Mercurial > repos > trinity_ctat > fusion_inspector
annotate fusion_inspector.xml @ 1:2e993ad06cf2 draft default tip
Removing mthod option from fusion_inspector tool. Only STAR is supported now.
| author | trinity_ctat |
|---|---|
| date | Thu, 25 Jan 2018 09:25:31 -0500 |
| parents | e4892a11c58d |
| children |
| rev | line source |
|---|---|
| 0 | 1 <tool id="fusion-inspector" name="Fusion Inspector" version="1.0.0" profile="17.05"> |
| 2 <description>In silico Validation of Fusion Transcript Predictions</description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="1.1.0">fusion-inspector</requirement> | |
| 5 </requirements> | |
| 6 <command detect_errors="default"> | |
| 7 <![CDATA[ | |
| 8 FusionInspector | |
| 9 --fusions $fusion_candidates_list | |
| 10 --genome_lib "${genome_ref_lib.fields.path}" | |
| 11 --left_fq $left_input | |
| 12 --right $right_input | |
| 13 --out_dir "subdir" | |
| 14 --out_prefix "finspector" | |
| 15 --prep_for_IGV | |
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2e993ad06cf2
Removing mthod option from fusion_inspector tool. Only STAR is supported now.
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16 --align_utils STAR |
| 0 | 17 #if $trinity_status.trinity=="true" |
| 18 --include_Trinity | |
| 19 #end if | |
| 20 ]]> | |
| 21 </command> | |
| 22 <stdio> | |
| 23 <exit_code range="1:" level="fatal" description="Error returned from pipeline" /> | |
| 24 </stdio> | |
| 25 <regex match="Must investigate error above." | |
| 26 source="stderr" | |
| 27 level="fatal" | |
| 28 description="Unknown error encountered" /> | |
| 29 <inputs> | |
| 30 <param format="tabular" name="fusion_candidates_list" type="data" multiple="True" label="Choose candidate list:" help="Fusion predictions"/> | |
| 31 <param format="fastq" name="left_input" type="data" label="Left/Forward strand reads" help=""/> | |
| 32 <param format="fastq" name="right_input" type="data" label="Right/Reverse strand reads" help=""/> | |
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2e993ad06cf2
Removing mthod option from fusion_inspector tool. Only STAR is supported now.
trinity_ctat
parents:
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changeset
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33 <!-- The HISAT and GSNAP methods are not supported and are being removed, leaving only STAR. |
| 0 | 34 <param name="method" type="select" label="Choose method:"> |
| 35 <option value="HISAT">HISAT</option> | |
| 36 <option value="STAR">STAR</option> | |
| 37 <option value="GSNAP">GSNAP</option> | |
| 38 </param> | |
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2e993ad06cf2
Removing mthod option from fusion_inspector tool. Only STAR is supported now.
trinity_ctat
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39 --> |
| 0 | 40 <conditional name="trinity_status"> |
| 41 <param name="trinity" type="select" label="Use Trinity:"> | |
| 42 <option value="true">True</option> | |
| 43 <option value="false">False</option> | |
| 44 </param> | |
| 45 </conditional> | |
| 46 <param name="genome_ref_lib" type="select" label="Select a reference genome"> | |
| 47 <options from_data_table="ctat_genome_ref_libs"> | |
| 48 <filter type="sort_by" column="2" /> | |
| 49 <validator type="no_options" message="No indexes are available" /> | |
| 50 </options> | |
| 51 </param> | |
| 52 </inputs> | |
| 53 <outputs> | |
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2e993ad06cf2
Removing mthod option from fusion_inspector tool. Only STAR is supported now.
trinity_ctat
parents:
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54 <data format="txt" name="finspector_idx" label="fidx" from_work_dir="subdir/finspector.fa.fai"/> |
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2e993ad06cf2
Removing mthod option from fusion_inspector tool. Only STAR is supported now.
