telescope</requirement>
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9 <requirement type="package" version="1.9">samtools</requirement>
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10 </requirements>
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11 <command detect_errors="exit_code"><![CDATA[
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12 mkdir tempdir &&
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13 mkdir outdir &&
71fcee7f54df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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14 telescope assign '$input_alignment' '$input_gtf'
71fcee7f54df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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15 --tempdir tempdir
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16 --outdir outdir
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17 --ncpu \${GALAXY_SLOTS:-1}
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18 $updated_sam
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19 #if str($advanced.advanced_options) == 'select':
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20 --reassign_mode $advanced.reassign_mode
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21 --conf_prob $advanced.conf_prob
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22 --overlap_mode $advanced.overlap_mode
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23 --overlap_threshold $advanced.overlap_threshold
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24 --annotation_class $advanced.annotation_class
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25 --pi_prior $advanced.pi_prior
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26 --theta_prior $advanced.theta_prior
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27 --em_epsilon $advanced.em_epsilon
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28 --max_iter $advanced.max_iter
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29 $advanced.use_likelihood
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30 #end if
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31 #if $updated_sam
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32 &&
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33 if [ -f outdir/telescope-updated.bam ] ; then
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34 samtools sort outdir/telescope-updated.bam > '$updated_alignment' ;
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35 else
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36 echo 'Updated alignment file not found.' ;
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37 exit 1 ;
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38 fi
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39 #end if
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40 ]]></command>
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41 <inputs>
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42 <param name="input_alignment" type="data" format="sam,bam" label="Input SAM or BAM file" />
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43 <param name="input_gtf" type="data" format="gtf" label="Input annotation" />
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44 <param argument="--updated_sam" type="boolean" truevalue="--updated_sam" falsevalue="" label="Also output an updated BAM file with reassigned reads" />
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45 <conditional name="advanced">
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46 <param name="advanced_options" type="select" label="Advanced options">
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47 <option value="defaults">Use defaults</option>
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48 <option value="select">Select values</option>
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49 </param>
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50 <when value="defaults" />
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51 <when value="select">
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52 <param argument="--reassign_mode" type="select" label="Reassignment mode"
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53 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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54 <option value="exclude">Exclude</option>
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55 <option value="choose">Choose</option>
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56 <option value="average">Average</option>
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57 <option value="conf">Conf</option>
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58 <option value="unique">Unique</option>
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59 </param>
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60 <param argument="--conf_prob" type="float" value="0.9" min="0" max="1" label="Minimum probability for high confidence assignment" />
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61 <param argument="--overlap_mode" type="select" label="Overlap mode" help="The method used to determine whether a fragment overlaps feature">
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62 <option value="threshold">Threshold</option>
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63 <option value="intersection-strict">Strict intersection</option>
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64 <option value="union">Union</option>
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65 </param>
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66 <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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67 <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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68 <option value="intervaltree">Interval tree</option>
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69 <option value="htseq">HTSeq</option>
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70 </param>
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71 <param argument="--pi_prior" type="integer" value="0" label="Prior on &#960;" help="Equivalent to adding n unique reads." />
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72 <param argument="--theta_prior" type="integer" value="0" label="Prior on &#952;" help="Equivalent to adding n non-unique reads." />
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73 <param argument="--em_epsilon" type="float" value="0.0000001" label="EM Algorithm &#965; cutoff" help="Default: 1e-7" />
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74 <param argument="--max_iter" type="integer" value="100" label="EM Algorithm maximum iterations" help="Default: 100" />
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75 <param argument="--use_likelihood" type="boolean" truevalue="--use_likelihood" falsevalue="" label="Use difference in log-likelihood as convergence criteria" />
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76 </when>
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77 </conditional>
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78 </inputs>
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79 <outputs>
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80 <data name="output" format="tabular" from_work_dir="outdir/telescope-telescope_report.tsv" />
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81 <data name="updated_alignment" format="bam">
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82 <filter>updated_sam</filter>
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83 </data>
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84 </outputs>
71fcee7f54df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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85 <tests>
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86 <test>
71fcee7f54df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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87 <param name="input_alignment" value="telescope-in1.bam" />
71fcee7f54df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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diff changeset
88 <param name="input_gtf" value="telescope-in1.gtf" />
71fcee7f54df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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89 <param name="updated_sam" value="true" />
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90 <output name="output" file="telescope-out1.tabular" />
71fcee7f54df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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91 <output name="updated_alignment" file="telescope-out1.bam" />
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92 </test>
71fcee7f54df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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93 </tests>
71fcee7f54df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
iuc
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94 <help><![CDATA[
71fcee7f54df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
iuc
parents:
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95 Output
71fcee7f54df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
iuc
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96 ------
71fcee7f54df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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97
71fcee7f54df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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98 Telescope has two main output files: the telescope report and an updated
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99 SAM file (optional). The report file is most important for downstream
71fcee7f54df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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100 differential expression analysis since it contains the fragment count
71fcee7f54df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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101 estimates. The updated SAM file is useful for downstream locus-specific
71fcee7f54df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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102 analyses.
