# HG changeset patch
# User saharlcc
# Date 1474336803 14400
# Node ID 7044191a603bc1e4ec98b78ff29f6af901b134f9
# Parent  babf45f7c9a35427292f5f01ec24aa77468ddc91
Uploaded

diff -r babf45f7c9a3 -r 7044191a603b isoem_wrapper.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/isoem_wrapper.xml	Mon Sep 19 22:00:03 2016 -0400
@@ -0,0 +1,161 @@
+<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 &gt; $Run 2&gt;&amp;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>
+
+
+
+