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author trinity_ctat
date Tue, 17 Jul 2018 11:51:18 -0400
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1 <tool id="ctat_fusion_inspector" name="ctat_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="1.2.0">fusion-inspector</requirement>
5 </requirements>
6 <command detect_errors="default">
7 <![CDATA[
8 FusionInspector
9 --fusions $fusion_candidates_list
10 --genome_lib "${genome_resource_lib.fields.path}"
11 --left_fq $left_input
12 --right $right_input
13 --out_dir "subdir"
14 --out_prefix "finspector"
15 --prep_for_IGV
16 #if $trinity_status.trinity=="true"
17 --include_Trinity
18 #end if
19 ]]>
20 </command>
21 <stdio>
22 <exit_code range="1:" level="fatal" description="Error returned from pipeline" />
23 </stdio>
24 <regex match="Must investigate error above."
25 source="stderr"
26 level="fatal"
27 description="Unknown error encountered" />
28 <inputs>
29 <param format="tabular" name="fusion_candidates_list" type="data" multiple="True" label="Choose candidate list:" help="Fusion predictions"/>
30 <param format="fastq" name="left_input" type="data" label="Left/Forward strand reads" help=""/>
31 <param format="fastq" name="right_input" type="data" label="Right/Reverse strand reads" help=""/>
32 <!-- The HISAT and GSNAP methods are not supported and are being removed, leaving only STAR.
33 <param name="method" type="select" label="Choose method:">
34 <option value="HISAT">HISAT</option>
35 <option value="STAR">STAR</option>
36 <option value="GSNAP">GSNAP</option>
37 </param>
38 -->
39 <conditional name="trinity_status">
40 <param name="trinity" type="select" label="Use Trinity:">
41 <option value="true">True</option>
42 <option value="false">False</option>
43 </param>
44 </conditional>
45 <param name="genome_resource_lib" type="select" label="Select a reference genome">
46 <options from_data_table="ctat_genome_resource_libs">
47 <filter type="sort_by" column="2" />
48 <validator type="no_options" message="No indexes are available" />
49 </options>
50 </param>
51 </inputs>
52 <outputs>
53 <data format="txt" name="finspector_idx" label="fidx" from_work_dir="subdir/finspector.fa.fai"/>
54 <data format="txt" name="cytoBand" label="cytoBand" from_work_dir="subdir/cytoBand.txt"/>
55 <data format="fasta" name="finspector_fa" label="finspector_fasta" from_work_dir="subdir/finspector.fa"/>
56 <data format="bed" name="finspector_bed" label="finspector_bed" from_work_dir="subdir/finspector.bed"/>
57 <data format="tabular" name="FusionJuncSpan" label="FusionJuncSpan" from_work_dir="subdir/finspector.igv.FusionJuncSpan"/>
58 <data format="bed" name="junction_bed" label="junction_bed" from_work_dir="subdir/finspector.junction_reads.bam.bed"/>
59 <data format="bam" name="junction_bam" label="junction_bam" from_work_dir="subdir/finspector.junction_reads.bam"/>
60 <data format="bam" name="spanning_bam" label="spanning_bam" from_work_dir="subdir/finspector.spanning_reads.bam"/>
61 <data format="bed" name="spanning_bed" label="spanning_bed" from_work_dir="subdir/finspector.spanning_reads.bam.bed"/>
62 <data format="bed" name="trinity_bed" label="trinity_bed" from_work_dir="subdir/finspector.gmap_trinity_GG.fusions.gff3.bed.sorted.bed">
63 <filter>trinity_status['trinity'] == "true"</filter>
64 </data>
65 <data format="txt" name="fusionPredictions" label="fusion_predictions.final" from_work_dir="subdir/finspector.fusion_predictions.final"/>
66 <data format="txt" name="fusionPredictionsAbridged" label="fusion_predictions_abridged" from_work_dir="subdir/finspector.fusion_predictions.final.abridged"/>
67 <data format="json" name="fusion_json" label="fusion_json" from_work_dir="subdir/finspector.fusion_inspector_web.json"/>
68 </outputs>
69 <tests>
70 <test>
71 <param name="fusion_candidates_list" value="FusionInspector/fusion_targets.A.txt,FusionInspector/fusion_targets.B.txt,FusionInspector/fusion_targets.C.txt" />
72 <param name="left_input" value="FusionInspector/test.reads_1.fastq.gz" />
73 <param name="right_input" value="FusionInspector/test.reads_2.fastq.gz" />
74 <!-- The HISAT and GSNAP methods are not supported and are being removed, leaving only STAR.
75 <param name="method" value="STAR" />
76 -->
77 <param name="trinity" value="false" />
78 <!-- FIX - now that we added the CTAT resource lib path as a parameter, how do we find it for testing?
