Mercurial > repos > yating-l > regtools_junctions_extract

annotate regtools_junctions_extract.xml @ 0:01ed8e112f2a draft

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author yating-l
date Wed, 12 Apr 2017 17:44:58 -0400
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children 06d9062f5430
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1 <tool id="regtools_junctions_extract" name="regtools junctions extract" version="0.1.0">
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2 <description>Extract splice junctions from a RNA-Seq BAM file</description>
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3 <requirements>
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4 <requirement type="package" version="0.3.0">regtools</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 ## regtools expects an indexed BAM file
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11 ## Use symlinks to link the BAM file and its index to the working directory
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12 ## See: https://biostar.usegalaxy.org/p/10128/
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13
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14 ln -sf '${input1}' infile.bam &&
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15 ln -sf '${input1.metadata.bam_index}' infile.bam.bai &&
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16
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17 regtools junctions extract
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18 -i $min_intron_length
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19 -I $max_intron_length
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20 -o $output1
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21 #if str($advanced_options.advanced_options_selector) == "on":
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22 -a $advanced_options.min_anchor_length
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23
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24 #if str($advanced_options.region):
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25 -r "$advanced_options.region"
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26 #end if
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27 #end if
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28 infile.bam &&
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29
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30 python $__tool_directory__/validator.py $output1 $fixed_output
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31 ]]></command>
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32 <inputs>
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33 <param name="input1" type="data" format="bam" />
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34
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35 <param name="min_intron_length" type="integer" label="Minimum intron length" value="20" min="1">
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36 <help>Only considers spliced RNA-Seq reads with this minimum intron length (-i)</help>
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37 </param>
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38 <param name="max_intron_length" type="integer" label="Maximum intron length" value="500000" min="1">
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39 <help>Only considers spliced RNA-Seq reads with this maximum intron length (-I)</help>
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40 </param>
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41
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42 <conditional name="advanced_options">
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43 <param name="advanced_options_selector" type="select" label="Advanced options">
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44 <option value="off" selected="true">Hide advanced options</option>
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45 <option value="on">Display advanced options</option>
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46 </param>
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47 <when value="on">
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48 <param name="min_anchor_length" type="integer" label="Minimum anchor length" value="8" min="1">
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49 <help>Only report splice junctions with this minimum anchor length on both sides of the junction (-a)</help>
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50 </param>
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51 <param name="region" type="text" optional="true" label="Only extract junctions in this region" value="">
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52 <help>Only report splice junctions within this region (format = chrom:start-end) (-r)</help>
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53 <validator type="regex"
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54 message="Region should be in the following format: chrom:start-end">^([^:]+):(\d+)-(\d+)$</validator>
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55 </param>
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56 </when>
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57
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58 <when value="off" />
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59 </conditional>
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60 </inputs>
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61 <outputs>
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62 <data name="output1" format="bed" label="${tool.name} on ${on_string}: original output"/>
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63 <data name="fixed_output" format="bed" label="${tool.name} on ${on_string}: fixed_output for HAC workflow"/>
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64 </outputs>
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65 <tests>
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66 <test>
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67 <!-- Test with default parameters -->
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68 <param name="input1" value="Dbia3_adult_males_shallow.bam" />
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69 <output name="output1" file="Dbia3_adult_males_junctions_i20_I500000.bed" />
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70 <output name="fixed_output" file="Dbia3_adult_males_junctions_i20_I500000_fixed.bed" />
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71 </test>
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72 <test>
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73 <!-- Test with custom intron length thresholds -->
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74 <param name="min_intron_length" value="50" />
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75 <param name="max_intron_length" value="50000" />
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76 <param name="input1" value="Dbia3_adult_males_shallow.bam" />
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77 <output name="output1" file="Dbia3_adult_males_junctions_i50_I50000.bed" />
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78 <output name="fixed_output" file="Dbia3_adult_males_junctions_i50_I50000_fixed.bed" />
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79 </test>
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80 <test>
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81 <!-- Test with advanced option and custom anchor size -->
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82 <param name="advanced_options_selector" value="on" />
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83 <param name="min_anchor_length" value="10" />
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84 <param name="input1" value="Dbia3_adult_males_shallow.bam" />
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85 <output name="output1"
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86 file="Dbia3_adult_males_junctions_i20_I500000_a10.bed" />
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87 <output name="fixed_output"
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88 file="Dbia3_adult_males_junctions_i20_I500000_a10_fixed.bed" />
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89 </test>
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90 <test>
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91 <!-- Test with advanced option and selected region -->
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92 <param name="advanced_options_selector" value="on" />
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93 <param name="region" value="contig2:10000-30000" />
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94 <param name="input1" value="Dbia3_adult_males_shallow.bam" />
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95 <output name="output1" file="Dbia3_adult_males_junctions_i20_I500000_rcontig2_10-30kb.bed" />
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96 <output name="fixed_output" file="Dbia3_adult_males_junctions_i20_I500000_rcontig2_10-30kb_fixed.bed"/>
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97 </test>
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98 <test>
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99 <!--Test with output having invalid strand -->
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100 <param name="input1" value="Dbia3.bam" />
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101 <output name="output1" file="Dbia3_i20_I500000.bed" />
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102 <output name="fixed_output" file="Dbia3_i20_I500000_fixed.bed" />
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103 </test>
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104 </tests>
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105 <help><![CDATA[
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106 **What it does**
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107
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108 The `regtools junctions extract <https://regtools.readthedocs.io/en/latest/commands/junctions-extract/>`_
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109 tool creates a list of exon-exon junctions from spliced RNA-Seq reads within a BAM
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110 alignment file. The format of the output BED file is similar to the ``junctions.bed``
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111 file produced by TopHat2.
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112
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113 The extent of each BED feature corresponds to the maximum overhang of each splice
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114 junction. The score of each BED feature corresponds to the number of spliced RNA-Seq
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115 reads that support each junction.
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116
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117 --------
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118
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119 .. class:: warningmark
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120
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121 By default, the minimum intron size is **20 bp** and the maximum intron size is
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122 **500,000 bp** so that they conform to the default intron size settings for
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123 `HISAT2 <https://ccb.jhu.edu/software/hisat2/manual.shtml#options>`_. The minimum
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124 intron size for the command-line version of ``regtools junctions extract`` is 70 bp.
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125
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126 ]]></help>
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127 <citations>
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128 <citation type="bibtex">
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129 @misc{githubregtools,
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130 author = {Griffith Lab},
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131 year = {2016},
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132 title = {regtools},
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133 publisher = {GitHub},
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134 journal = {GitHub repository},
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135 url = {https://github.com/griffithlab/regtools},
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136 }</citation>
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137 </citations>
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138 </tool>