71fcee7f54df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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103
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104 Telescope report
71fcee7f54df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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105 ~~~~~~~~~~~~~~~~
71fcee7f54df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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106
71fcee7f54df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
iuc
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107 The first line in the telescope report is a comment (starting with a
71fcee7f54df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
iuc
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108 “#”) that contains information about the run such as the number of
71fcee7f54df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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109 fragments processed, number of mapped fragments, number of uniquely and
71fcee7f54df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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110 ambiguously mapped fragments, and number of fragments mapping to the
71fcee7f54df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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111 annotation. The total number of mapped fragments may be useful for
71fcee7f54df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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112 normalization.
71fcee7f54df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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113
71fcee7f54df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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114 The rest of the report is a table with calculated expression values for
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115 individual transposable element locations. The columns of the table are:
71fcee7f54df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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116
71fcee7f54df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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117 - ``transcript`` - Transcript ID, by default from "locus" field. See
71fcee7f54df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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118 --attribute argument to use a different attribute.
71fcee7f54df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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119 - ``transcript_length`` - Approximate length of transcript. This is
71fcee7f54df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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120 calculated from the annotation, not the data, and is equal to the
71fcee7f54df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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121 spanning length of the annotation minus any non-model regions.
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122 - ``final_count`` - Total number of fragments assigned to transcript
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123 after fitting the Telescope model. This is the column to use for
71fcee7f54df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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124 downstream analysis that models data as negative binomial, i.e.
71fcee7f54df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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125 DESeq2.
71fcee7f54df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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126 - ``final_conf`` - Final confident fragments. The number of fragments
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127 assigned to transcript whose posterior probability exceeds a cutoff,
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128 0.9 by default. Set this using the --conf_prob argument.
71fcee7f54df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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129 - ``final_prop`` - Final proportion of fragments represented by
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130 transcript. This is the final estimate of the π parameter.
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131 - ``init_aligned`` - Initial number of fragments aligned to transcript.
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132 A given fragment will contribute +1 to each transcript that it is
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133 aligned to, thus the sum of this will be greater than the number of
71fcee7f54df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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134 fragments if there are multimapped reads.
71fcee7f54df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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135 - ``unique_count`` - Unique count. Number of fragments aligning
71fcee7f54df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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136 uniquely to this transcript.
71fcee7f54df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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137 - ``init_best`` - Initial number of fragments aligned to transcript
71fcee7f54df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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diff changeset
138 that have the "best" alignment score for that fragment. Fragments
71fcee7f54df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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139 that have the same best alignment score to multiple transcripts will
71fcee7f54df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
iuc
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140 contribute +1 to each transcript.
71fcee7f54df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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141 - ``init_best_random`` - Initial number of fragments aligned to
71fcee7f54df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
iuc
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142 transcript that have the "best" alignment score for that fragment.
71fcee7f54df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
iuc
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143 Fragments that have the same best alignment score to multiple
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144 transcripts will be randomly assigned to one transcript.
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145
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146 Updated BAM file
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147 ~~~~~~~~~~~~~~~~
71fcee7f54df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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148
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149 The updated BAM file contains those fragments that has at least 1
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150 initial alignment to a transposable element. The final assignment and
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151 probabilities are encoded in the SAM tags:
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152
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153 - ``ZF:Z`` Assigned Feature - The name of the feature that alignment is
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154 assigned to.
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155 - ``ZT:Z`` Telescope tag - A value of ``PRI`` indicates that this
71fcee7f54df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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156 alignment is the best hit for the feature and is used in the
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157 likelihood calculations. Otherwise the value will be ``SEC``, meaning
71fcee7f54df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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158 that another alignment to the same feature has a higher score.
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159 - ``ZB:Z`` Best Feature = The name(s) of the highest scoring feature(s)
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160 for the fragment.
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161 - ``YC:Z`` Specifies color for alignment as R,G,B. UCSC sanctioned tag,
71fcee7f54df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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162 see documentation `here.`_
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163 - ``XP:Z`` Alignment probability - estimated posterior probability for
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164 this alignment.
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165
71fcee7f54df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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166 .. _here.: http://genome.ucsc.edu/goldenpath/help/hgBamTrackHelp.html
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167
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168 ]]>
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169 </help>
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170 <citations>
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171 <citation type="doi">10.1101/398172</citation>
71fcee7f54df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope commit 2ad29725263c29d7612d2e150801c212eb9a2463"
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172 </citations>
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173 </tool>