# HG changeset patch
# User iuc
# Date 1461592957 14400
# Node ID de0af39266efde1fcf283f19b236a0dcfb41cba2
# Parent  0067c78f49dc83c7052fe22dd9873348378a51df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45

diff -r 0067c78f49dc -r de0af39266ef abundance_estimates_to_matrix.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/abundance_estimates_to_matrix.xml	Mon Apr 25 10:02:37 2016 -0400
@@ -0,0 +1,206 @@
+<tool id="abundance_estimates_to_matrix" name="Build expression matrix" version="2.1.1">
+    <description>for a de novo assembly of RNA-Seq data by Trinity</description>
+    <requirements>
+        <requirement type="package" version="2.1.1">trinity</requirement>
+        <requirement type="package" version="1.1.2">bowtie</requirement>
+        <requirement type="package" version="1.2">samtools</requirement>
+        <requirement type="package" version="3.12.0">edger</requirement>
+        <requirement type="package" version="3.12.0">bioconductor-edger</requirement>
+        <requirement type="package" version="1.2.28">rsem</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range="1:"/>
+    </stdio>
+    <command><![CDATA[
+        #for $entry in $samples:
+            ln -s "${entry.file}" "${entry.sample_name}.tsv" &&
+        #end for
+
+        abundance_estimates_to_matrix.pl
+
+        --est_method ${est_method}
+        --cross_sample_norm ${additional_params.cross_sample_norm}
+
+        #for $entry in $samples:
+            "${entry.sample_name}.tsv"
+        #end for
+    ]]></command>
+    <inputs>
+        <repeat name="samples" title="RSEM abundance estimates for samples">
+            <param name="file" label="Add file" type="data" format="tabular"/>
+            <param name="sample_name" label="Sample name" type="text">
+                <validator type="regex" message="Value must be a not empty string composed by alphanumeric characters and underscores">^\w+$</validator>
+            </param>
+        </repeat>
+        
+        <param type="select" name="est_method" label="Abundance estimation method">
+            <option value="RSEM">RSEM</option>
+            <option value="eXpress">eXpress</option>
+        </param>
+
+        <section name="additional_params" title="Additional Options" expanded="False">
+            <param type="select" name="cross_sample_norm" label="Cross sample normalization">
+                <option value="TMM">TMM</option>
+                <option value="UpperQuartile">UpperQuartile</option>
+                <option value="none">None</option>
+            </param>
+        </section>
+    </inputs>
+    <outputs>
+        <data format="tabular" name="trans_counts" label="${tool.name} on ${on_string}: estimated RNA-Seq fragment counts (raw counts)" from_work_dir="matrix.counts.matrix"/>
+        <data format="tabular" name="TPM_no_norm" label="${tool.name} on ${on_string}: matrix of TPM expression values (not cross-sample normalized)" from_work_dir="matrix.TPM.not_cross_norm"/>
+        <data format="tabular" name="norm" label="${tool.name} on ${on_string}: matrix of TMM-normalized expression values" from_work_dir="matrix.TMM.EXPR.matrix">
+            <filter>additional_params['cross_sample_norm'] == "TMM"</filter>
+        </data>
+        <data format="tabular" name="norm" label="${tool.name} on ${on_string}: matrix of UpperQuartile-normalized expression values" from_work_dir="matrix.UpperQuartile.EXPR.matrix">
+            <filter>additional_params['cross_sample_norm'] == "UpperQuartile"</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="samples_0|file" value="count/rsem_bowtie/RSEM.genes.results"/>
+            <param name="samples_0|sample_name" value="sample_A"/>
+            <param name="samples_1|file" value="count/rsem_bowtie/RSEM.genes_B.results"/>
+            <param name="samples_1|sample_name" value="sample_B"/>
+            <param name="est_method" value="RSEM"/>
+            <param name="cross_sample_norm" value="TMM"/>
+            <output name="trans_counts">
+                <assert_contents>
+                    <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
+                    <has_n_columns n="3" />
+                </assert_contents>
+            </output>
+            <output name="TPM_no_norm">
+                <assert_contents>
+                    <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
+                    <has_n_columns n="3" />
+                </assert_contents>
+            </output>
+            <output name="norm">
+                <assert_contents>
+                    <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
+                    <has_n_columns n="3" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="samples_0|file" value="count/rsem_bowtie2/RSEM.genes.results"/>
+            <param name="samples_0|sample_name" value="sample_A"/>
+            <param name="samples_1|file" value="count/rsem_bowtie2/RSEM.genes_B.results"/>
+            <param name="samples_1|sample_name" value="sample_B"/>
+            <param name="est_method" value="RSEM"/>
+            <param name="cross_sample_norm" value="TMM"/>
+            <output name="trans_counts">
+                <assert_contents>
+                    <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
+                    <has_n_columns n="3" />
+                </assert_contents>
+            </output>
+            <output name="TPM_no_norm">
+                <assert_contents>
+                    <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
+                    <has_n_columns n="3" />
+                </assert_contents>
+            </output>
+            <output name="norm">
+                <assert_contents>
+                    <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
+                    <has_n_columns n="3" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="samples_0|file" value="count/express_bowtie/results.xprs.genes"/>
+            <param name="samples_0|sample_name" value="sample_A"/>
+            <param name="samples_1|file" value="count/express_bowtie/results_B.xprs.genes"/>
+            <param name="samples_1|sample_name" value="sample_B"/>
+            <param name="est_method" value="eXpress"/>
+            <param name="cross_sample_norm" value="TMM"/>
+            <output name="trans_counts">
+                <assert_contents>
+                    <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
+                    <has_n_columns n="3" />
+                </assert_contents>
+            </output>
+            <output name="TPM_no_norm">
+                <assert_contents>
+                    <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
+                    <has_n_columns n="3" />
+                </assert_contents>
+            </output>
+            <output name="norm">
+                <assert_contents>
+                    <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
+                    <has_n_columns n="3" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="samples_0|file" value="count/rsem_bowtie/RSEM.genes.results"/>
+            <param name="samples_0|sample_name" value="sample_A"/>
+            <param name="samples_1|file" value="count/rsem_bowtie/RSEM.genes_B.results"/>
+            <param name="samples_1|sample_name" value="sample_B"/>
+            <param name="est_method" value="RSEM"/>
+            <param name="cross_sample_norm" value="UpperQuartile"/>
+            <output name="trans_counts">
+                <assert_contents>
+                    <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
+                    <has_n_columns n="3" />
+                </assert_contents>
+            </output>
+            <output name="TPM_no_norm">
+                <assert_contents>
+                    <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
+                    <has_n_columns n="3" />
+                </assert_contents>
+            </output>
+            <output name="norm" file="count/matrix_rsem_bowtie_UpperQuartile/matrix.UpperQuartile.EXPR.matrix" />
+        </test>
+        <test>
+            <param name="samples_0|file" value="count/rsem_bowtie/RSEM.genes.results"/>
+            <param name="samples_0|sample_name" value="sample_A"/>
+            <param name="samples_1|file" value="count/rsem_bowtie/RSEM.genes_B.results"/>
+            <param name="samples_1|sample_name" value="sample_B"/>
+            <param name="est_method" value="RSEM"/>
+            <param name="cross_sample_norm" value="none"/>
+            <output name="trans_counts">
+                <assert_contents>
+                    <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
+                    <has_n_columns n="3" />
+                </assert_contents>
+            </output>
+            <output name="TPM_no_norm">
+                <assert_contents>
+                    <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
+                    <has_n_columns n="3" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+Trinity_ assembles transcript sequences from Illumina RNA-Seq data.
+This tool will combine abundance estimations (produced by 'Align reads and estimate abundance on a de novo assembly of RNA-Seq data' tool) from multiple samples into a single tabular file.
+This matrix can then be used by 'RNASeq samples quality check for transcript quantification' and 'Differential Expression Analysis using a Trinity assembly' tools.
+
+**Inputs**
+
+It takes as input multiple results from 'Align reads and estimate abundance on a de novo assembly of RNA-Seq data' tool/
+Each sample must have a name, that should be used in subsequent tools.
