Mercurial > repos > saharlcc > isoem2_isode2
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author | saharlcc |
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date | Mon, 19 Sep 2016 22:04:15 -0400 |
parents | 7044191a603b |
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<tool id="isoem" name="IsoEM2" version="1.0.0"> <description> Infers isoform and gene expression levels from high-throughput transcriptome sequencing (RNA-Seq) data</description> <requirements> </requirements> <command interpreter="bash"> isoem_wrapper.sh ## Provide outputs. --out_gene_fpkm $out_gene_fpkm --out_gene_tpm $out_gene_tpm --out_iso_fpkm $out_iso_fpkm --out_iso_tpm $out_iso_tpm --out_bootstrap $out_bootstrap ## Handle reference file . #if $referenceSource.CCDSsource == "history": --fastaFile $referenceSource.fastaFile #else: --GTF $referenceSource.index.fields.GTF --TMAP_INDEX $referenceSource.index.fields.TMAP_INDEX --HISAT2_INDEX $referenceSource.index.fields.HISAT2_INDEX --Cluster $referenceSource.index.fields.Cluster #end if ## First input file always required fastq1. --input1 $Data.input1 ## Set params based on whether reads are single-end or paired. #if $Data.RNAseqType == "Illumina-paired-end": --input2 $Data.input2 #else: -m $Data.lengthMean -d $Data.lengthSd #end if ## RNA-Seq type based on sequencing platform. --RNA_type $Data.RNAseqType > $Run 2>&1 </command> <inputs> <conditional name="referenceSource"> <param name="CCDSsource" type="select" label="Will you upload a reference transcriptome fasta file from your history or use a built-in reference?" help="Built-ins were indexed using default options"> <option value="indexed">Use a built-in reference</option> <option value="history">Use reference from the history</option> </param> <when value="indexed"> <param name="index" type="select" label="Select a reference dataset" help="If your reference of interest is not listed, contact the Galaxy team"> <options from_data_table="IsoEM" /> </param> </when> <when value="history"> <param name="fastaFile" type="data" format="fasta" metadata_name="dbkey" label="Select CCDS fasta file from your history" /> </when> <!-- history --> </conditional> <!-- referenceSource --> <conditional name="Data"> <!-- <param name="sPaired" type="select" label="Is this library Single-end or Paired-end?"> <option value="single">Single-end</option> <option value="paired">Paired-end</option> </param> --> <param name="RNAseqType" type="select" label="Select RNA-seq type"> <option value="Ion-Torrent-Proton">Ion Torrent single-end</option> <option value="Illumina-paired-end">Illumina paired-end</option> <option value="Illumina-single-end">Illumina single-end</option> </param> <!-- RNAseqType --> <when value="Illumina-paired-end"> <param name="input1" type="data" label="RNA-Seq file1, fastq or bam format" /> <param name="input2" type="data" label="RNA-Seq file2, fastq or bam format" /> </when> <when value="Ion-Torrent-Proton"> <param name="input1" type="data" label="RNA-Seq file, fastq or bam format" /> <param name="lengthMean" type="text" label="m (RNA-Seq fragment length mean)" /> <param name="lengthSd" type="text" label="d (RNA-Seq fragment length standard deviation)" /> </when> <when value="Illumina-single-end"> <param name="input1" type="data" label="RNA-Seq file, fastq or bam format" /> <param name="lengthMean" type="text" label="m (RNA-Seq fragment length mean)" /> <param name="lengthSd" type="text" label="d (RNA-Seq fragment length standard deviation)" /> </when> </conditional> <!-- Data --> <!-- <param name="RNAseqType" type="select" label="Select RNA-seq type"> <option value="Ion-Torrent-Proton">Ion Torrent Proton</option> <option value="Illumina-paired-end">Illumina paired-end</option> <option value="Illumina-single-end">Illumina single-end</option> </param> --> </inputs> <outputs> <data name="out_gene_fpkm" format="tabular" label="Gene_fpkm"/> <data name="out_gene_tpm" format="tabular" label="Gene_tpm"/> <data name="out_iso_fpkm" format="tabular" label="Iso_fpkm"/> <data name="out_iso_tpm" format="tabular" label="Iso_tpm"/> <data name="out_bootstrap" format="toolshed.gz" label="Bootstrap.tar.gz"/> <data name="Run" format="log" label="isoem_wrapper: The log file" /> </outputs> <help> **What it does** * The IsoEM can be used to infer isoform and gene expression levels from high-throughput transcriptome sequencing (RNA-Seq) data. **Input Format** * The tool accept the fastq, fastq.gz, bam formats. Extension must be specified at the end of the file names. * RNA-seq data must be Ion Torrent Proton or Illumina sequncing data. ----- **BUILT-IN REFERENCE documentation** **mm10_C57BL/6:** * GTF file: /import1/CCDS/Mm38.1/CCDS_nucleotide.20140407.fna.GTF * TMAP_index:/import1/tmap-index/tmap3.4.1/mm10/CCDS_nucleotide.20140407.fna * HISAT2_index: /import1/hisat2-index/mm10_CCDS/mm10_CCDS_nucleotide.20140407 * Cluster file: /import1/CCDS/Mm38.1/CCDS_nucleotide.20140407.fna_transcriptID_geneName.txt **mm10_BALB/c:** * GTF file: /import1/CCDS/Mm38.1/CCDS_nucleotide.20140407.fna.GTF * TMAP_index: /import1/tmap-index/tmap3.4.1/mm10/mm10_CCDS_nucleotide.20140407_BALBc.fna * HISAT2_index: /import1/hisat2-index/mm10_CCDS/mm10_CCDS_nucleotide.20140407_BALBc * Cluster file: /import1/CCDS/Mm38.1/CCDS_nucleotide.20140407.fna_transcriptID_geneName.txt **hg19** * GTF file: /import1/CCDS/HsGRCh37.1/HsGRCh37.1_CCDS_nucleotide.20131129.fa.GTF * TMAP_index: /import1/tmap-index/tmap3.4.1/hg19/hg19_CCDS_nucleotide.20131129.fa * HISAT2_index: /import1/hisat2-index/hg19/hg19_CCDS_nucleotide.20131129.fna * Cluster file: /import1/CCDS/HsGRCh37.1/HsGRCh37.1_CCDS.20131129_transcriptID_geneName.txt **hg38** * GTF file: /import1/CCDS/GRCh38.p2/GRCh38.p2_CCDS_nucleotide.20150512.fna.GTF * TMAP_index: /import1/tmap-index/tmap3.4.1/hg38/hg38_CCDS_nucleotide.20150512.fna * HISAT2_index: /import1/hisat2-index/hg38_CCDS_downloadedRef/h19_CCDS_nucleotide.20150512.fna * Cluster file: /import1/CCDS/GRCh38.p2/GRCh38.p2_CCDS.20150512_transcriptID_geneName.txt ----- **Output Format** * Four output files containinag results for **Gene FPKM**, **Gene TPM**, **Isoform FPKM**, and **Isoform TPM**. The four files have identical format with the following fields. * 1 Gene/Isoform ID * 2 Gene/Isoform FPKM (Fragments Per Kilobase per Million reads) or TPM (Transcripts per Million reads) * 3 Min FPKM/TPM * 4 Max FPKM/TPM * And one compressed **Bootstrap.tar** file will be used in IsoDE2 to compute gene differential expression. </help> </tool>