Mercurial > repos > saharlcc > isoem2_isode2
diff isoem2_isode2/isoem_wrapper.xml @ 10:78d03bf22a1f draft
- Add prinseq command to filter RNA-Seq data
- Fix in interpreting p-value when replicates are used
author | saharlcc |
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date | Thu, 16 Mar 2017 13:44:03 -0400 |
parents | |
children | be08c88b353e |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/isoem2_isode2/isoem_wrapper.xml Thu Mar 16 13:44:03 2017 -0400 @@ -0,0 +1,135 @@ +<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 + + --MinReadLength $MinReadLength + + ## 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="MinReadLength" label="Min. read length" type="text" value="50" /> + + +<!-- + <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. + +----- + + +**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> + + + +