+
+**Output**
+
+This tool will produce a single matrix file. More details on this page:
+
+.. _Trinity manual: https://github.com/trinityrnaseq/trinityrnaseq/wiki/Trinity-Transcript-Quantification
+
+
+.. _Trinity: http://trinityrnaseq.github.io
+]]>
+    </help>
+    
+     <citations>
+        <citation type="doi">doi:10.1038/nbt.1883</citation>
+    </citations>
+</tool>
+
diff -r 0067c78f49dc -r de0af39266ef align_and_estimate_abundance.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/align_and_estimate_abundance.xml	Mon Apr 25 10:02:37 2016 -0400
@@ -0,0 +1,260 @@
+<tool id="align_and_estimate_abundance" name="Align reads and estimate abundance" version="2.1.1">
+    <description>on a de novo assembly of RNA-Seq data</description>
+    <requirements>
+        <requirement type="package" version="2.1.1">trinity</requirement>
+        <requirement type="package" version="1.1.2">bowtie</requirement>
+        <requirement type="package" version="2.2.6">bowtie2</requirement>
+        <requirement type="package" version="1.2">samtools</requirement>
+        <requirement type="package" version="1.2.28">rsem</requirement>
+        <requirement type="package" version="1.5.1">express</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range="1:"/>
+    </stdio>
+    <command><![CDATA[
+        ln -s $transcripts input.fa
+
+        &&
+
+        align_and_estimate_abundance.pl
+       
+        --transcripts input.fa
+
+        --est_method $method.est_method
+        #if $method.est_method == "RSEM" or $method.est_method == "eXpress":
+            --aln_method $method.aln_method
+        #end if
+
+        #if $inputs.paired_or_single == "paired":
+            --left $inputs.left_input --right $inputs.right_input
+            
+            #if $inputs.left_input.is_of_type('fasta'):
+                --seqType fa
+            #else:
+                --seqType fq
+            #end if
+            
+            #if $inputs.strand.is_strand_specific:
+                --SS_lib_type $inputs.strand.library_type
+            #end if
+
+        #else:
+            --single $inputs.input
+            
+            #if $inputs.input.is_of_type('fasta'):
+                --seqType fa
+            #else:
+                --seqType fq
+            #end if
+            
+            #if $inputs.strand.is_strand_specific:
+                --SS_lib_type $inputs.strand.library_type
+            #end if
+        #end if
+        
+        --max_ins_size $inputs.paired_fragment_length
+
+        ## Additional parameters.
+        #if $additional_params.gene_map.has_gene_map == "yes":
+            --gene_trans_map $additional_params.gene_map.gene_trans_map
+        #else
+            --trinity_mode
+        #end if
+        
+        --prep_reference
+        
+        --output_dir .
+
+        ## CPU
+        --thread_count \${GALAXY_SLOTS:-4}
+    ]]></command>
+    <inputs>
+        <param format="fasta" name="transcripts" type="data" label="Transcripts" help="de novo assembly of RNA-Seq data"/>
+        <conditional name="inputs">
+            <param name="paired_or_single" type="select" label="Paired or Single-end data?">
+                <option value="paired">Paired</option>
+                <option value="single">Single</option>
+            </param>
+            <when value="paired">
+                <param format="fasta,fastqsanger" name="left_input" type="data" label="Left/Forward strand reads" help=""/>
+                <param format="fasta,fastqsanger" name="right_input" type="data" label="Right/Reverse strand reads" help=""/>
+                <conditional name="strand">
+                    <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/>
+                    <when value="false">
+                    </when>
+                    <when value="true">
+                        <param name="library_type" type="select" label="Strand-specific Library Type">
+                            <option value="FR">Forward-Reverse</option>
+                            <option value="RF">Reverse-Forward</option>
+                        </param>
+                    </when>
+                </conditional>
+                <param name="paired_fragment_length" type="integer" value="800" min="1" label="Maximum insert size" help="bowtie -X parameter"/>
+            </when>
+            <when value="single">
+                <param format="fasta,fastqsanger" name="input" type="data" label="Single-end reads" help=""/>
+                <conditional name="strand">
+                    <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/>
+                    <when value="false">
+                    </when>
+                    <when value="true">
+                        <param name="library_type" type="select" label="Strand-specific Library Type">
+                            <option value="F">F</option>
+                            <option value="R">R</option>
+                        </param>
+                    </when>
+                </conditional>
+            </when>
+        </conditional>
+        
+        <conditional name="method">
+            <param type="select" name="est_method" label="Abundance estimation method">
+                <option value="RSEM">RSEM</option>
+                <option value="eXpress">eXpress</option>
+            </param>
+            <when value="RSEM">
+                <param type="select" name="aln_method" label="Alignment method">
+                    <option value="bowtie">Bowtie</option>
+                    <option value="bowtie2">Bowtie2</option>
+                </param>
+            </when>
+            <when value="eXpress">
+                <param type="select" name="aln_method" label="Alignment method">
+                    <option value="bowtie">Bowtie</option>
+                    <option value="bowtie2">Bowtie2</option>
+                </param>
+            </when>
+        </conditional>
+
+        <section name="additional_params" title="Additional Options" expanded="False">
+            <conditional name="gene_map">
+                <param name="has_gene_map" type="select" label="Trinity assembly?" help="If the transcripts were not assembled by trinity, additional information is needed">
+                    <option value="no">No</option>
+                    <option value="yes">Yes</option>
+                </param>
+                <when value="no">
+                </when>
+                <when value="yes">
+                    <param format="tabular" name="gene_trans_map" type="data" label="Gene to transcript correspondence ('gene(tab)transcript' lines)" />
+                </when>
+            </conditional>
+            
+        </section>
+    </inputs>
+    <outputs>
+        <data format="tabular" name="isoforms_counts_rsem" label="${tool.name} on ${on_string}: isoforms counts" from_work_dir="RSEM.isoforms.results">
+            <filter>method['est_method'] == "RSEM"</filter>
+        </data>
+        <data format="tabular" name="genes_counts_rsem" label="${tool.name} on ${on_string}: genes counts" from_work_dir="RSEM.genes.results">
+            <filter>method['est_method'] == "RSEM"</filter>
+        </data>
+        
+        <data format="tabular" name="isoforms_counts_express" label="${tool.name} on ${on_string}: isoforms counts" from_work_dir="results.xprs">
+            <filter>method['est_method'] == "eXpress"</filter>
+        </data>
+        <data format="tabular" name="genes_counts_express" label="${tool.name} on ${on_string}: genes counts" from_work_dir="results.xprs.genes">
+            <filter>method['est_method'] == "eXpress"</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="paired_or_single" value="paired"/>
+            <param name="left_input" value="reads.left.fq"/>
+            <param name="right_input" value="reads.right.fq"/>
+            <param name="transcripts" value="raw/Trinity.fasta"/>
+            <param name="library_type" value="RF"/>
+            <param name="est_method" value="RSEM"/>
+            <param name="aln_method" value="bowtie"/>
+            <param name="has_gene_map" value="no"/>
+            <output name="isoforms_counts_rsem">
+                <assert_contents>
+                    <has_line_matching expression="TRINITY_DN0_c0_g1_i1&#009;.*" />
+                    <has_n_columns n="8" />
+                </assert_contents>
+            </output>
+            <output name="genes_counts_rsem">
+                <assert_contents>
+                    <has_line_matching expression="TRINITY_DN0_c0_g1&#009;.*" />
+                    <has_n_columns n="7" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="paired_or_single" value="paired"/>
+            <param name="left_input" value="reads.left.fq"/>
+            <param name="right_input" value="reads.right.fq"/>
+            <param name="transcripts" value="raw/Trinity.fasta"/>
+            <param name="library_type" value="RF"/>
+            <param name="est_method" value="RSEM"/>
+            <param name="aln_method" value="bowtie2"/>
+            <param name="has_gene_map" value="no"/>
+            <output name="isoforms_counts_rsem">
+                <assert_contents>
+                    <has_line_matching expression="TRINITY_DN0_c0_g1_i1&#009;.*" />
+                    <has_n_columns n="8" />
+                </assert_contents>
+            </output>
+            <output name="genes_counts_rsem">
+                <assert_contents>
+                    <has_line_matching expression="TRINITY_DN0_c0_g1&#009;.*" />
+                    <has_n_columns n="7" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="paired_or_single" value="paired"/>
+            <param name="left_input" value="reads.left.fq"/>
+            <param name="right_input" value="reads.right.fq"/>
+            <param name="transcripts" value="raw/Trinity.fasta"/>
+            <param name="library_type" value="RF"/>
+            <param name="est_method" value="eXpress"/>
+            <param name="aln_method" value="bowtie"/>
+            <param name="has_gene_map" value="no"/>
+            <output name="isoforms_counts_express">
+                <assert_contents>
+                    <has_line_matching expression=".*&#009;TRINITY_DN2_c3_g1_i1&#009;.*" />
+                    <has_n_columns n="15" />
+                </assert_contents>
+            </output>
+            <output name="genes_counts_express">
+                <assert_contents>
+                    <has_line_matching expression="NA&#009;TRINITY_DN3_c0_g1.*" />
+                    <has_n_columns n="15" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+Trinity_ assembles transcript sequences from Illumina RNA-Seq data.
