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annotate pizzly.xml @ 1:3658798275bd draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pizzly/ commit 0ad49d906b38e290b860310e73b1f8585ac65d09
author iuc
date Tue, 03 Oct 2017 18:04:29 -0400
parents 6095717c185d
children
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3658798275bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pizzly/ commit 0ad49d906b38e290b860310e73b1f8585ac65d09
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1 <tool id="pizzly" name="pizzly" version="0.37.3.1">
0
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2 <description>- fast fusion detection using kallisto</description>
6095717c185d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pizzly/ commit a9f602d697c570bc40c6b6ab8e873a11e0eb703d
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3 <requirements>
6095717c185d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pizzly/ commit a9f602d697c570bc40c6b6ab8e873a11e0eb703d
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4 <requirement type="package" version="0.37.3">pizzly</requirement>
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5 </requirements>
6095717c185d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pizzly/ commit a9f602d697c570bc40c6b6ab8e873a11e0eb703d
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6 <version_command>pizzly --version</version_command>
6095717c185d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pizzly/ commit a9f602d697c570bc40c6b6ab8e873a11e0eb703d
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7 <command detect_errors="exit_code"><![CDATA[
1
3658798275bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pizzly/ commit 0ad49d906b38e290b860310e73b1f8585ac65d09
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3658798275bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pizzly/ commit 0ad49d906b38e290b860310e73b1f8585ac65d09
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9 ## Get reference FASTA
0
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1
3658798275bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pizzly/ commit 0ad49d906b38e290b860310e73b1f8585ac65d09
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11 #if $ref_fa.rfasta.rfasta_source == "history":
3658798275bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pizzly/ commit 0ad49d906b38e290b860310e73b1f8585ac65d09
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12 ln -s '$ref_fa.rfasta.ref_fa_hist' reference.fa &&
3658798275bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pizzly/ commit 0ad49d906b38e290b860310e73b1f8585ac65d09
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13 #else:
3658798275bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pizzly/ commit 0ad49d906b38e290b860310e73b1f8585ac65d09
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14 ln -s '$ref_fa.rfasta.ref_fa_builtin.fields.path' reference.fa &&
3658798275bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pizzly/ commit 0ad49d906b38e290b860310e73b1f8585ac65d09
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15 #end if
0
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1
3658798275bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pizzly/ commit 0ad49d906b38e290b860310e73b1f8585ac65d09
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3658798275bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pizzly/ commit 0ad49d906b38e290b860310e73b1f8585ac65d09
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18 ## Get reference GTF
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1
3658798275bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pizzly/ commit 0ad49d906b38e290b860310e73b1f8585ac65d09
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20 #if $ref_gtf.rgtf.rgtf_source == "history":
3658798275bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pizzly/ commit 0ad49d906b38e290b860310e73b1f8585ac65d09
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21 ln -s '$ref_gtf.rgtf.ref_gtf_hist' reference.gtf &&
3658798275bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pizzly/ commit 0ad49d906b38e290b860310e73b1f8585ac65d09
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22 #else:
3658798275bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pizzly/ commit 0ad49d906b38e290b860310e73b1f8585ac65d09
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23 ln -s '$ref_gtf.rgtf.ref_gtf_builtin.fields.path' reference.gtf &&
3658798275bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pizzly/ commit 0ad49d906b38e290b860310e73b1f8585ac65d09
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24 #end if
0
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25
1
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3658798275bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pizzly/ commit 0ad49d906b38e290b860310e73b1f8585ac65d09
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27 ## Run pizzly
0
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1
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29 pizzly
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30 --fasta reference.fa
3658798275bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pizzly/ commit 0ad49d906b38e290b860310e73b1f8585ac65d09
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31 --gtf reference.gtf
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32 --align-score '$adv.align_score'
3658798275bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pizzly/ commit 0ad49d906b38e290b860310e73b1f8585ac65d09
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33 --insert-size '$adv.insert_size'
3658798275bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pizzly/ commit 0ad49d906b38e290b860310e73b1f8585ac65d09
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34 --k '$adv.kmer_size'
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35 $adv.ignore_protein
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36 --output out
3658798275bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pizzly/ commit 0ad49d906b38e290b860310e73b1f8585ac65d09
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37 '$kinput.input' &&
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38
1
3658798275bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pizzly/ commit 0ad49d906b38e290b860310e73b1f8585ac65d09
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3658798275bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pizzly/ commit 0ad49d906b38e290b860310e73b1f8585ac65d09
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40 ## Convert json output to tabular
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3658798275bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pizzly/ commit 0ad49d906b38e290b860310e73b1f8585ac65d09
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42 pizzly_flatten_json.py out.json > out.fusions.tab
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43
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44 ]]></command>
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45 <inputs>
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46 <section name="kinput" expanded="false" title="Select kallisto fusions file">
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47 <param name="input" type="data" format="tabular" label="Output from kallisto quant --fusion" />
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48 </section>
1
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49 <section name="ref_fa" expanded="false" title="Select Reference FASTA">
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50 <conditional name="rfasta">
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51 <param name="rfasta_source" type="select" label="Reference transcriptome FASTA" help="Make sure the FASTA corresponds to the same file used with kallisto quant --fusion">
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52 <option value="cached" selected="true">Use a built-in transcriptome</option>
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53 <option value="history">Use a FASTA from history</option>
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54 </param>
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55 <when value="cached">
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56 <param name="ref_fa_builtin" type="select" label="Select a built-in FASTA" help="If your transcriptome of interest is not listed, contact your Galaxy administrator">
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57 <options from_data_table="all_fasta">
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58 <filter type="sort_by" column="2" />
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59 <validator type="no_options" message="No FASTA is available for the selected input dataset" />
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60 </options>
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61 </param>
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62 </when>
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63 <when value="history">
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64 <param name="ref_fa_hist" type="data" format="fasta" label="Select a history FASTA" />
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65 </when>
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66 </conditional>
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67 </section>
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68 <section name="ref_gtf" expanded="false" title="Select Reference GTF">
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69 <conditional name="rgtf">
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70 <param name="rgtf_source" type="select" label="Reference GTF">
