Mercurial > repos > iuc > chira_merge

annotate chira_merge.xml @ 6:7f9cf152cf8f draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit cc81372929ffba1f5ab8cf620911425c832fb120"
author iuc
date Thu, 16 Apr 2020 13:23:11 -0400
parents 0170de5072d4
children 35f433d0bd7f
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rev   line source
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5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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1 <tool id="chira_merge" name="ChiRA merge" version="@WRAPPER_VERSION@0">
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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2 <description>merge aligned positions</description>
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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3 <macros>
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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4 <import>macros.xml</import>
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5 </macros>
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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6 <expand macro="requirements" />
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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7 <command><![CDATA[
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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8 chira_merge.py
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9 -b '$alignments'
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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10 #if str($annotation.choice) == "yes":
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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11 -g '$annotation.gtf'
4
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12 #end if
0
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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13 -so '$segment_overlap'
4
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14 #if str($merge.mode) == "blockbuster":
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15 -bb
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16 -d '$merge.distance'
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17 -mc '$merge.min_cluster_height'
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18 -mb '$merge.min_block_height'
0170de5072d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit aafb8e5de9023eeddd7f4683909f418ef5aae086"
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19 -sc '$merge.scale'
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20 #else:
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21 -ao '$merge.alignment_overlap'
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22 #end if
0
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23 -o ./
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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24 ]]></command>
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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25
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26 <inputs>
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27 <param format="bed" name="alignments" type="data" label="Input BED file of alignments"/>
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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28 <conditional name="annotation">
1
ce26b5a859ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit 6845f3b028a42acbefb07c5f59fd2e558f50a768"
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29 <param name="choice" type="select" label="Do you have an annotation in GTF format?">
0
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30 <option value="yes">Yes</option>
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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31 <option value="no">No</option>
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32 </param>
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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33 <when value="yes">
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34 <param format="gtf,gff" name="gtf" type="data" label="Annotations in GTF format"/>
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35 </when>
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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36 <when value="no">
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37 <!-- Do nothing -->
4
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38 </when>
0
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39 </conditional>
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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40 <param name="segment_overlap" type="float" value="0.7" label="Overlap fraction for merging mapped read positions to segments" min="0" max="1"
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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41 help="Matching read positions with greater than this fraction overlap are merged into a segment"/>
4
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42 <conditional name="merge">
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43 <param name="mode" type="select" label="Select the mode of merging">
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44 <option value="overlap">Overlap based</option>
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45 <option value="blockbuster">Gaussian based (blockbuster)</option>
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46 </param>
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47 <when value="overlap">
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48 <param name="alignment_overlap" type="float" value="0.7" label="Overlap fraction for merging alignments" min="0" max="1"
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49 help="Minimum fraction of BED entries that must overlap inorder to merge"/>
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50 </when>
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51 <when value="blockbuster">
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52 <param name="distance" type="integer" value="30" label="Blockbuster parameter distance"
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53 help="Minimum distance between two clusters"/>
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54 <param name="min_cluster_height" type="float" value="10" label="Blockbuster parameter minClusterHeight"
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55 help="minimum height (readno) of a cluster"/>
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56 <param name="min_block_height" type="float" value="1" label="Blockbuster parameter minBlockHeight"
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57 help="minimum height (readno) of a block"/>
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58 <param name="scale" type="float" value="0.4" label="Blockbuster parameter scale" min="0" max="1"
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59 help="scale stddev for a single read"/>
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60 </when>
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61 </conditional>
0
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62 </inputs>
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63 <outputs>
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64 <data format="bed" name="segments_bed" from_work_dir="segments.bed" label="ChiRA aligned read segments on ${on_string}"/>
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65 <data format="tabular" name="merged_bed" from_work_dir="merged.bed" label="ChiRA merged alignments on ${on_string}"/>
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66 </outputs>
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67