+This tool estimates the abundance of isoforms and genes of a transcriptome assembled with Trinity, using FastQ of a specific sample.
+
+**Inputs**
+
+It takes as input a transcriptome assembled with Trinity and the reads from a RNASeq sample.
+You have to choose between several counting methods.
+
+If you dont align on a Trinity assembly, you need to provide a file of the following (tabular) format to map gene ids to transcript ids:
+
+=========== ================
+gene1       transcript1
+----------- ----------------
+gene2       transcript2
+=========== ================
+
+**Output**
+
+This tool will produce 2 tabular files, with counts for isoforms and genes respectively. More details on this page:
+
+.. _Trinity manual: https://github.com/trinityrnaseq/trinityrnaseq/wiki/Trinity-Transcript-Quantification
+
+
+.. _Trinity: http://trinityrnaseq.github.io
+]]>
+    </help>
+    
+     <citations>
+        <citation type="doi">doi:10.1038/nbt.1883</citation>
+    </citations>
+</tool>
+
diff -r 0067c78f49dc -r de0af39266ef run_DE_analysis.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/run_DE_analysis.xml	Mon Apr 25 10:02:37 2016 -0400
@@ -0,0 +1,146 @@
+<tool id="run_DE_analysis" name="Differential expression analysis" version="2.1.1">
+    <description>using a Trinity assembly</description>
+    <requirements>
+        <requirement type="package" version="2.1.1">trinity</requirement>
+        <!-- odering is crucial, otherwise R will override the ENV variables from deseq2 -->
+        <requirement type="package" version="1.10.0">deseq2</requirement>
+        <requirement type="package" version="1.10.0">bioconductor-deseq2</requirement>
+        <requirement type="package" version="3.12.0">edger</requirement>
+        <requirement type="package" version="3.12.0">bioconductor-edger</requirement>
+        <requirement type="package" version="3.25.3">limma</requirement>
+        <requirement type="package" version="3.27.4">bioconductor-limma</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range="1:"/>
+    </stdio>
+    <command><![CDATA[
+        
+        ln -s "${matrix}" "input.matrix"
+        
+        &&
+        
+        run_DE_analysis.pl
+        
+        --matrix "input.matrix"
+
+        --samples_file "${samples}"
+        
+        --method ${method_choice.method}
+        
+        #if $method_choice.method == "edgeR":
+            --dispersion ${method_choice.edger_dispersion}
+        #end if
+        
+        #if $method_choice.method == "ROTS":
+            --ROTS_B ${method_choice.rots_b}
+            --ROTS_K ${method_choice.rots_k}
+        #end if
+        
+        --min_rowSum_counts ${additional_params.min_rowSum_counts}
+        
+        #if $additional_params.reference_sample:
+            --reference_sample ${additional_params.reference_sample}
+        #end if
+        
+        #if $additional_params.contrasts:
+            --contrasts ${additional_params.contrasts}
+        #end if
+        
+        --output results
+        
+    ]]></command>
+    <inputs>
+        <param format="tabular" name="matrix" type="data" label="Expression matrix" help="output of abundance_estimates_to_matrix tool"/>
+        <param format="tabular" name="samples" type="data" label="Sample description" help="file describing samples and replicates"/>
+        
+        <conditional name="method_choice">
+            <param type="select" name="method" label="Differential analysis method">
+                <option value="edgeR">edgeR</option>
+                <option value="DESeq2">DESeq2</option>
+                <option value="voom">voom</option>
+                <option value="ROTS">ROTS</option>
+            </param>
+            <when value="edgeR">
+                <param name="edger_dispersion" type="float" value="0.1" label="edgeR dispersion value" help="Read edgeR manual to guide your value choice" />
+            </when>
+            <when value="ROTS">
+                <param name="rots_b" type="integer" value="500" label="number of bootstraps and permutation resampling" />
+                <param name="rots_k" type="integer" value="5000" label="largest top genes size" />
+            </when>
+            <when value="voom">
+            </when>
+            <when value="DESeq2">
+            </when>
+        </conditional>
+        
+        <section name="additional_params" title="Additional Options" expanded="False">
+            <param name="min_rowSum_counts" type="integer" value="2" label="Minimum count" help="Only those rows of matrix meeting requirement will be tested"/>
+            <param name="reference_sample" type="text" optional="true" value="" label="Name of a sample to which all other samples should be compared" help="default is doing all pairwise-comparisons among samples"/>
+            <param format="tabular" name="contrasts" optional="true" type="data" label="Pairs of sample comparisons to perform" help="A 2-column tabular with lists of pairs of samples to compare"/>
+        </section>
+    </inputs>
+    <outputs>
+        <collection name="DE_results" type="list" label="Differential expression results on ${on_string}">
+            <discover_datasets pattern="(?P&lt;name&gt;.+)\.DE_results" ext="tabular" directory="results" visible="true" />
+        </collection>
+        <collection name="PDF_results" type="list" label="Differential expression plots on ${on_string}">
+            <discover_datasets pattern="(?P&lt;name&gt;.+)\.pdf" ext="pdf" directory="results" visible="true" />
+        </collection>
+    </outputs>
+    <tests>
+        <test>
+            <param name="matrix" value="count/qcheck/matrix.counts.matrix"/>
+            <param name="samples" value="count/samples.txt"/>
+            <param name="method" value="DESeq2"/>
+            <output_collection name="DE_results">
+                <element name="input.matrix.wt_37_vs_wt_ph8.DESeq2" compare="sim_size" file="count/exp_diff/matrix.counts.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results"/>
+                <element name="input.matrix.wt_37_vs_wt_ph8.DESeq2" compare="sim_size" file="count/exp_diff/matrix.counts.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results"/>
+                <element name="input.matrix.wt_GSNO_vs_wt_ph8.DESeq2" compare="sim_size" file="count/exp_diff/matrix.counts.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results"/>
+            </output_collection>
+            <output_collection name="PDF_results">
+                <element name="input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano" compare="sim_size" delta="100" file="count/exp_diff/matrix.counts.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.MA_n_Volcano.pdf"/>
+                <element name="input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano" compare="sim_size" delta="100" file="count/exp_diff/matrix.counts.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano.pdf"/>
+                <element name="input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano" compare="sim_size" delta="100" file="count/exp_diff/matrix.counts.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano.pdf"/>
+            </output_collection>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+Trinity_ assembles transcript sequences from Illumina RNA-Seq data.
+This tool performs differential expression analyses on a transcriptome assembled with Trinity.
+
+**Inputs**
+
+This tool uses the matrix produced by 'Build expression matrix for a de novo assembly of RNA-Seq data by Trinity' tool.
+
+You must describe your samples and replicates with a tabular file looking like this:
+
+=========== ================
+ConditionA  CondA_replicate1
+----------- ----------------
+ConditionA  CondA_replicate2
+----------- ----------------
+ConditionB  CondB_replicate1
+----------- ----------------
+ConditionB  CondB_replicate2
+----------- ----------------
+ConditionC  CondC_replicate1
+----------- ----------------
+ConditionC  CondC_replicate2
+----------- ----------------
+ConditionC  CondC_replicate3
+=========== ================
+
+It will probably be the same file as used in the tool 'RNASeq samples quality check for transcript quantification'.
+The names in column 2 must match the names given in the tool 'Build expression matrix for a de novo assembly of RNA-Seq data by Trinity'.
