Mercurial > repos > trinity_ctat > ctat_star_fusion
annotate ctat_star_fusion.xml @ 10:fe24128ef413 draft default tip
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| author | trinity_ctat |
|---|---|
| date | Sun, 08 Jul 2018 16:18:09 -0400 |
| parents | 690a6696ce11 |
| children |
| rev | line source |
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dc3454ad7e09
Trying to fix invalid repository tag error for ctat_star_fusion.
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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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dc3454ad7e09
Trying to fix invalid repository tag error for ctat_star_fusion.
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| 0 | 3 <description>Fusion-finding Pipeline Using the STAR Aligner</description> |
| 4 <requirements> | |
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New ctat_star_fusion.xml to use new bioconda recipe.
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5 <requirement type="package" version="1.4.0">star-fusion</requirement> |
| 0 | 6 </requirements> |
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3268b5e6ab4a
Trying to fix problems with ctat_star_fusion and ctat_metagenomics.
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7 <!-- Using command's detect_errors instead of below. |
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3268b5e6ab4a
Trying to fix problems with ctat_star_fusion and ctat_metagenomics.
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8 <stdio> |
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3268b5e6ab4a
Trying to fix problems with ctat_star_fusion and ctat_metagenomics.
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9 <exit_code range="1:" level="fatal" description="Error returned from pipeline" /> |
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3268b5e6ab4a
Trying to fix problems with ctat_star_fusion and ctat_metagenomics.
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10 </stdio> |
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3268b5e6ab4a
Trying to fix problems with ctat_star_fusion and ctat_metagenomics.
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11 <regex match="Must investigate error above." |
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3268b5e6ab4a
Trying to fix problems with ctat_star_fusion and ctat_metagenomics.
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12 source="stderr" |
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3268b5e6ab4a
Trying to fix problems with ctat_star_fusion and ctat_metagenomics.
trinity_ctat
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13 level="fatal" |
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3268b5e6ab4a
Trying to fix problems with ctat_star_fusion and ctat_metagenomics.
trinity_ctat
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14 description="Unknown error encountered" /> |
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3268b5e6ab4a
Trying to fix problems with ctat_star_fusion and ctat_metagenomics.
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15 --> |
| 0 | 16 <command detect_errors="default"> |
| 17 <![CDATA[ | |
| 18 STAR-Fusion | |
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31beded40e1a
Updating star_fusion and gmap_fusion to work with the new datamanager (the tablename was changed to be consistent with other naming).
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19 --genome_lib_dir "${genome_resource_lib.fields.path}" |
| 0 | 20 --left_fq "${left_input}" |
| 21 --right_fq "${right_input}" | |
| 22 --output_dir subdir | |
| 9 | 23 --STAR_SortedByCoordinate |
| 0 | 24 ]]> |
| 25 </command> | |
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dc3454ad7e09
Trying to fix invalid repository tag error for ctat_star_fusion.
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26 |
| 0 | 27 <inputs> |
| 28 <param format="fastq" name="left_input" type="data" label="Left/Forward strand reads" help=""/> | |
| 29 <param format="fastq" name="right_input" type="data" label="Right/Reverse strand reads" help=""/> | |
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31beded40e1a
Updating star_fusion and gmap_fusion to work with the new datamanager (the tablename was changed to be consistent with other naming).
trinity_ctat
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30 <param name="genome_resource_lib" type="select" label="Select a reference genome"> |
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31beded40e1a
Updating star_fusion and gmap_fusion to work with the new datamanager (the tablename was changed to be consistent with other naming).
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31 <options from_data_table="ctat_genome_resource_libs"> |
| 0 | 32 <filter type="sort_by" column="2" /> |
| 33 <validator type="no_options" message="No indexes are available" /> | |
| 34 </options> | |
| 35 </param> | |
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dc3454ad7e09
Trying to fix invalid repository tag error for ctat_star_fusion.
trinity_ctat
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36 </inputs> |
| 0 | 37 |
| 38 <outputs> | |
| 39 <data format="txt" name="starfusion_log" label="${tool.name} on ${on_string}: log" from_work_dir="subdir/Log.out"/> | |
| 10 | 40 <data format="bam" name="aligned_bam" label="${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"/> | |
| 0 | 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? | |
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31beded40e1a
Updating star_fusion and gmap_fusion to work with the new datamanager (the tablename was changed to be consistent with other naming).
trinity_ctat
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53 <param name="genome_resource_lib.fields.path" value="?????" /> |
| 0 | 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> |