trinity_ctat
parents:
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diff
changeset
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55 <data format="txt" name="cytoBand" label="cytoBand" from_work_dir="subdir/cytoBand.txt"/> |
| 0 | 56 <data format="fasta" name="finspector_fa" label="finspector_fasta" from_work_dir="subdir/finspector.fa"/> |
| 57 <data format="bed" name="finspector_bed" label="finspector_bed" from_work_dir="subdir/finspector.bed"/> | |
| 58 <data format="tabular" name="FusionJuncSpan" label="FusionJuncSpan" from_work_dir="subdir/finspector.igv.FusionJuncSpan"/> | |
| 59 <data format="bed" name="junction_bed" label="junction_bed" from_work_dir="subdir/finspector.junction_reads.bam.bed"/> | |
| 60 <data format="bam" name="junction_bam" label="junction_bam" from_work_dir="subdir/finspector.junction_reads.bam"/> | |
| 61 <data format="bam" name="spanning_bam" label="spanning_bam" from_work_dir="subdir/finspector.spanning_reads.bam"/> | |
| 62 <data format="bed" name="spanning_bed" label="spanning_bed" from_work_dir="subdir/finspector.spanning_reads.bam.bed"/> | |
| 63 <data format="bed" name="trinity_bed" label="trinity_bed" from_work_dir="subdir/finspector.gmap_trinity_GG.fusions.gff3.bed.sorted.bed"> | |
| 64 <filter>trinity_status['trinity'] == "true"</filter> | |
| 65 </data> | |
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2e993ad06cf2
Removing mthod option from fusion_inspector tool. Only STAR is supported now.
trinity_ctat
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66 <data format="txt" name="fusionPredictions" label="fusion_predictions.final" from_work_dir="subdir/finspector.fusion_predictions.final"/> |
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2e993ad06cf2
Removing mthod option from fusion_inspector tool. Only STAR is supported now.
trinity_ctat
parents:
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diff
changeset
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67 <data format="txt" name="fusionPredictionsAbridged" label="fusion_predictions_abridged" from_work_dir="subdir/finspector.fusion_predictions.final.abridged"/> |
| 0 | 68 <data format="json" name="fusion_json" label="fusion_json" from_work_dir="subdir/finspector.fusion_inspector_web.json"/> |
| 69 </outputs> | |
| 70 <tests> | |
| 71 <test> | |
| 72 <param name="fusion_candidates_list" value="FusionInspector/fusion_targets.A.txt,FusionInspector/fusion_targets.B.txt,FusionInspector/fusion_targets.C.txt" /> | |
| 73 <param name="left_input" value="FusionInspector/test.reads_1.fastq.gz" /> | |
| 74 <param name="right_input" value="FusionInspector/test.reads_2.fastq.gz" /> | |
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1
2e993ad06cf2
Removing mthod option from fusion_inspector tool. Only STAR is supported now.
trinity_ctat
parents:
0
diff
changeset
|
75 <!-- The HISAT and GSNAP methods are not supported and are being removed, leaving only STAR. |
| 0 | 76 <param name="method" value="STAR" /> |
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2e993ad06cf2
Removing mthod option from fusion_inspector tool. Only STAR is supported now.
trinity_ctat
parents:
0
diff
changeset
|
77 --> |
| 0 | 78 <param name="trinity" value="false" /> |
| 79 <output name="finspector_idx" file="FusionInspector/test.reads_1_2.fa.fai" /> | |
| 80 <output name="cytoBand" file="FusionInspector/test.reads_1_2.cytoBand.tail.txt" compare="contains" /> | |
| 81 <output name="finspector_fa" file="FusionInspector/test.reads_1_2.fa" /> | |
| 82 <output name="finspector_bed" file="FusionInspector/test.reads_1_2.bed.sorted" sort="true" /> | |
| 83 <output name="FusionJuncSpan" > | |
| 84 <assert_contents> | |
| 85 <has_line_matching expression=".+" /> | |
| 86 <has_line line="#scaffold	fusion_break_name	break_left	break_right	num_junction_reads	num_spanning_frags	spanning_frag_coords" /> | |
| 87 </assert_contents> | |
| 88 </output> | |
| 89 <!-- sorted output sometimes matches, but simetimes not, so now I just test for similar size. --> | |
| 90 <output name="junction_bed" file="FusionInspector/test.reads_1_2.junction_reads.bam.bed.sorted" sort="true" compare="sim_size" > | |
| 91 <assert_contents> | |
| 92 <has_line_matching expression=".+" /> | |
| 93 <has_n_columns n="12" /> | |
| 94 </assert_contents> | |