+
+
+.. _Trinity: http://trinityrnaseq.github.io
+]]>
+    </help>
+    
+     <citations>
+        <citation type="doi">doi:10.1038/nbt.1883</citation>
+    </citations>
+</tool>
+
diff -r 0067c78f49dc -r de0af39266ef samples_qccheck.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/samples_qccheck.xml	Mon Apr 25 10:02:37 2016 -0400
@@ -0,0 +1,114 @@
+<tool id="samples_qccheck" name="RNASeq samples quality check" version="2.1.1">
+    <description>for transcript quantification</description>
+    <requirements>
+        <requirement type="package" version="2.1.1">trinity</requirement>
+        <requirement type="package" version="2.30.0">bioconductor-biobase</requirement>
+        <requirement type="package" version="2.2.2">bioconductor-qvalue</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range="1:"/>
+    </stdio>
+    <command><![CDATA[
+        
+        ln -s "${matrix}" "input.matrix"
+        
+        &&
+        
+        PtR
+        --matrix "input.matrix"
+        
+        --samples "${samples}"
+        
+        --CPM --log2 --compare_replicates
+        
+        &&
+        
+        PtR
+        --matrix "input.matrix"
+        
+        --samples "${samples}"
+        
+        --CPM --log2 --sample_cor_matrix
+        
+        &&
+        
+        PtR
+        --matrix "input.matrix"
+        
+        --samples "${samples}"
+        
+        --CPM --log2 --prin_comp 3
+        
+        && mkdir out_pdf
+        && mv *rep_compare.pdf out_pdf/
+        && mv *sample_cor_matrix.pdf out_pdf/
+        && mv *principal_components.pdf out_pdf/
+        
+    ]]></command>
+    <inputs>
+        <param format="tabular" name="matrix" type="data" label="Expression matrix" help="output of abundance_estimates_to_matrix tool"/>
+        <param format="tabular" name="samples" type="data" label="Samples description" help="file describing samples and replicates"/>
+    </inputs>
+    <outputs>
+        <collection name="reports" type="list" label="Quality check result files on ${on_string}">
+            <discover_datasets pattern="__name__" ext="pdf" directory="out_pdf" visible="true" />
+        </collection>
+    </outputs>
+    <tests>
+        <test>
+            <param name="matrix" value="count/qcheck/matrix.counts.matrix"/>
+            <param name="samples" value="count/samples.txt"/>
+            <output_collection name="reports">
+                <element name="wt_37.rep_compare.pdf" compare="sim_size" delta="100" file="count/qcheck/wt_37.rep_compare.pdf"/>
+                <element name="wt_GSNO.rep_compare.pdf" compare="sim_size" delta="100" file="count/qcheck/wt_GSNO.rep_compare.pdf"/>
+                <element name="wt_ph8.rep_compare.pdf" compare="sim_size" delta="100" file="count/qcheck/wt_ph8.rep_compare.pdf"/>
+                <element name="input.matrix.minCol10.minRow10.CPM.log2.principal_components.pdf" compare="sim_size" delta="100" file="count/qcheck/matrix.counts.matrix.minCol10.minRow10.CPM.log2.principal_components.pdf"/>
+                <element name="input.matrix.minCol10.minRow10.CPM.log2.sample_cor_matrix.pdf" compare="sim_size" delta="100" file="count/qcheck/matrix.counts.matrix.minCol10.minRow10.CPM.log2.sample_cor_matrix.pdf"/>
+            </output_collection>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+Trinity_ assembles transcript sequences from Illumina RNA-Seq data.
+This tool performs some Quality Checks on a RNASeq experiment, analysing the abundance estimation for different samples using a transcriptome assembled with Trinity.
+
+**Inputs**
+
+This tool uses the matrix produced by 'Build expression matrix for a de novo assembly of RNA-Seq data by Trinity' tool.
+
+You must describe your samples and replicates with a tabular file looking like this:
+
+=========== ================
+ConditionA  CondA_replicate1
+----------- ----------------
+ConditionA  CondA_replicate2
+----------- ----------------
+ConditionB  CondB_replicate1
+----------- ----------------
+ConditionB  CondB_replicate2
+----------- ----------------
+ConditionC  CondC_replicate1
+----------- ----------------
+ConditionC  CondC_replicate2
+----------- ----------------
+ConditionC  CondC_replicate3
+=========== ================
+
+The names in column 2 must match the names given in the tool 'Build expression matrix for a de novo assembly of RNA-Seq data by Trinity'.
+
+**Output**
+
+This tool will produce several PDF files, see the following page for more information:
+
+.. _Trinity manual: https://github.com/trinityrnaseq/trinityrnaseq/wiki/QC-Samples-and-Replicates
+
+
+.. _Trinity: http://trinityrnaseq.github.io
+]]>
+    </help>
+    
+     <citations>
+        <citation type="doi">doi:10.1038/nbt.1883</citation>
+    </citations>
+</tool>
+
diff -r 0067c78f49dc -r de0af39266ef test-data/count/exp_diff/matrix.counts.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/exp_diff/matrix.counts.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results	Mon Apr 25 10:02:37 2016 -0400
@@ -0,0 +1,39 @@
+id	baseMeanA	baseMeanB	baseMean	log2FoldChange	lfcSE	stat	pvalue	padj
+TR4277|c0_g1_i1	3852.97388871986	161.116814813422	2007.04535176664	-4.57259674791206	0.121601866332754	-37.6030145409076	0	0
+TR131|c0_g1_i1	26.1866396538608	1340.30918254958	683.247911101723	5.67372481552909	0.187406695960058	30.274931140872	2.45144211418965e-201	4.04487948841292e-200
+TR4761|c0_g1_i1	1645.20640957447	193.196157329029	919.201283451752	-3.08847487551254	0.143642016580712	-21.5011940728159	1.51733402752078e-102	1.66906743027286e-101
+TR3091|c0_g1_i1	16.7444693227929	328.569936894811	172.657203108802	4.29039998257063	0.240421038467916	17.8453599980735	3.14072644239509e-71	2.59109931497595e-70
+TR3638|c0_g1_i1	583.00358519031	183.754416330029	383.37900076017	-1.66018915730897	0.144484444213305	-11.4904352945982	1.47367477630653e-30	9.72625352362312e-30
+TR2487|c0_g1_i1	342.210853400436	920.407318992504	631.30908619647	1.42690938766606	0.124693202553469	11.4433614539188	2.5385551583546e-30	1.39620533709503e-29
+TR3788|c0_g1_i1	19.5075441237117	134.95369713876	77.2306206312357	2.77038513264018	0.262760026053246	10.5434040871909	5.44900939296595e-26	2.56881871382681e-25
+TR1479|c0_g1_i1	129.593534475689	371.064629188207	250.329081831948	1.51441163103673	0.145431922863633	10.4131995315551	2.1584296431011e-25	8.90352227779205e-25
