Mercurial > repos > yboursin > rsem_eba
comparison rsem_prepare_reference.xml @ 1:73a9e9df80da draft
Uploaded
| author | yboursin |
|---|---|
| date | Wed, 25 May 2016 10:08:02 -0400 |
| parents | 7146e81bc886 |
| children | 67c078448bea |
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| 0:7146e81bc886 | 1:73a9e9df80da |
|---|---|
| 1 <tool id="rsem_prepare_reference" name="RSEM prepare reference" version="1.1.17"> | 1 <tool id="rsem_prepare_reference" name="RSEM prepare reference" version="EBA2016-v1"> |
| 2 <description></description> | 2 <description></description> |
| 3 <requirements> | 3 <requirements> |
| 4 <requirement type="package" version="1.2.28">rsem</requirement> | 4 <requirement type="package" version="1.2.28">rsem</requirement> |
| 5 <requirement type="package" version="1.1.2">bowtie</requirement> | 5 <requirement type="package" version="1.1.2">bowtie</requirement> |
| 6 <requirement type="package" version="2.2.6">bowtie2</requirement> | 6 <requirement type="package" version="2.2.6">bowtie2</requirement> |
| 21 #end if | 21 #end if |
| 22 #elif $polya.polya_use == 'none': | 22 #elif $polya.polya_use == 'none': |
| 23 --no-polyA | 23 --no-polyA |
| 24 #end if | 24 #end if |
| 25 $ntog | 25 $ntog |
| 26 $bowtie | |
| 27 $bowtietwo | |
| 26 #if $transcript_to_gene_map: | 28 #if $transcript_to_gene_map: |
| 27 --transcript-to-gene-map $transcript_to_gene_map | 29 --transcript-to-gene-map $transcript_to_gene_map |
| 28 #end if | 30 #end if |
| 29 #if $reference.ref_type == 'transcripts': | 31 #if $reference.ref_type == 'transcripts': |
| 30 $reference.reference_fasta_file | 32 $reference.reference_fasta_file |
| 31 #else: | 33 #else: |
| 34 #if $reference.gtf.extension == 'gtf': | |
| 32 --gtf $reference.gtf | 35 --gtf $reference.gtf |
| 36 #elif $reference.gtf.extension == 'gff3': | |
| 37 --gff3 $reference.gtf | |
| 38 #end if | |
| 33 $reference.reference_fasta_file | 39 $reference.reference_fasta_file |
| 34 #end if | 40 #end if |
| 35 $reference_name | 41 $reference_name |
| 36 > ${reference_name}.log | 42 > ${reference_name}.log |
| 37 </command> | 43 </command> |
| 46 help="The files should contain the sequences of transcripts."/> | 52 help="The files should contain the sequences of transcripts."/> |
| 47 </when> | 53 </when> |
| 48 <when value="genomic"> | 54 <when value="genomic"> |
| 49 <param name="reference_fasta_file" type="data" format="fasta" label="reference fasta file" | 55 <param name="reference_fasta_file" type="data" format="fasta" label="reference fasta file" |
| 50 help="The file should contain the sequence of an entire genome."/> | 56 help="The file should contain the sequence of an entire genome."/> |
| 51 <param name="gtf" type="data" format="gtf" label="gtf" | 57 <param name="gtf" type="data" format="gtf,gff3" label="gtf or gff3 file" |
| 52 help="extract transcript reference sequences using the gene annotations specified in this GTF" /> | 58 help="extract transcript reference sequences using the gene annotations specified in this GTF or GFF3 file" /> |
| 53 </when> | 59 </when> |
| 54 </conditional> | 60 </conditional> |
| 55 <param name="transcript_to_gene_map" type="data" format="tabular" optional="true" label="Map of gene ids to transcript (isoform) ids" > | 61 <param name="transcript_to_gene_map" type="data" format="tabular" optional="true" label="Map of gene ids to transcript (isoform) ids" > |
| 56 <help> | 62 <help> |
| 57 Each line of should be of the form: gene_id transcript_id ( with the two fields separated by a tab character ) | 63 Each line of should be of the form: gene_id transcript_id ( with the two fields separated by a tab character ) |
| 84 <validator type="in_range" message="must be positive " min="1"/> | 90 <validator type="in_range" message="must be positive " min="1"/> |
| 85 </param> | 91 </param> |
| 86 </when> | 92 </when> |
| 87 <when value="none"/> | 93 <when value="none"/> |
| 88 </conditional> | 94 </conditional> |
| 95 <param name="bowtie" type="boolean" truevalue="--bowtie" falsevalue="" checked="false" label="Use bowtie" /> | |
| 96 <param name="bowtietwo" type="boolean" truevalue="--bowtie2" falsevalue="" checked="false" label="Use bowtie2" /> | |
| 89 <param name="ntog" type="boolean" truevalue="--no-ntog" falsevalue="" checked="false" label="Disable the conversion of 'N' characters to 'G' characters in the reference sequences" help="Bowite uses the automatic N to G conversion to to align against all positions in the reference."/> | 97 <param name="ntog" type="boolean" truevalue="--no-ntog" falsevalue="" checked="false" label="Disable the conversion of 'N' characters to 'G' characters in the reference sequences" help="Bowite uses the automatic N to G conversion to to align against all positions in the reference."/> |
| 90 </inputs> | 98 </inputs> |
| 91 <stdio> | 99 <stdio> |
| 92 <exit_code range="1:" level="fatal" description="Error Running RSEM" /> | 100 <exit_code range="1:" level="fatal" description="Error Running RSEM" /> |
| 93 </stdio> | 101 </stdio> |