view isoem2_isode2/isoem_wrapper.xml @ 21:b07d4238ba9b draft default tip

Updating README

<tool id="isoem" name="IsoEM2" version="1.0.0">
    <description> Infers isoform and gene expression levels with bootstrap based confidence intervals from 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.TranscriptomeSource == "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 &gt; $Run 2&gt;&amp;1

        
                          
    </command>
    <inputs>
	    <param name="sampleName"  size="10" type="text"  label="Sample name" value="Sample" help="Output files label"/>

        <conditional name="referenceSource">
          <param name="TranscriptomeSource" 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 transcriptome 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" format="fastq" label="RNA-Seq file1, fastq format" />
              <param name="input2" type="data" format="fastq" label="RNA-Seq file2, fastq format" /> 
	    </when>
            <when value="Ion-Torrent-Proton">
	      <param name="input1" type="data" format="fastq" label="RNA-Seq file, fastq 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" format="fastq" label="RNA-Seq file, fastq 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="${sampleName}-Gene_fpkm"/>
    	<data name="out_gene_tpm" format="tabular" label="${sampleName}-Gene_tpm"/>
    	<data name="out_iso_fpkm" format="tabular" label="${sampleName}-Iso_fpkm"/>
    	<data name="out_iso_tpm" format="tabular" label="${sampleName}-Iso_tpm"/>
	<data name="out_bootstrap" format="toolshed.gz" label="${sampleName}-Bootstrap.tar.gz"/>
        <data name="Run" format="log"  label="${sampleName}: The log file" />
    </outputs>
<help>
**What it does**

* IsoEM2 infers isoform and gene expression levels (along with bootstrapping based confidence intervals) from high-throughput transcriptome sequencing (RNA-Seq) data. 
*

**Input Format**

* The IsoEM2 tool can process RNA-seq reads generated by both Ion Torrent and Illumina platforms. RNA-Seq reads must be provided in fastq format. 

**Output Format**

* IsoEM2 generates four output files containinag results for **Isoform FPKM**, **Isoform TPM**, **Gene FPKM**, and **Gene TPM**. The four tab delimited files have identical format, including the following fields:


* 1- Isoform/Gene ID 
* 2- Isoform/Gene FPKM (Fragments Per Kilobase per Million reads) or TPM (Transcripts per Million reads) 
* 3- Lower-bound for the 95% confidence interval of the Isoform/Gene FPKM/TPM estimate determined by bootstrapping
* 4- Upper-bound for the 95% confidence interval of the Isoform/Gene FPKM/TPM estimate determined by bootstrapping
* 5- A compressed tar archive containing bootstrap samples used to determine confidence intervals. These archives can be used as input to the IsoDE2 tool for computing differentially expressed isoforms/genes.
*

-----

**BUILT-IN REFERENCES**

* All reference files used in this pipeline can be found at http://dna.engr.uconn.edu/tmp/galaxy/tool-data/IsoEM.loc
*
	
</help>


</tool>