+TR2107|c1_g1_i1	48.9228907410258	7.40521775805688	28.1640542495414	-2.6949883047084	0.431525668867458	-6.24525607429428	4.23106352657394e-10	1.55138995974378e-09
+TR3854|c0_g1_i1	1573.69549271337	2374.56159860719	1974.12854566028	0.593513416954248	0.111306645736399	5.33223701987958	9.70102011419466e-08	3.20133663768424e-07
+TR2122|c0_g2_i2	119.534640490118	199.143666337033	159.339153413576	0.738656537188098	0.168436715892782	4.38536534788702	1.15791268060543e-05	3.47373804181628e-05
+TR1449|c0_g1_i1	180.814952011467	104.755290736358	142.785121373912	-0.784194659361461	0.185749133486416	-4.2217944420118	2.42365089281258e-05	6.61949164163031e-05
+TR4163|c0_g1_i1	347.283468916919	232.772947466212	290.028208191566	-0.576744528291395	0.137147958253208	-4.20527243450891	2.60767852549073e-05	6.61949164163031e-05
+TR2672|c0_g1_i1	18.3155337236093	2.26581902751323	10.2906763755613	-2.88818323474529	0.724350842979802	-3.98727117216294	6.68376171815065e-05	0.000157545811927837
+TR127|c1_g1_i1	13.461799216177	1.21881296083961	7.34030608850831	-3.33218181130749	0.914685635912973	-3.64298036448506	0.000269499403689035	0.000576210779000196
+TR5055|c0_g2_i1	23.3590211688541	5.52768338415684	14.4433522765055	-2.04478780320925	0.562727305023446	-3.63370994255211	0.00027937492315161	0.000576210779000196
+TR2844|c0_g1_i1	158.206282615139	231.762548186068	194.984415400603	0.550641897280872	0.154759496937021	3.55804915484414	0.000373619406412113	0.000725261200682336
+TR5212|c0_g1_i1	65.7079302129484	107.875371765755	86.7916509893515	0.713884138135847	0.209708011296715	3.40418152707468	0.000663626354411326	0.00121664831642076
+TR1894|c2_g1_i1	13.3497721959996	2.96749216411516	8.15863218005739	-2.04982326482473	0.714661961266818	-2.8682417365424	0.00412760030232129	0.00716898999876856
+TR24|c0_g1_i1	69.9065207344592	41.2394742844514	55.5729975094553	-0.760369639593845	0.269117661787534	-2.8254170853868	0.00472191070589177	0.00779115266472142
+TR4669|c0_g2_i1	0	167.096667347181	83.5483336735905	4.37844609928899	2.00484514683835	2.18393231327309	0.0289672221614669	0.0455199205394479
+TR2779|c0_g1_i1	155.915506826481	205.619872596257	180.767689711369	0.402360429872658	0.188906223389576	2.12994798505331	0.0331759079102528	0.0497638618653791
+TR1492|c0_g1_i2	1640.89375005483	1435.64893261411	1538.27134133447	-0.192484740220531	0.101376439014472	-1.89871277874588	0.0576022504671541	0.0796285639028554
+TR3807|c0_g1_i1	3.48709246029019	0.350050334268211	1.9185713972792	-2.70461238638113	1.4262081182078	-1.89636586123194	0.0579116828384403	0.0796285639028554
+TR4084|c0_g1_i1	93.2264707954139	121.352438036668	107.289454416041	0.3802042378315	0.213056828958299	1.78452030704877	0.0743391580521785	0.0981276886288757
+TR1891|c0_g1_i1	107.628573623499	135.399287466928	121.513930545214	0.328806752550927	0.189034600977243	1.73939982866159	0.0819644583677276	0.104031812543654
+TR1837|c2_g1_i1	0.308903905435236	2.22601224010275	1.26745807276899	2.42365647560727	1.53486167088074	1.57907160077593	0.114319634794044	1
+TR5075|c0_g1_i1	15.8633018853512	9.23822794034992	12.5507649128506	-0.764079585128418	0.506894456921462	-1.50737411840904	0.131714788977897	0.158065100778825
+TR4859|c0_g1_i1	7.32690480813971	3.17910584569163	5.25300532691567	-1.18284590433612	0.789581441931072	-1.49806700299749	0.134115843085064	0.158065100778825
+TR939|c0_g1_i1	84.2568220960088	96.9171174594069	90.5869697777078	0.202696971338398	0.202184598546511	1.00253418309589	0.316085665578007	0.354180332604713
+TR2278|c0_g1_i1	486.5272515724	448.140178813055	467.333715192727	-0.118822731208233	0.119975347874694	-0.990392887481645	0.321982120549739	0.354180332604713
+TR2011|c5_g1_i1	5.60408627995835	7.88255079488408	6.74331853742122	0.488779860259128	0.689341019893534	0.70905378637502	0.478291099766969	0.509148590074515
+TR2182|c3_g2_i6	2.24974854180929	1.3031439398571	1.77644624083319	-0.780861388045469	1.28191780274725	-0.609135302101293	0.54243475986365	0.559385846109389
+TR3249|c0_g1_i1	1.12573841927462	2.128954842887	1.62734663108081	0.761533075632955	1.28978972955114	0.590431958159547	0.554901090261946	1
+TR1678|c0_g1_i1	0.595141051681226	0.700100668536423	0.647620860108824	0.247986780508542	1.73527723872539	0.142909026277954	0.886362029808798	1
+TR1122|c0_g1_i1	1.41370386226057	1.3031439398571	1.35842390105883	-0.16283641618004	1.43170451886811	-0.113736049606644	0.909447034479058	1
+TR1982|c2_g1_i1	5.73684100209948	5.71221669652109	5.72452884931028	0.0102126833240523	0.713573951255734	0.0143120181252136	0.988581051536513	0.988581051536513
+TR2090|c0_g1_i1	0	9.55638889228537	4.77819444614269	3.06235120305875	2.04796345977052	1.49531535264887	NA	1
diff -r 0067c78f49dc -r de0af39266ef test-data/count/exp_diff/matrix.counts.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.MA_n_Volcano.pdf
Binary file test-data/count/exp_diff/matrix.counts.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.MA_n_Volcano.pdf has changed
diff -r 0067c78f49dc -r de0af39266ef test-data/count/exp_diff/matrix.counts.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/exp_diff/matrix.counts.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results	Mon Apr 25 10:02:37 2016 -0400
@@ -0,0 +1,39 @@
+id	baseMeanA	baseMeanB	baseMean	log2FoldChange	lfcSE	stat	pvalue	padj
+TR4277|c0_g1_i1	4705.34614971641	162.902721493704	2434.12443560506	-4.84860951090545	0.124597307945428	-38.9142397284305	0	0
+TR131|c0_g1_i1	32.0461070493257	1436.30905989883	734.177583474076	5.48367743370229	0.196017912869615	27.9753893581648	3.23827538807456e-172	6.15272323734167e-171
+TR4761|c0_g1_i1	2012.6141923276	384.620292965437	1198.61724264652	-2.38450946693381	0.143863830576436	-16.5747669680385	1.06073316501088e-61	1.34359534234711e-60
+TR3091|c0_g1_i1	20.4914097091341	321.651020117047	171.071214913091	3.96886910507283	0.256323110469072	15.4838519937191	4.45952081812589e-54	4.2365447772196e-53
+TR2779|c0_g1_i1	191.51955185349	1058.15934185376	624.839446853626	2.46616535412611	0.177102083131526	13.9251064161374	4.4587691300744e-44	3.38866453885655e-43
+TR1492|c0_g1_i2	2006.11782336441	890.823502721036	1448.47066304272	-1.17029110983798	0.12207086547883	-9.58698134274255	9.06997941755552e-22	5.74432029778516e-21
+TR5075|c0_g1_i1	19.3833722195684	136.98672801182	78.1850501156942	2.80049241151413	0.293976352213923	9.52625063350759	1.63066468983638e-21	8.85217974482605e-21
