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1 <tool id="ctat_star_fusion" name="ctat_star_fusion" version="1.0.1" profile="17.05">
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2
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3 <description>Fusion-finding Pipeline Using the STAR Aligner</description>
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4 <requirements>
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5 <requirement type="package" version="1.4.0">star-fusion</requirement>
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6 </requirements>
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7 <!-- Using command's detect_errors instead of below.
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8 <stdio>
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9 <exit_code range="1:" level="fatal" description="Error returned from pipeline" />
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10 </stdio>
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11 <regex match="Must investigate error above."
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12 source="stderr"
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13 level="fatal"
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14 description="Unknown error encountered" />
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15 -->
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16 <command detect_errors="default">
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17 <![CDATA[
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18 STAR-Fusion
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19 --genome_lib_dir "${genome_resource_lib.fields.path}"
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20 --left_fq "${left_input}"
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21 --right_fq "${right_input}"
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22 --output_dir subdir
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23 --STAR_SortedByCoordinate
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24 ]]>
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25 </command>
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26
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27 <inputs>
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28 <param format="fastq" name="left_input" type="data" label="Left/Forward strand reads" help=""/>
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29 <param format="fastq" name="right_input" type="data" label="Right/Reverse strand reads" help=""/>
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30 <param name="genome_resource_lib" type="select" label="Select a reference genome">
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31 <options from_data_table="ctat_genome_resource_libs">
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32 <filter type="sort_by" column="2" />
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33 <validator type="no_options" message="No indexes are available" />
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34 </options>
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35 </param>
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36 </inputs>
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37
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38 <outputs>
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39 <data format="txt" name="starfusion_log" label="${tool.name} on ${on_string}: log" from_work_dir="subdir/Log.out"/>
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40 <data format="bam" name="aligned_bam" label="${tool.name} on ${on_string}: Aligned Bam" from_work_dir="subdir/std.STAR.bam"/>
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41 <data format="tabular" name="candidates" label="${tool.name} on ${on_string}: Fusion candidates" from_work_dir="subdir/star-fusion.fusion_predictions.abridged.tsv"/>
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42 <data format="tabular" name="chimeric_junc" label="${tool.name} on ${on_string}: Chimeric.out.junction" from_work_dir="subdir/std.Chimeric.out.junction"/>
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43 </outputs>
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44 <tests>
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45 <test>
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46 <param name="left_input" value="StarFusion/reads_1.fq.gz" />
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47 <param name="right_input" value="StarFusion/reads_2.fq.gz" />
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48 <!--
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49 <param name="left_input" value="reads.left.simPE.fq" />
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50 <param name="right_input" value="reads.right.simPE.fq" />
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51 -->
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52 <!-- FIX - now that we added the CTAT ref lib path as a parameter, how do we find it for testing?
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53 <param name="genome_resource_lib.fields.path" value="?????" />
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54 -->
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55 <!--
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56 <output name="aligned_bam" file="SF_out_aligned.bam" />
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57 <output name="candidates" file="SF_out_fusion_candidates.dat" />
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58 <output name="chimeric_junc" file="SF_out_chimeric.junction" />
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59 <output name="starfusion_log" file="SF_out.log" />
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60 -->
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61 <output name="starfusion_log">
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62 <assert_contents>
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63 <has_line_matching expression=".+" />
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64 <has_line line="ALL DONE!" />
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65 </assert_contents>
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66 </output>
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67 <output name="aligned_bam">
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68 <assert_contents>
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69 <has_line_matching expression=".+" />
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70 <!-- The following checks for the magic number at the start of the bam file -->
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71 <!-- At first I thought "\x8B\x1F" was the number, but it turns out the file
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72 produced by the StarFusion test had that sequence in the file somewhere else.
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73 -->
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74 <has_text_matching expression="\x1F\x8B" />
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75 </assert_contents>
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76 </output>
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77 <output name="candidates">
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78 <assert_contents>
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79 <has_line_matching expression=".+" />
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80 <has_line line="#fusion_name	JunctionReads	SpanningFrags	Splice_type	LeftGene	LeftBreakpoint	RightGene	RightBreakpoint	Long_double_anchor_support" />
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81 </assert_contents>
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82 </output>
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83 <output name="chimeric_junc">
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84 <assert_contents>
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85 <has_line_matching expression=".+" />
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86 <has_line_matching expression="^chr20.*" />
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87 </assert_contents>
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88 </output>
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89 </test>
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90 </tests>
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91 <help>
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92 .. class:: infomark
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93
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94 STAR-Fusion is a component of the Trinity Cancer Transcriptome Analysis Toolkit (CTAT). STAR-Fusion uses the STAR aligner to identify candidate fusion transcripts supported by Illumina reads. STAR-Fusion further processes the output generated by the STAR aligner to map junction reads and spanning reads to a reference annotation set. Please read more here_.
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95
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96 .. _here: https://github.com/STAR-Fusion/STAR-Fusion/wiki
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97
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98 </help>
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99 </tool>
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