Mercurial > repos > trinity_ctat > fusion_inspector
comparison 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 |
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| 0:e4892a11c58d | 1:2e993ad06cf2 |
|---|---|
| 11 --left_fq $left_input | 11 --left_fq $left_input |
| 12 --right $right_input | 12 --right $right_input |
| 13 --out_dir "subdir" | 13 --out_dir "subdir" |
| 14 --out_prefix "finspector" | 14 --out_prefix "finspector" |
| 15 --prep_for_IGV | 15 --prep_for_IGV |
| 16 --align_utils $method | 16 --align_utils STAR |
| 17 #if $trinity_status.trinity=="true" | 17 #if $trinity_status.trinity=="true" |
| 18 --include_Trinity | 18 --include_Trinity |
| 19 #end if | 19 #end if |
| 20 ]]> | 20 ]]> |
| 21 </command> | 21 </command> |
| 28 description="Unknown error encountered" /> | 28 description="Unknown error encountered" /> |
| 29 <inputs> | 29 <inputs> |
| 30 <param format="tabular" name="fusion_candidates_list" type="data" multiple="True" label="Choose candidate list:" help="Fusion predictions"/> | 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=""/> | 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=""/> | 32 <param format="fastq" name="right_input" type="data" label="Right/Reverse strand reads" help=""/> |
| 33 | 33 <!-- The HISAT and GSNAP methods are not supported and are being removed, leaving only STAR. |
| 34 <param name="method" type="select" label="Choose method:"> | 34 <param name="method" type="select" label="Choose method:"> |
| 35 <option value="HISAT">HISAT</option> | 35 <option value="HISAT">HISAT</option> |
| 36 <option value="STAR">STAR</option> | 36 <option value="STAR">STAR</option> |
| 37 <option value="GSNAP">GSNAP</option> | 37 <option value="GSNAP">GSNAP</option> |
| 38 </param> | 38 </param> |
| 39 --> | |
| 39 <conditional name="trinity_status"> | 40 <conditional name="trinity_status"> |
| 40 <param name="trinity" type="select" label="Use Trinity:"> | 41 <param name="trinity" type="select" label="Use Trinity:"> |
| 41 <option value="true">True</option> | 42 <option value="true">True</option> |
| 42 <option value="false">False</option> | 43 <option value="false">False</option> |
| 43 </param> | 44 </param> |
| 48 <validator type="no_options" message="No indexes are available" /> | 49 <validator type="no_options" message="No indexes are available" /> |
| 49 </options> | 50 </options> |
| 50 </param> | 51 </param> |
| 51 </inputs> | 52 </inputs> |
| 52 <outputs> | 53 <outputs> |
| 53 <data format="text" name="finspector_idx" label="fidx" from_work_dir="subdir/finspector.fa.fai"/> | 54 <data format="txt" name="finspector_idx" label="fidx" from_work_dir="subdir/finspector.fa.fai"/> |
| 54 <data format="text" name="cytoBand" label="cytoBand" from_work_dir="subdir/cytoBand.txt"/> | 55 <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="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="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="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="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="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="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="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 <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 <filter>trinity_status['trinity'] == "true"</filter> |
| 64 </data> | 65 </data> |
| 65 <data format="text" name="fusionPredictions" label="fusion_predictions.final" from_work_dir="subdir/finspector.fusion_predictions.final"/> | 66 <data format="txt" name="fusionPredictions" label="fusion_predictions.final" from_work_dir="subdir/finspector.fusion_predictions.final"/> |
| 66 <data format="text" name="fusionPredictionsAbridged" label="fusion_predictions_abridged" from_work_dir="subdir/finspector.fusion_predictions.final.abridged"/> | 67 <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 <data format="json" name="fusion_json" label="fusion_json" from_work_dir="subdir/finspector.fusion_inspector_web.json"/> |
| 68 </outputs> | 69 </outputs> |
| 69 <tests> | 70 <tests> |
| 70 <test> | 71 <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="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="left_input" value="FusionInspector/test.reads_1.fastq.gz" /> |
| 73 <param name="right_input" value="FusionInspector/test.reads_2.fastq.gz" /> | 74 <param name="right_input" value="FusionInspector/test.reads_2.fastq.gz" /> |
| 75 <!-- The HISAT and GSNAP methods are not supported and are being removed, leaving only STAR. | |
| 74 <param name="method" value="STAR" /> | 76 <param name="method" value="STAR" /> |
| 77 --> | |
| 75 <param name="trinity" value="false" /> | 78 <param name="trinity" value="false" /> |
| 76 <output name="finspector_idx" file="FusionInspector/test.reads_1_2.fa.fai" /> | 79 <output name="finspector_idx" file="FusionInspector/test.reads_1_2.fa.fai" /> |
| 77 <output name="cytoBand" file="FusionInspector/test.reads_1_2.cytoBand.tail.txt" compare="contains" /> | 80 <output name="cytoBand" file="FusionInspector/test.reads_1_2.cytoBand.tail.txt" compare="contains" /> |
| 78 <output name="finspector_fa" file="FusionInspector/test.reads_1_2.fa" /> | 81 <output name="finspector_fa" file="FusionInspector/test.reads_1_2.fa" /> |
| 79 <output name="finspector_bed" file="FusionInspector/test.reads_1_2.bed.sorted" sort="true" /> | 82 <output name="finspector_bed" file="FusionInspector/test.reads_1_2.bed.sorted" sort="true" /> |