# HG changeset patch
# User trinity_ctat
# Date 1516816485 18000
# Node ID e4892a11c58daeb04f561c379f16727178209d7f
Adding fusion_inspector tool.
diff -r 000000000000 -r e4892a11c58d fusion_inspector.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/fusion_inspector.xml Wed Jan 24 12:54:45 2018 -0500
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+ In silico Validation of Fusion Transcript Predictions
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+ fusion-inspector
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+ trinity_status['trinity'] == "true"
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+.. class:: infomark
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+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_.
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+.. _here: https://github.com/FusionInspector/FusionInspector/wiki
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+**To Visualize Output**
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+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.
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+**There are several output files for the CTAT Fusion Inspector Pipeline. Files of interest include:**
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+1. **fidx**: Finspector_fasta index file (required for visualization).
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+2. **cytoBand**: Cytogenetic information for hg19.
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+3. **finspector_fasta**: The candidate fusion-gene contigs.
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+4. **finspector_bed**: The reference gene structure annotations for fusion partners.
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+5. **FusionJuncSpan**: Tabular details on junction reads and spanning reads.
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+6. **junction_bed**: Alignments of the breakpoint-junction supporting reads.
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+7. **junction_bam**: Alignments of the breakpoint-junction supporting reads.
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+8. **spanning_bam**: Alignments of the breakpoint-spanning paired-end reads.
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+9. **spanning_bed**: Alignments of the breakpoint-spanning paired-end reads.
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+10. **trinity_bed**: Fusion-guided Trinity assembly.
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+11. **fusion_predictions.final**: All fusion evidence described.
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+12. **fusion_predictions_abridged**: encompasses all information in fusion_predictions.final excluding the names of the reads.
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+13. **fusion_json**: A logistical file that enables the visualization.
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diff -r 000000000000 -r e4892a11c58d test-data/FusionInspector/fusion_targets.A.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/FusionInspector/fusion_targets.A.txt Wed Jan 24 12:54:45 2018 -0500
@@ -0,0 +1,24 @@
+ACACA--STAC2
+AHCTF1--NAAA
+CTD-2328D6.1--MT-CO1
+DIDO1--TTI1
+FITM2--UQCC1
+GLB1--CMTM7
+LAMP1--MCF2L
+MED1--ACSF2
+MED1--STXBP4
+MT-ND5--MT-RNR2
+PIP4K2B--RAD51C
+RAB22A--MYO9B
+RP11-96H19.1--RP11-446N19.1
+RPS6KB1--SNF8
+STARD3--DOK5
+STX16--RAE1
+STX16-NPEPL1--RAE1
+THRA--AC090627.1
+TOB1--SYNRG
+TRIM37--MYO19
+TRPC4AP--MRPL45
+TULP4--RP11-732M18.3
+VAPB--IKZF3
+ZMYND8--CEP250
diff -r 000000000000 -r e4892a11c58d test-data/FusionInspector/fusion_targets.B.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/FusionInspector/fusion_targets.B.txt Wed Jan 24 12:54:45 2018 -0500
@@ -0,0 +1,22 @@
+ACACA--STAC2
+AHCTF1--NAAA
+ASTN2--RP11-281A20.1
+CPNE1--PI3
+CTD-2319I12.2--HEATR6
+CTD-2328D6.1--MT-CO1
+DIDO1--TTI1
+FITM2--UQCC1
+GLB1--CMTM7
+RAB22A--MYO9B
+RP11-96H19.1--RP11-446N19.1
+RPS6KB1--SNF8
+STARD3--DOK5
+STX16--RAE1
+STX16-NPEPL1--RAE1
+THRA--AC090627.1
+TOB1--SYNRG
+TRIM37--MYO19
+TRPC4AP--MRPL45
+TULP4--RP11-732M18.3
+VAPB--IKZF3
+ZMYND8--CEP250
diff -r 000000000000 -r e4892a11c58d test-data/FusionInspector/fusion_targets.C.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/FusionInspector/fusion_targets.C.txt Wed Jan 24 12:54:45 2018 -0500
@@ -0,0 +1,24 @@
+ACACA--STAC2
+AHCTF1--NAAA
+ASTN2--RP11-281A20.1
+CPNE1--PI3
+CTD-2319I12.2--HEATR6
+CTD-2328D6.1--MT-CO1
+DIDO1--TTI1
+FITM2--UQCC1
+GLB1--CMTM7
+LAMP1--MCF2L
+MED1--ACSF2
+MED1--STXBP4
+MT-ND5--MT-RNR2
+PIP4K2B--RAD51C
+RAB22A--MYO9B
+RP11-96H19.1--RP11-446N19.1
+RPS6KB1--SNF8
+STARD3--DOK5
+STX16--RAE1
+STX16-NPEPL1--RAE1
+THRA--AC090627.1
+TOB1--SYNRG
+TRIM37--MYO19
+ZMYND8--CEP250
diff -r 000000000000 -r e4892a11c58d test-data/FusionInspector/test.reads_1.fastq.gz
Binary file test-data/FusionInspector/test.reads_1.fastq.gz has changed
diff -r 000000000000 -r e4892a11c58d test-data/FusionInspector/test.reads_2.fastq.gz
Binary file test-data/FusionInspector/test.reads_2.fastq.gz has changed
diff -r 000000000000 -r e4892a11c58d tool-data/ctat_genome_ref_libs.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/ctat_genome_ref_libs.loc.sample Wed Jan 24 12:54:45 2018 -0500
@@ -0,0 +1,12 @@
+# This file lists the locations of CTAT Genome Reference Libraries
+# Usually there will only be one library, but it is concievable
+# that there could be multiple libraries.
+# This file format is as follows
+# (white space characters are TAB characters):
+#
+#
+#
+#ctat_genome_ref_libs.loc could look like:
+#
+#CTAT_RESOURCE_LIB GRCh38_gencode_v26 /ctat/genome/resource/lib/path
+#
diff -r 000000000000 -r e4892a11c58d tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Wed Jan 24 12:54:45 2018 -0500
@@ -0,0 +1,6 @@
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