+TR1891|c0_g1_i1	131.416087212132	376.595292171713	254.005689691923	1.51493508389526	0.17090866237033	8.86400409952692	7.71909159725621e-19	3.6665685086967e-18
+TR2487|c0_g1_i1	418.818667162757	965.862817209246	692.340742186001	1.20547893236143	0.136832960243688	8.80985787499278	1.25304626500959e-18	5.29063978559604e-18
+TR3638|c0_g1_i1	713.131183384274	326.063958913919	519.597571149096	-1.1281436752687	0.141731779309567	-7.95970868893582	1.72444792020844e-15	6.55290209679206e-15
+TR2107|c1_g1_i1	59.5986596731862	1.89840873462066	30.7485342039034	-4.81058600791914	0.641850436461167	-7.49487066557473	6.63637683134955e-14	2.29256654173894e-13
+TR2122|c0_g2_i2	146.135958637131	360.821667264163	253.478812950647	1.30334955915215	0.177300500792357	7.35107658087526	1.96616724778278e-13	6.22619628464548e-13
+TR1479|c0_g1_i1	158.005105094407	334.827472148091	246.416288621249	1.07882286721986	0.173458235018578	6.2194963940704	4.98753084614221e-10	1.45789363194926e-09
+TR24|c0_g1_i1	85.6614643869141	199.923709280262	142.792586833588	1.22623657127381	0.213504266341901	5.74338205172044	9.2804014146814e-09	2.51896609827067e-08
+TR4163|c0_g1_i1	424.593720981574	227.471218917767	326.03246994967	-0.900786056392834	0.160721595544993	-5.60463609969988	2.08692952426197e-08	5.28688812813031e-08
+TR2278|c0_g1_i1	594.657329919233	348.341653317169	471.499491618201	-0.772446091346236	0.159105007190944	-4.85494520244241	1.20420038267752e-06	2.79113819122931e-06
+TR1449|c0_g1_i1	220.782434528097	117.26089394399	169.021664236043	-0.913694497348233	0.188477876305836	-4.84775462911953	1.24866708554995e-06	2.79113819122931e-06
+TR127|c1_g1_i1	16.3791628279609	1.58772512712498	8.98344397754296	-3.19771077466237	0.834376974262452	-3.83245328346816	0.00012687169720824	0.000267840249661839
+TR1894|c2_g1_i1	16.2826445742552	1.67571344127509	8.97917900776516	-3.15659686337855	0.834779400611257	-3.7813545244015	0.00015597736029041	0.000307529893573321
+TR5055|c0_g2_i1	28.6665933385886	6.05959103586122	17.3630921872249	-2.17768048931004	0.577307428800381	-3.77213314894485	0.000161857838722801	0.000307529893573321
+TR4084|c0_g1_i1	113.2594381118	173.837287636503	143.548362874151	0.609755827935052	0.219803235717165	2.7740985065373	0.00553549140639085	0.00984268771318224
+TR2090|c0_g1_i1	0	5.87877087384675	2.93938543692337	4.81114433617716	1.74023660764341	2.76464953963491	0.00569839814973709	0.00984268771318224
+TR1678|c0_g1_i1	0.738899982352077	7.85275634721875	4.29582816478541	3.12892233414853	1.14660116223239	2.72886722708063	0.00635522860739327	0.0104999429165628
+TR4859|c0_g1_i1	8.91205730249659	1.28188505334354	5.09697117792006	-2.61274053843141	0.973661400721484	-2.68341801009608	0.00728738414676855	0.0115383582323835
+TR2672|c0_g1_i1	22.3129914439134	7.89947501226409	15.1062332280887	-1.45907440559266	0.562189545530202	-2.59534247335852	0.0094496708578661	0.0143634997039565
+TR3807|c0_g1_i1	4.23896204531587	0.352255997713617	2.29560902151474	-3.05008419968594	1.43726100452922	-2.12215052803511	0.0338250994349076	0.0494366837894803
+TR3249|c0_g1_i1	1.36481976577862	4.37661229401476	2.87071602989669	1.51948727816201	1.15409756308282	1.31660210260141	0.187972033660362	0.255148785128113
+TR1859|c3_g1_i1	0.361569353912422	2.25550826604853	1.30853880998047	2.09887277242766	1.59427549709957	1.31650569568817	0.188004367989136	0.255148785128113
+TR1982|c2_g1_i1	7.00144976454503	11.520013112092	9.26073143831853	0.70490953188932	0.647715898283926	1.0883004937148	0.276462472665158	0.362261171078483
+TR3854|c0_g1_i1	1925.26464813324	2107.16376011081	2016.21420412203	0.130534071096341	0.124633726123269	1.04734147936199	0.29494211171073	0.373593341500258
+TR5212|c0_g1_i1	80.2050001877881	94.8352723753388	87.5201362815635	0.236773654582184	0.240888724170321	0.982917134862537	0.325648223857982	0.399181693761397
+TR1837|c2_g1_i1	0.377330628439655	1.67813520813222	1.02773291828594	1.63744709452968	1.70484764845029	0.960465350682869	0.336821061516539	0.39997501055089
+TR2844|c0_g1_i1	193.030766468894	213.82243412349	203.426600296192	0.144163413939115	0.182129405153131	0.791543868591151	0.428626687374099	0.493570124855023
+TR1122|c0_g1_i1	1.69354093201913	0.660517838352177	1.17702938518565	-1.10951489814723	1.57444243758247	-0.704703374135971	0.48099485111646	0.537582480659573
+TR2011|c5_g1_i1	6.84875389533898	4.81927837273561	5.8340161340373	-0.467994718304978	0.83497566164615	-0.560489053516039	0.575145904101733	0.62444412445331
+TR2182|c3_g2_i6	2.76248771922916	1.94482465855284	2.353656188891	-0.463555959442342	1.17585679724627	-0.394228243207794	0.69341253558072	0.731935454224094
+TR3788|c0_g1_i1	23.7579432209456	26.0024682525169	24.8802057367313	0.125242792795277	0.407913046833573	0.307033064442226	0.75881820512208	0.779326805260514
+TR939|c0_g1_i1	103.002135647151	102.820214322362	102.911174984756	-0.00127076378479059	0.216917077821033	-0.00585829293643274	0.995325785249569	0.995325785249569
diff -r 0067c78f49dc -r de0af39266ef test-data/count/exp_diff/matrix.counts.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano.pdf
Binary file test-data/count/exp_diff/matrix.counts.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano.pdf has changed
diff -r 0067c78f49dc -r de0af39266ef test-data/count/exp_diff/matrix.counts.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/exp_diff/matrix.counts.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results	Mon Apr 25 10:02:37 2016 -0400
@@ -0,0 +1,40 @@
+id	baseMeanA	baseMeanB	baseMean	log2FoldChange	lfcSE	stat	pvalue	padj
+TR2779|c0_g1_i1	195.849684476753	966.924129135581	581.386906806167	2.25621220756415	0.156114979193812	14.4522467940961	2.42639762934434e-47	5.82335431042642e-46
+TR1891|c0_g1_i1	128.246229498835	343.028289972482	235.637259735659	1.40479466067472	0.104376051709838	13.4589749052781	2.72672776456232e-41	3.27207331747478e-40
+TR4761|c0_g1_i1	184.029205648389	351.782300021135	267.905752834762	0.934185686537064	0.0945413616088594	9.88123791152932	5.0208774429335e-23	4.0167019543468e-22
+TR24|c0_g1_i1	39.3724575919554	183.288101009647	111.330279300801	2.11680322693425	0.240338854880295	8.80757806717753	1.27878744153922e-18	7.67272464923531e-18
+TR3638|c0_g1_i1	174.266398355818	297.555274221606	235.910836288712	0.75598517202537	0.0975355931355663	7.75086455848598	9.12689947000201e-15	3.81892706573808e-14