| 95 </output> | |
| 96 <output name="junction_bam" > | |
| 97 <assert_contents> | |
| 98 <has_line_matching expression=".+" /> | |
| 99 <!-- The following checks for the magic number at the start of the bam file --> | |
| 100 <has_text_matching expression="\x1F\x8B" /> | |
| 101 </assert_contents> | |
| 102 </output> | |
| 103 <output name="spanning_bam" > | |
| 104 <assert_contents> | |
| 105 <has_line_matching expression=".+" /> | |
| 106 <!-- The following checks for the magic number at the start of the bam file --> | |
| 107 <has_text_matching expression="\x1F\x8B" /> | |
| 108 </assert_contents> | |
| 109 </output> | |
| 110 <output name="spanning_bed" file="FusionInspector/test.reads_1_2.spanning_reads.bam.bed.sorted" sort="true" /> | |
| 111 <!-- | |
| 112 Since trinity is false in this test, trinity_bed does not exist. | |
| 113 <output name="trinity_bed" /> | |
| 114 <assert_contents> | |
| 115 <has_line_matching expression=".+" /> | |
| 116 </assert_contents> | |
| 117 </output> | |
| 118 --> | |
| 119 <output name="fusionPredictions" > | |
| 120 <assert_contents> | |
| 121 <has_line_matching expression=".+" /> | |
| 122 <has_line line="#fusion_name	JunctionReads	SpanningFrags	Splice_type	LeftGene	LeftBreakpoint	RightGene	RightBreakpoint	JunctionReads	SpanningFrags	Annotations	TrinityGG" /> | |
| 123 </assert_contents> | |
| 124 </output> | |
| 125 <output name="fusionPredictionsAbridged" > | |
| 126 <assert_contents> | |
| 127 <has_line_matching expression=".+" /> | |
| 128 <has_line line="#fusion_name	JunctionReads	SpanningFrags	Splice_type	LeftGene	LeftBreakpoint	RightGene	RightBreakpoint	Annotations	TrinityGG" /> | |
| 129 </assert_contents> | |
| 130 </output> | |
| 131 <!-- So far in my testing of the fusion_json, I have had up to 18 different lines | |
| 132 (9 positions values switched between two entries)- 64 gives some padding. --> | |
| 133 <output name="fusion_json" file="FusionInspector/test.reads_1_2.web.json" lines_diff="64" /> | |
| 134 | |
| 135 </test> | |
| 136 </tests> | |
| 137 <help> | |
| 138 .. class:: infomark | |
| 139 | |
| 140 FusionInspector is a component of the Trinity Cancer Transcriptome Analysis Toolkit (CTAT). FusionInspector assists in fusion transcript discovery by performing a supervised analysis of fusion predictions, attempting to recover and re-score evidence for such predictions. Please read more here_. | |
| 141 | |
| 142 .. _here: https://github.com/FusionInspector/FusionInspector/wiki | |
| 143 | |
| 144 **To Visualize Output** | |
| 145 | |
| 146 After completion, results can be visualized in galaxy. Click on the output json file name in the history (on the right). A more detailed view of that file will be shown. Click on the button in the middle that looks like a bar chart. The visualization should now open for you to explore results. | |
| 147 | |
| 148 **There are several output files for the CTAT Fusion Inspector Pipeline. Files of interest include:** | |
| 149 | |
| 150 1. **fidx**: Finspector_fasta index file (required for visualization). | |
| 151 | |
| 152 2. **cytoBand**: Cytogenetic information for hg19. | |
| 153 | |
| 154 3. **finspector_fasta**: The candidate fusion-gene contigs. | |
| 155 | |
| 156 4. **finspector_bed**: The reference gene structure annotations for fusion partners. | |
| 157 | |
| 158 5. **FusionJuncSpan**: Tabular details on junction reads and spanning reads. | |
| 159 | |
| 160 6. **junction_bed**: Alignments of the breakpoint-junction supporting reads. | |
| 161 | |
| 162 7. **junction_bam**: Alignments of the breakpoint-junction supporting reads. | |
| 163 | |
| 164 8. **spanning_bam**: Alignments of the breakpoint-spanning paired-end reads. | |
| 165 | |
| 166 9. **spanning_bed**: Alignments of the breakpoint-spanning paired-end reads. | |
| 167 | |
| 168 10. **trinity_bed**: Fusion-guided Trinity assembly. | |
| 169 | |
| 170 11. **fusion_predictions.final**: All fusion evidence described. | |
| 171 | |
| 172 12. **fusion_predictions_abridged**: encompasses all information in fusion_predictions.final excluding the names of the reads. | |
| 173 | |
| 174 13. **fusion_json**: A logistical file that enables the visualization. | |
| 175 | |
| 176 </help> | |
| 177 <cite> | |
| 178 </cite> | |
| 179 </tool> |