Mercurial > repos > jjohnson > arriba
comparison arriba.xml @ 2:7420753b0671 draft
"planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 7dbe725aaa7b4b84d7b14ea52f38f63d362bf09c"
author | jjohnson |
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date | Fri, 08 Oct 2021 19:23:48 +0000 |
parents | 9f2665b32c45 |
children | 2d32e6c86c48 |
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1:9f2665b32c45 | 2:7420753b0671 |
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17 #set read2 = 'input_2.fastq.gz' | 17 #set read2 = 'input_2.fastq.gz' |
18 #else: | 18 #else: |
19 #set read2 = 'input_2.fastq' | 19 #set read2 = 'input_2.fastq' |
20 #end if | 20 #end if |
21 ln -f -s '${input_params.right_fq}' ${read2} && | 21 ln -f -s '${input_params.right_fq}' ${read2} && |
22 #if str($input_params.index.index_source) == "history" | |
23 #set $star_index_dir = $input_params.index.star_index.files_path | |
24 #end if | |
22 STAR | 25 STAR |
23 --runThreadN \${GALAXY_SLOTS:-1} | 26 --runThreadN \${GALAXY_SLOTS:-1} |
24 --genomeDir /path/to/STAR_index | 27 --genomeDir $star_index_dir |
25 --genomeLoad NoSharedMemory | 28 --genomeLoad NoSharedMemory |
26 --readFilesIn $read1 $read2 | 29 --readFilesIn $read1 $read2 |
27 --readFilesCommand zcat | 30 --readFilesCommand zcat |
28 --outStd BAM_Unsorted | 31 --outStd BAM_Unsorted |
29 --outSAMtype BAM Unsorted | 32 --outSAMtype BAM Unsorted |
68 -o fusions.tsv | 71 -o fusions.tsv |
69 -O fusions.discarded.tsv | 72 -O fusions.discarded.tsv |
70 ]]></command> | 73 ]]></command> |
71 <inputs> | 74 <inputs> |
72 <conditional name="input_params"> | 75 <conditional name="input_params"> |
73 <param name="input_source" | 76 <param name="input_source" type="select" label="Use output from earlier STAR run or let Arriba running STAR"> |
74 type="select" | |
75 label="Use output from earlier STAR run or let Arriba running STAR"> | |
76 <option value="use_star">Use output from earlier STAR</option> | 77 <option value="use_star">Use output from earlier STAR</option> |
77 <option value="use_fastq">Let Arriba control running STAR</option> | 78 <option value="use_fastq">Let Arriba control running STAR</option> |
78 </param> | 79 </param> |
79 <when value="use_star"> | 80 <when value="use_star"> |
80 <param name="input" argument="-x" type="data" format="sam,bam,cram" label="STAR Aligned.out.sam"/> | 81 <param name="input" argument="-x" type="data" format="sam,bam,cram" label="STAR Aligned.out.sam"/> |
91 <param name="right_fq" | 92 <param name="right_fq" |
92 type="data" | 93 type="data" |
93 format="fastqsanger,fastqsanger.gz" | 94 format="fastqsanger,fastqsanger.gz" |
94 argument="--right_fq" | 95 argument="--right_fq" |
95 label="right.fq file"/> | 96 label="right.fq file"/> |
97 <conditional name="index"> | |
98 <param name="index_source" type="select" label="Arriba STAR index source"> | |
99 <option value="history">Arriba STAR index from your history</option> | |
100 </param> | |
101 <when value="history"> | |
102 <param name="star_index" argument="--genomeDir" type="data" format="txt" label="Arriba STAR index" | |
103 help="generated by: Arriba Reference"/> | |
104 </when> | |
105 </conditional> | |
96 </when> | 106 </when> |
97 </conditional> | 107 </conditional> |
98 <param name="genome_assembly" argument="-a" type="data" format="fasta" label="genome assembly fasta"/> | 108 <param name="genome_assembly" argument="-a" type="data" format="fasta" label="genome assembly fasta"/> |
99 <param name="gtf" argument="-g" type="data" format="gtf" label="GTF file with gene annotation"/> | 109 <param name="gtf" argument="-g" type="data" format="gtf" label="GTF file with gene annotation"/> |
100 <param name="blacklist" argument="-b" type="data" format="tabular" label="File containing blacklisted ranges."/> | 110 <param name="blacklist" argument="-b" type="data" format="tabular" label="File containing blacklisted ranges."/> |
217 | 227 |
218 The file must be in GFF3 format and may optionally be gzip-compressed. The ninth column must at least contain the following attributes: | 228 The file must be in GFF3 format and may optionally be gzip-compressed. The ninth column must at least contain the following attributes: |
219 * Name=PROTEIN_DOMAIN_NAME; | 229 * Name=PROTEIN_DOMAIN_NAME; |
220 * gene_id=GENE_ID; | 230 * gene_id=GENE_ID; |
221 * gene_name=GENE_NAME | 231 * gene_name=GENE_NAME |
232 | |
222 The attribute Name is reported in the column retained_protein_domains of Arriba's output file. Some special characters in the name are replaced with underscores (_). The columns gene_id and gene_name are used to match the protein domains to the genes given in the gene annotation. If a match cannot be found, Arriba cannot determine the retained protein domains of the respective gene and a warning is issued. There may be many warnings if RefSeq annotation is used, because the protein domains file distributed with Arriba uses ENSEMBL gene names/IDs. | 233 The attribute Name is reported in the column retained_protein_domains of Arriba's output file. Some special characters in the name are replaced with underscores (_). The columns gene_id and gene_name are used to match the protein domains to the genes given in the gene annotation. If a match cannot be found, Arriba cannot determine the retained protein domains of the respective gene and a warning is issued. There may be many warnings if RefSeq annotation is used, because the protein domains file distributed with Arriba uses ENSEMBL gene names/IDs. |
223 | 234 |
224 - Structural variant calls from WGS | 235 - Structural variant calls from WGS |
225 | 236 |
226 If whole-genome sequencing (WGS) data is available, the sensitivity and specificity of Arriba can be improved by passing a list of structural variants detected from WGS to Arriba via the parameter -d. This has the following effects: | 237 If whole-genome sequencing (WGS) data is available, the sensitivity and specificity of Arriba can be improved by passing a list of structural variants detected from WGS to Arriba via the parameter -d. This has the following effects: |