+TR2122|c0_g2_i2	190.673533226329	328.707071692642	259.690302459485	0.782528370953275	0.101034702024136	7.74514454218254	9.54731766434521e-15	3.81892706573808e-14
+TR2278|c0_g1_i1	426.804298570637	315.99710709695	371.400702833793	-0.429046906426044	0.106511998284025	-4.02815563822158	5.62161256784655e-05	0.000192741002326167
+TR4084|c0_g1_i1	115.544575735664	157.970364768418	136.757470252041	0.435378746345168	0.157905703989027	2.75720721510747	0.00582973950434901	0.017489218513047
+TR3788|c0_g1_i1	128.115824993653	24.010679388938	76.0632521912957	-1.20076602288383	0.555078500739638	-2.16323640941564	0.0305230012251409	0.0813946699337092
+TR1678|c0_g1_i1	0.695005959508731	7.10082184137838	3.89791390044355	1.13542782611345	0.54389306361848	2.08759387104432	0.0368344853417399	1
+TR1859|c3_g1_i1	0	2.05957798928713	1.02978899464357	1.08547672488113	0.52169423531112	2.08067609609255	0.0374635634690378	1
+TR1479|c0_g1_i1	353.92669362375	305.546165789569	329.736429706659	-0.210273055725041	0.101401657889395	-2.07366487000044	0.0381104459877385	0.0914650703705724
+TR1492|c0_g1_i2	1368.89238848897	813.514514376559	1091.20345143276	-0.673957173112486	0.33643480733027	-2.00323259790084	0.0451523282811554	0.0985141707952481
+TR2844|c0_g1_i1	220.566338218013	194.214843050373	207.390590634193	-0.1851823349888	0.101213323108161	-1.8296240979155	0.0673061677634479	0.134612335526896
+TR5075|c0_g1_i1	8.81552188359314	126.23137395943	67.5234479215117	0.86620707327725	0.498591364017662	1.73730861741634	0.0823327113057556	0.151998851641395
+TR2107|c1_g1_i1	7.08292121571621	1.78415791317121	4.43353956444371	-0.87765751535477	0.553196716703176	-1.58651974759584	0.112621456124343	1
+TR2672|c0_g1_i1	2.07518941673641	7.44710458698621	4.76114700186131	0.652733502871168	0.537764458916032	1.21379070715621	0.224827655823799	1
+TR4859|c0_g1_i1	3.10763825129944	1.1806627783491	2.14415051482427	-0.587630876626665	0.551071114588281	-1.06634309269812	0.28626857627862	1
+TR3091|c0_g1_i1	312.47018793986	293.531643106953	303.000915523406	-0.0879738435317154	0.0902971665647824	-0.97427025540829	0.329922369379669	0.501282895914669
+TR4163|c0_g1_i1	221.469120691076	207.118822998308	214.293971844692	-0.0959599050588562	0.0987561344325879	-0.97168551209707	0.331207026506115	0.501282895914669
+TR4669|c0_g2_i1	165.630009730314	0	82.8150048651569	-0.322459466822447	0.333908718519009	-0.965711432311973	0.334188597276446	0.501282895914669
+TR1894|c2_g1_i1	2.85762748931802	1.47338219762144	2.16550484346973	-0.426208431542948	0.551264679640795	-0.773146634064541	0.439435604855973	1
+TR3249|c0_g1_i1	2.06512931203634	4.15451161800812	3.10982046502223	0.3941103325595	0.539435464341514	0.730597742661558	0.465024891244583	1
+TR5212|c0_g1_i1	102.736339436612	86.4452993262187	94.5908193814151	-0.222704356323449	0.346653224187607	-0.642441324021618	0.520586675617895	0.734945894989969
+TR1122|c0_g1_i1	1.29006258579706	0.5946183773076	0.942340481552333	-0.302591524122929	0.512417527863229	-0.590517512905403	0.554843748171664	1
+TR2011|c5_g1_i1	7.597917075274	4.42090354598533	6.00941031062966	-0.246737820349972	0.517913150509813	-0.476407714511773	0.633783939711306	1
+TR1837|c2_g1_i1	2.16507864525674	1.46465683073113	1.81486773799393	-0.235474161889615	0.546181064177423	-0.431128388246582	0.666375020163124	1
+TR2182|c3_g2_i6	1.29006258579706	1.76655578876639	1.52830918728173	0.209843639881372	0.537581597903129	0.390347513195914	0.696279593847798	1
+TR1449|c0_g1_i1	98.9943307118646	106.843279101242	102.918804906553	0.100194141469895	0.276715374273995	0.362083753867198	0.717289443676285	0.9108498942696
+TR4277|c0_g1_i1	153.969096204861	149.159426886469	151.564261545665	-0.0459267760105497	0.128823197370029	-0.356510139075578	0.721458560376159	0.9108498942696
+TR1982|c2_g1_i1	5.5352448786851	10.687042573374	8.11114372602957	0.110416157924497	0.359967068804195	0.306739608962835	0.759041578558	0.9108498942696
+TR127|c1_g1_i1	1.20754470361908	1.49113571265046	1.34934020813477	0.142968860758062	0.541343527667515	0.26410006484066	0.791702813929264	1
+TR3854|c0_g1_i1	2260.55060252051	1927.46472630351	2094.00766441201	-0.135348942475858	0.546438760787258	-0.247692792291784	0.804372109047297	0.919282410339768
+TR2090|c0_g1_i1	9.46045896251181	5.6546754787973	7.55756722065455	-0.0586395744056909	0.302337767579782	-0.193953851267414	0.846212017000596	1
+TR3807|c0_g1_i1	0.347502979754365	0.292870809896544	0.320186894825454	-0.0640837282416973	0.445995787050203	-0.143686846608001	0.885747758296628	1
+TR131|c0_g1_i1	1275.67603302799	1312.2934796972	1293.9847563626	0.0343724958045096	0.405262489992082	0.0848153891695754	0.932408158838271	0.963782835492881
+TR5055|c0_g2_i1	5.17791343714095	5.60171771495863	5.38981557604979	0.043552763660028	0.53975688204026	0.0806895939805349	0.935688812631814	1
+TR939|c0_g1_i1	92.2508462008296	94.0990807885678	93.1749634946987	0.0253693962827489	0.353966153466169	0.0716718139130601	0.942863087697354	0.963782835492881
+TR2487|c0_g1_i1	875.181494043204	882.631049341941	878.906271692572	0.0115839334384507	0.255112918612705	0.0454070828770402	0.963782835492881	0.963782835492881
diff -r 0067c78f49dc -r de0af39266ef test-data/count/exp_diff/matrix.counts.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano.pdf
Binary file test-data/count/exp_diff/matrix.counts.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano.pdf has changed
diff -r 0067c78f49dc -r de0af39266ef test-data/count/express_bowtie/results.xprs
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/express_bowtie/results.xprs	Mon Apr 25 10:02:37 2016 -0400
@@ -0,0 +1,8 @@
+bundle_id	target_id	length	eff_length	tot_counts	uniq_counts	est_counts	eff_counts	ambig_distr_alpha	ambig_distr_beta	fpkm	fpkm_conf_low	fpkm_conf_high	solvable	tpm
+1	TRINITY_DN2_c3_g1_i1	202	0.000000	0	0	0.000000	0.000000	0.000000e00	0.000000e00	0.000000e00	0.000000e00	0.000000e00	F	0.000000e+00
+2	TRINITY_DN1_c0_g1_i1	380	109.247050	5	5	5.000000	17.391774	0.000000e00	0.000000e00	4.160711e06	4.160711e06	4.160711e06	T	6.610131e+05
+3	TRINITY_DN2_c0_g1_i1	279	0.000000	0	0	0.000000	0.000000	0.000000e00	0.000000e00	0.000000e00	0.000000e00	0.000000e00	F	0.000000e+00
+4	TRINITY_DN0_c0_g1_i1	229	0.000000	0	0	0.000000	0.000000	0.000000e00	0.000000e00	0.000000e00	0.000000e00	0.000000e00	F	0.000000e+00
+5	TRINITY_DN2_c1_g1_i1	541	259.008053	5	5	5.000000	10.443691	0.000000e00	0.000000e00	1.754947e06	1.754947e06	1.754947e06	T	2.788088e+05
