Mercurial > repos > trinity_ctat > ctat_star_fusion
comparison ctat_star_fusion.xml @ 0:a530fa18e9e8 draft default tip
Upload ctat tools.
author | trinity_ctat |
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date | Tue, 17 Jul 2018 11:51:50 -0400 |
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-1:000000000000 | 0:a530fa18e9e8 |
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1 <tool id="ctat_star_fusion" name="ctat_star_fusion" version="1.0.1" profile="17.05"> | |
2 | |
3 <description>Fusion-finding Pipeline Using the STAR Aligner</description> | |
4 <requirements> | |
5 <requirement type="package" version="1.4.0">star-fusion</requirement> | |
6 </requirements> | |
7 <!-- Using command's detect_errors instead of below. | |
8 <stdio> | |
9 <exit_code range="1:" level="fatal" description="Error returned from pipeline" /> | |
10 </stdio> | |
11 <regex match="Must investigate error above." | |
12 source="stderr" | |
13 level="fatal" | |
14 description="Unknown error encountered" /> | |
15 --> | |
16 <command detect_errors="default"> | |
17 <![CDATA[ | |
18 STAR-Fusion | |
19 --genome_lib_dir "${genome_resource_lib.fields.path}" | |
20 --left_fq "${left_input}" | |
21 --right_fq "${right_input}" | |
22 --output_dir subdir | |
23 --STAR_SortedByCoordinate | |
24 ]]> | |
25 </command> | |
26 | |
27 <inputs> | |
28 <param format="fastq" name="left_input" type="data" label="Left/Forward strand reads" help=""/> | |
29 <param format="fastq" name="right_input" type="data" label="Right/Reverse strand reads" help=""/> | |
30 <param name="genome_resource_lib" type="select" label="Select a reference genome"> | |
31 <options from_data_table="ctat_genome_resource_libs"> | |
32 <filter type="sort_by" column="2" /> | |
33 <validator type="no_options" message="No indexes are available" /> | |
34 </options> | |
35 </param> | |
36 </inputs> | |
37 | |
38 <outputs> | |
39 <data format="txt" name="starfusion_log" label="${tool.name} on ${on_string}: log" from_work_dir="subdir/Log.out"/> | |
40 <data format="bam" name="aligned_bam" label="${tool.name} on ${on_string}: Aligned Bam" from_work_dir="subdir/std.STAR.bam"/> | |
41 <data format="tabular" name="candidates" label="${tool.name} on ${on_string}: Fusion candidates" from_work_dir="subdir/star-fusion.fusion_predictions.abridged.tsv"/> | |
42 <data format="tabular" name="chimeric_junc" label="${tool.name} on ${on_string}: Chimeric.out.junction" from_work_dir="subdir/std.Chimeric.out.junction"/> | |
43 </outputs> | |
44 <tests> | |
45 <test> | |
46 <param name="left_input" value="StarFusion/reads_1.fq.gz" /> | |
47 <param name="right_input" value="StarFusion/reads_2.fq.gz" /> | |
48 <!-- | |
49 <param name="left_input" value="reads.left.simPE.fq" /> | |
50 <param name="right_input" value="reads.right.simPE.fq" /> | |
51 --> | |
52 <!-- FIX - now that we added the CTAT ref lib path as a parameter, how do we find it for testing? | |
53 <param name="genome_resource_lib.fields.path" value="?????" /> | |
54 --> | |
55 <!-- | |
56 <output name="aligned_bam" file="SF_out_aligned.bam" /> | |
57 <output name="candidates" file="SF_out_fusion_candidates.dat" /> | |
58 <output name="chimeric_junc" file="SF_out_chimeric.junction" /> | |
59 <output name="starfusion_log" file="SF_out.log" /> | |
60 --> | |
61 <output name="starfusion_log"> | |
62 <assert_contents> | |
63 <has_line_matching expression=".+" /> | |
64 <has_line line="ALL DONE!" /> | |
65 </assert_contents> | |
66 </output> | |
67 <output name="aligned_bam"> | |
68 <assert_contents> | |
69 <has_line_matching expression=".+" /> | |
70 <!-- The following checks for the magic number at the start of the bam file --> | |
71 <!-- At first I thought "\x8B\x1F" was the number, but it turns out the file | |
72 produced by the StarFusion test had that sequence in the file somewhere else. | |
73 --> | |
74 <has_text_matching expression="\x1F\x8B" /> | |
75 </assert_contents> | |
76 </output> | |
77 <output name="candidates"> | |
78 <assert_contents> | |
79 <has_line_matching expression=".+" /> | |
80 <has_line line="#fusion_name	JunctionReads	SpanningFrags	Splice_type	LeftGene	LeftBreakpoint	RightGene	RightBreakpoint	Long_double_anchor_support" /> | |
81 </assert_contents> | |
82 </output> | |
83 <output name="chimeric_junc"> | |
84 <assert_contents> | |
85 <has_line_matching expression=".+" /> | |
86 <has_line_matching expression="^chr20.*" /> | |
87 </assert_contents> | |
88 </output> | |
89 </test> | |
90 </tests> | |
91 <help> | |
92 .. class:: infomark | |
93 | |
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_. | |
95 | |
96 .. _here: https://github.com/STAR-Fusion/STAR-Fusion/wiki | |
97 | |
98 </help> | |
99 </tool> |