79 <param name="genome_resource_lib.fields.path" value="?????" />
80 -->
81 <output name="finspector_idx" file="FusionInspector/test.reads_1_2.fa.fai" />
82 <output name="cytoBand" file="FusionInspector/test.reads_1_2.cytoBand.tail.txt" compare="contains" />
83 <output name="finspector_fa" file="FusionInspector/test.reads_1_2.fa" />
84 <output name="finspector_bed" file="FusionInspector/test.reads_1_2.bed.sorted" sort="true" />
85 <output name="FusionJuncSpan" >
86 <assert_contents>
87 <has_line_matching expression=".+" />
88 <has_line line="#scaffold&#009;fusion_break_name&#009;break_left&#009;break_right&#009;num_junction_reads&#009;num_spanning_frags&#009;spanning_frag_coords" />
89 </assert_contents>
90 </output>
91 <!-- sorted output sometimes matches, but simetimes not, so now I just test for similar size. -->
92 <output name="junction_bed" file="FusionInspector/test.reads_1_2.junction_reads.bam.bed.sorted" sort="true" compare="sim_size" >
93 <assert_contents>
94 <has_line_matching expression=".+" />
95 <has_n_columns n="12" />
96 </assert_contents>
97 </output>
98 <output name="junction_bam" >
99 <assert_contents>
100 <has_line_matching expression=".+" />
101 <!-- The following checks for the magic number at the start of the bam file -->
102 <has_text_matching expression="\x1F\x8B" />
103 </assert_contents>
104 </output>
105 <output name="spanning_bam" >
106 <assert_contents>
107 <has_line_matching expression=".+" />
108 <!-- The following checks for the magic number at the start of the bam file -->
109 <has_text_matching expression="\x1F\x8B" />
110 </assert_contents>
111 </output>
112 <output name="spanning_bed" file="FusionInspector/test.reads_1_2.spanning_reads.bam.bed.sorted" sort="true" />
113 <!--
114 Since trinity is false in this test, trinity_bed does not exist.
115 <output name="trinity_bed" />
116 <assert_contents>
117 <has_line_matching expression=".+" />
118 </assert_contents>
119 </output>
120 -->
121 <output name="fusionPredictions" >
122 <assert_contents>
123 <has_line_matching expression=".+" />
124 <has_line line="#fusion_name&#009;JunctionReads&#009;SpanningFrags&#009;Splice_type&#009;LeftGene&#009;LeftBreakpoint&#009;RightGene&#009;RightBreakpoint&#009;JunctionReads&#009;SpanningFrags&#009;Annotations&#009;TrinityGG" />
125 </assert_contents>
126 </output>
127 <output name="fusionPredictionsAbridged" >
128 <assert_contents>
129 <has_line_matching expression=".+" />
130 <has_line line="#fusion_name&#009;JunctionReads&#009;SpanningFrags&#009;Splice_type&#009;LeftGene&#009;LeftBreakpoint&#009;RightGene&#009;RightBreakpoint&#009;Annotations&#009;TrinityGG" />
131 </assert_contents>
132 </output>
133 <!-- So far in my testing of the fusion_json, I have had up to 18 different lines
134 (9 positions values switched between two entries)- 64 gives some padding. -->
135 <output name="fusion_json" file="FusionInspector/test.reads_1_2.web.json" lines_diff="64" />
136
137 </test>
138 </tests>
139 <help>
140 .. class:: infomark
141
142 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_.
143
144 .. _here: https://github.com/FusionInspector/FusionInspector/wiki
145
146 **To Visualize Output**
147
148 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.
149
150 **There are several output files for the CTAT Fusion Inspector Pipeline. Files of interest include:**
151
152 1. **fidx**: Finspector_fasta index file (required for visualization).
153
154 2. **cytoBand**: Cytogenetic information for hg19.
155
156 3. **finspector_fasta**: The candidate fusion-gene contigs.
157
158 4. **finspector_bed**: The reference gene structure annotations for fusion partners.
159
160 5. **FusionJuncSpan**: Tabular details on junction reads and spanning reads.
161
162 6. **junction_bed**: Alignments of the breakpoint-junction supporting reads.
163
164 7. **junction_bam**: Alignments of the breakpoint-junction supporting reads.
165
166 8. **spanning_bam**: Alignments of the breakpoint-spanning paired-end reads.
167
168 9. **spanning_bed**: Alignments of the breakpoint-spanning paired-end reads.
169
170 10. **trinity_bed**: Fusion-guided Trinity assembly.
171
172 11. **fusion_predictions.final**: All fusion evidence described.
173
174 12. **fusion_predictions_abridged**: encompasses all information in fusion_predictions.final excluding the names of the reads.
175
176 13. **fusion_json**: A logistical file that enables the visualization.
177
178 </help>
179 <cite>
180 </cite>
181 </tool>