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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68 <tests>
4
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69 <!-- Test: Merge without annotation -->
0
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70 <test expect_num_outputs="2">
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71 <param name="alignments" value="alignments.bed"/>
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72 <param name="choice" value="no" />
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73 <output name="segments_bed" >
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74 <assert_contents>
4
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75 <has_text_matching expression="ENSMUST00000160533\t69\t82\t34\|1\|2,ENSMUST00000160533,69,82,\+,42S13M\t1\t\+" />
0
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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76 </assert_contents>
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77 </output>
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78 <output name="merged_bed" >
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79 <assert_contents>
4
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80 <has_text_matching expression="ENSMUST00000182010\t408\t477\t\+" />
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81 <has_text_matching expression="mmu-miR-106a-3p\t4\t15\t\+" />
0
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82 </assert_contents>
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83 </output>
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84 </test>
4
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85 <!-- Test: Merge with annotation -->
0
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86 <test expect_num_outputs="2">
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87 <param name="alignments" value="alignments.bed" />
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88 <param name="choice" value="yes" />
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89 <param name="gtf" value="annotation.gtf" />
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90 <output name="segments_bed" >
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91 <assert_contents>
4
0170de5072d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit aafb8e5de9023eeddd7f4683909f418ef5aae086"
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92 <has_text_matching expression="5\t137142331\t137142344\t34\|1\|2,ENSMUST00000160533,69,82,\+,42S13M\t1\t-" />
0
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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93 </assert_contents>
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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94 </output>
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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95 <output name="merged_bed" >
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96 <assert_contents>
4
0170de5072d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit aafb8e5de9023eeddd7f4683909f418ef5aae086"
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97 <has_text_matching expression="17\t39846957\t39847016\t\+" />
0170de5072d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit aafb8e5de9023eeddd7f4683909f418ef5aae086"
iuc
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98 <has_text_matching expression="5\t137142331\t137142344\t-" />
0170de5072d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit aafb8e5de9023eeddd7f4683909f418ef5aae086"
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99 </assert_contents>
0170de5072d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit aafb8e5de9023eeddd7f4683909f418ef5aae086"
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100 </output>
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101 </test>
0170de5072d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit aafb8e5de9023eeddd7f4683909f418ef5aae086"
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102 <!-- Test: Merge using blockbuster -->
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103 <test expect_num_outputs="2">
0170de5072d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit aafb8e5de9023eeddd7f4683909f418ef5aae086"
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104 <param name="alignments" value="alignments.bed" />
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105 <param name="choice" value="yes" />
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106 <param name="gtf" value="annotation.gtf" />
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107 <param name="mode" value="blockbuster" />
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108 <param name="min_cluster_height" value="5" />
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109 <output name="segments_bed" >
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110 <assert_contents>
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111 <has_text_matching expression="5\t137142331\t137142344\t34\|1\|2,ENSMUST00000160533,69,82,\+,42S13M\t1\t-" />
0170de5072d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit aafb8e5de9023eeddd7f4683909f418ef5aae086"
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112 </assert_contents>
0170de5072d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit aafb8e5de9023eeddd7f4683909f418ef5aae086"
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113 </output>
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114 <output name="merged_bed" >
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115 <assert_contents>
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116 <has_text_matching expression="17\t39846957\t39847016\t\+" />
0
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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117 </assert_contents>
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118 </output>
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119 </test>
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120 </tests>
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121
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122 <help>
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123
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124 .. class:: infomark
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125
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126 **What it does**
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127
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128 This tool merges the overlapping aligned positions to define the read concentrated loci. If an annotation GTF file produced, the transcriptomic alignment positions are first converted to their corresponding genomic positions.
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129
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130 **Inputs**
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131
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132 * Alignments in BED format
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133 * An annotation GTF file contaning reference genomic positions.
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134
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135 **Output**
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136
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137 * BED file containing the alignments with reads categorized into segments depending on which part of the read is aligned.
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138 * Tabular file containing merged alignments. 4th column contains all the alignments merged into that location.
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139
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140 </help>
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141 <expand macro="citations" />
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142 </tool>