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71 <option value="cached" selected="true">Use a built-in transcriptome</option>
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72 <option value="history">Use a GTF from history</option>
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73 </param>
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74 <when value="cached">
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75 <param name="ref_gtf_builtin" type="select" label="Select a built-in GTF" help="If the GTF file for your transcriptome of interest is not listed, contact your Galaxy administrator">
1
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76 <options from_data_table="gene_sets">
0
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77 <filter type="sort_by" column="2" />
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78 <validator type="no_options" message="No GTF file is available." />
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79 </options>
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80 </param>
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81 </when>
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82 <when value="history">
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83 <param name="ref_gtf_hist" type="data" format="gtf" label="Select a history GTF" />
0
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84 </when>
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85 </conditional>
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86 </section>
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87 <section name="adv" expanded="false" title="Advanced Options">
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88 <param name="insert_size" argument="--insert-size" type="integer" value="400" min="0" label="Maximum insert size of the paired-end library" help="kallisto will estimate this from the reads, default: 400" />
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89 <param name="align_score" argument="--align-score" type="integer" value="2" min="0" label="Number of mismatches allowed" help="default: 2" />
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90 <param name="kmer_size" argument="--k" type="integer" value="31" min="0" label="K-mer size used to create the kallisto index" help="default: 31" />
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91 <param name="ignore_protein" argument="--ignore-protein" type="boolean" truevalue="--ignore-protein" falsevalue="" checked="false" label="Ignore protein coding information in annotation" help="Warning: this will probably lead to an increase in the number of false positives reported"/>
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92 </section>
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93 </inputs>
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94 <outputs>
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95 <data name="fusions_tab" format="tabular" from_work_dir="out.fusions.tab" label="${tool.name} on ${on_string}: Table"/>
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96 <data name="fusions_fa" format="fasta" from_work_dir="out.fusions.fasta" label="${tool.name} on ${on_string}: Fasta"/>
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97 </outputs>
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98 <tests>
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99 <test><!-- Ensure history fasta and gtf work -->
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100 <param name="rfasta_source" value="history" />
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101 <param name="rgtf_source" value="history" />
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102 <param name="input" ftype="tabular" value="fusion.txt" />
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103 <param name="ref_fa_hist" ftype="fasta" value="ref.trans.fasta.gz" />
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104 <param name="ref_gtf_hist" ftype="gtf" value="ref.gtf.gz" />
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105 <output name="fusions_tab" file="out.fusions.tab" ftype="tabular" />
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106 <output name="fusions_fa" file="out.fusions.fasta" ftype="fasta" />
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107 </test>
1
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108 <test><!-- Ensure built-in fasta and gtf work -->
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109 <param name="rfasta_source" value="cached" />
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110 <param name="rgtf_source" value="cached" />
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111 <param name="input" ftype="tabular" dbkey="hg38" value="fusion.txt" />
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112 <output name="fusions_tab" file="out.fusions.tab" ftype="tabular" />
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113 <output name="fusions_fa" file="out.fusions.fasta" ftype="fasta" />
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114 </test>
0
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115 </tests>
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116 <help><![CDATA[
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117
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118 .. class:: infomark
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119
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120 **What it does**
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121
1
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122 pizzly_ is a program for detecting gene fusions from RNA-Seq data of cancer samples.
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123
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124 pizzly introduces a novel approach to fusion detection, it builds on the pseudoalignment idea (that simplifies and accelerates transcript quantification) by inspecting paired reads that cannot be pseudoaligned due to conflicting matches. pizzly filters false positives, assembles new transcripts from the fusion reads, and reports candidate fusions.
0
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125
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126 With pizzly, fusion detection from RNA-Seq reads can be performed **in a matter of minutes**.
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127
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128 .. _pizzly: https://github.com/pmelsted/pizzly
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129
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130 -----
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131
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132 **Inputs**
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133
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134 - one or more tabular files from kallisto quant (run with the --fusion parameter on paired-end fastqs)
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135 - a FASTA file containing the reference transcriptome. This must be the same fasta that was used to build the kallisto index.
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136 - a GTF file describing the transcriptome. Ensembl transcriptomes recommended.
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137
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138 pizzly has been tested on Ensembl (versions 75+) and Gencode (version 19+) annotations. The latest Ensembl annotations (version 87 GTF, FASTA) are recommended for running with pizzly.
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139
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140 -----
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141
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142 **Outputs**
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143
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144 Two output files are created containing the filtered fusion calls
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145
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146 - a tabular file
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147 - a FASTA file
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148
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149 -----
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150
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151 **More Information**
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152
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153 Fusion junctions are detected by pizzly using a two-stage method. The first stage is implemented in kallisto and detects individual reads or read pairs, whose constituent parts pseudoalign to a reference transcriptome but that in combination fail to pseudoalign. pizzly takes the output of the potential fusion junctions found by kallisto and performs a detailed analysis of the associated reads by aligning them across the putative junctions. Additionally, pizzly is annotation aware, i.e. it uses information about the genomic coordinates and gene identities of each isoform to identify possible false positives arising from repetitive sequences across the genome.
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154
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155 ]]></help>
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156 <citations>
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157 <citation type="doi">10.1101/166322</citation>
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158 </citations>
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159 </tool>