+6	TRINITY_DN2_c2_g1_i1	240	240.000000	1	1	1.000000	1.000000	0.000000e00	0.000000e00	3.787879e05	3.787879e05	3.787879e05	T	6.017811e+04
+7	TRINITY_DN3_c0_g1_i1	216	0.000000	0	0	0.000000	0.000000	0.000000e00	0.000000e00	0.000000e00	0.000000e00	0.000000e00	F	0.000000e+00
diff -r 0067c78f49dc -r de0af39266ef test-data/count/express_bowtie/results.xprs.genes
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/express_bowtie/results.xprs.genes	Mon Apr 25 10:02:37 2016 -0400
@@ -0,0 +1,8 @@
+bundle_id	target_id	length	eff_length	tot_counts	uniq_counts	est_counts	eff_counts	ambig_distr_alpha	ambig_distr_beta	fpkm	fpkm_conf_low	fpkm_conf_high	solvable	tpm
+NA	TRINITY_DN3_c0_g1	216.00	1.00	NA	NA	NA	0.00	NA	NA	0.00	NA	NA	NA	0
+NA	TRINITY_DN2_c2_g1	240.00	240.00	NA	NA	NA	1.00	NA	NA	378787.90	NA	NA	NA	60178.11
+NA	TRINITY_DN2_c3_g1	202.00	1.00	NA	NA	NA	0.00	NA	NA	0.00	NA	NA	NA	0
+NA	TRINITY_DN0_c0_g1	229.00	1.00	NA	NA	NA	0.00	NA	NA	0.00	NA	NA	NA	0
+NA	TRINITY_DN2_c0_g1	279.00	1.00	NA	NA	NA	0.00	NA	NA	0.00	NA	NA	NA	0
+NA	TRINITY_DN1_c0_g1	380.00	109.25	NA	NA	NA	17.39	NA	NA	4160711.00	NA	NA	NA	661013.1
+NA	TRINITY_DN2_c1_g1	541.00	259.01	NA	NA	NA	10.44	NA	NA	1754947.00	NA	NA	NA	278808.8
diff -r 0067c78f49dc -r de0af39266ef test-data/count/express_bowtie/results_B.xprs
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/express_bowtie/results_B.xprs	Mon Apr 25 10:02:37 2016 -0400
@@ -0,0 +1,8 @@
+bundle_id	target_id	length	eff_length	tot_counts	uniq_counts	est_counts	eff_counts	ambig_distr_alpha	ambig_distr_beta	fpkm	fpkm_conf_low	fpkm_conf_high	solvable	tpm
+1	TRINITY_DN0_c0_g1_i1	380	109.247050	5	5	5.000000	17.391774	0.000000e+00	0.000000e+00	4.160711e+06	4.160711e+06	4.160711e+06	T	6.610131e+05
+2	TRINITY_DN2_c0_g1_i1	279	0.000000	0	0	0.000000	0.000000	0.000000e+00	0.000000e+00	0.000000e+00	0.000000e+00	0.000000e+00	F	0.000000e+00
+3	TRINITY_DN2_c1_g1_i1	240	240.000000	1	1	1.000000	1.000000	0.000000e+00	0.000000e+00	3.787879e+05	3.787879e+05	3.787879e+05	T	6.017811e+04
+4	TRINITY_DN1_c0_g1_i1	229	0.000000	0	0	0.000000	0.000000	0.000000e+00	0.000000e+00	0.000000e+00	0.000000e+00	0.000000e+00	F	0.000000e+00
+5	TRINITY_DN3_c0_g1_i1	216	0.000000	0	0	0.000000	0.000000	0.000000e+00	0.000000e+00	0.000000e+00	0.000000e+00	0.000000e+00	F	0.000000e+00
+6	TRINITY_DN2_c3_g1_i1	202	0.000000	0	0	0.000000	0.000000	0.000000e+00	0.000000e+00	0.000000e+00	0.000000e+00	0.000000e+00	F	0.000000e+00
+7	TRINITY_DN2_c2_g1_i1	541	259.008053	5	5	5.000000	10.443691	0.000000e+00	0.000000e+00	1.754947e+06	1.754947e+06	1.754947e+06	T	2.788088e+05
diff -r 0067c78f49dc -r de0af39266ef test-data/count/express_bowtie/results_B.xprs.genes
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/express_bowtie/results_B.xprs.genes	Mon Apr 25 10:02:37 2016 -0400
@@ -0,0 +1,8 @@
+bundle_id	target_id	length	eff_length	tot_counts	uniq_counts	est_counts	eff_counts	ambig_distr_alpha	ambig_distr_beta	fpkm	fpkm_conf_low	fpkm_conf_high	solvable	tpm
+NA	TRINITY_DN3_c0_g1	216.00	1.00	NA	NA	NA	0.00	NA	NA	0.00	NA	NA	NA	0
+NA	TRINITY_DN2_c1_g1	240.00	240.00	NA	NA	NA	1.00	NA	NA	378787.90	NA	NA	NA	60178.11
+NA	TRINITY_DN2_c3_g1	202.00	1.00	NA	NA	NA	0.00	NA	NA	0.00	NA	NA	NA	0
+NA	TRINITY_DN0_c0_g1	380.00	109.25	NA	NA	NA	17.39	NA	NA	4160711.00	NA	NA	NA	661013.1
+NA	TRINITY_DN1_c0_g1	229.00	1.00	NA	NA	NA	0.00	NA	NA	0.00	NA	NA	NA	0
+NA	TRINITY_DN2_c0_g1	279.00	1.00	NA	NA	NA	0.00	NA	NA	0.00	NA	NA	NA	0
+NA	TRINITY_DN2_c2_g1	541.00	259.01	NA	NA	NA	10.44	NA	NA	1754947.00	NA	NA	NA	278808.8
diff -r 0067c78f49dc -r de0af39266ef test-data/count/matrix_express_bowtie/matrix.TMM.EXPR.matrix
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/matrix_express_bowtie/matrix.TMM.EXPR.matrix	Mon Apr 25 10:02:37 2016 -0400
@@ -0,0 +1,8 @@
+	sample_A.tsv	sample_B.tsv
+TRINITY_DN2_c1_g1_i1	278808.8	60178.11
+TRINITY_DN1_c0_g1_i1	0	0
+TRINITY_DN2_c2_g1_i1	60178.11	278808.8
+TRINITY_DN2_c0_g1_i1	0	0
+TRINITY_DN3_c0_g1_i1	0	0
+TRINITY_DN2_c3_g1_i1	0	0
+TRINITY_DN0_c0_g1_i1	661013.1	661013.1
diff -r 0067c78f49dc -r de0af39266ef test-data/count/matrix_express_bowtie/matrix.TPM.not_cross_norm
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/matrix_express_bowtie/matrix.TPM.not_cross_norm	Mon Apr 25 10:02:37 2016 -0400
@@ -0,0 +1,8 @@
+	sample_A.tsv	sample_B.tsv
+TRINITY_DN2_c1_g1_i1	278808.8	60178.11
+TRINITY_DN1_c0_g1_i1	0	0
+TRINITY_DN2_c2_g1_i1	60178.11	278808.8
+TRINITY_DN2_c0_g1_i1	0	0
+TRINITY_DN3_c0_g1_i1	0	0
+TRINITY_DN2_c3_g1_i1	0	0
+TRINITY_DN0_c0_g1_i1	661013.1	661013.1
diff -r 0067c78f49dc -r de0af39266ef test-data/count/matrix_express_bowtie/matrix.counts.matrix
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/matrix_express_bowtie/matrix.counts.matrix	Mon Apr 25 10:02:37 2016 -0400
@@ -0,0 +1,8 @@
+	sample_A.tsv	sample_B.tsv
+TRINITY_DN2_c1_g1_i1	10.443691	1.000000
+TRINITY_DN1_c0_g1_i1	0.000000	0.000000
+TRINITY_DN2_c2_g1_i1	1.000000	10.443691
+TRINITY_DN2_c0_g1_i1	0.000000	0.000000
+TRINITY_DN3_c0_g1_i1	0.000000	0.000000
+TRINITY_DN2_c3_g1_i1	0.000000	0.000000
+TRINITY_DN0_c0_g1_i1	17.391774	17.391774
diff -r 0067c78f49dc -r de0af39266ef test-data/count/matrix_rsem_bowtie/matrix.TMM.EXPR.matrix
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/matrix_rsem_bowtie/matrix.TMM.EXPR.matrix	Mon Apr 25 10:02:37 2016 -0400
@@ -0,0 +1,8 @@
+	sample_A.tsv	sample_B.tsv
+TRINITY_DN3_c0_g1	0	0
+TRINITY_DN4_c0_g1	0	0
+TRINITY_DN0_c0_g1	331152.79	331152.79
+TRINITY_DN2_c0_g1	0	0
+TRINITY_DN3_c2_g1	524034.76	144812.45
+TRINITY_DN3_c1_g1	144812.45	524034.76
+TRINITY_DN3_c3_g1	0	0
diff -r 0067c78f49dc -r de0af39266ef test-data/count/matrix_rsem_bowtie/matrix.TPM.not_cross_norm
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/matrix_rsem_bowtie/matrix.TPM.not_cross_norm	Mon Apr 25 10:02:37 2016 -0400
@@ -0,0 +1,8 @@
+	sample_A.tsv	sample_B.tsv
+TRINITY_DN3_c0_g1	0	0
+TRINITY_DN4_c0_g1	0	0
+TRINITY_DN0_c0_g1	331152.79	331152.79
+TRINITY_DN2_c0_g1	0	0
+TRINITY_DN3_c2_g1	524034.76	144812.45
+TRINITY_DN3_c1_g1	144812.45	524034.76
+TRINITY_DN3_c3_g1	0	0
diff -r 0067c78f49dc -r de0af39266ef test-data/count/matrix_rsem_bowtie/matrix.counts.matrix
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/matrix_rsem_bowtie/matrix.counts.matrix	Mon Apr 25 10:02:37 2016 -0400
@@ -0,0 +1,8 @@
+	sample_A.tsv	sample_B.tsv
+TRINITY_DN3_c0_g1	0.00	0.00
+TRINITY_DN4_c0_g1	0.00	0.00
+TRINITY_DN0_c0_g1	5.00	5.00
+TRINITY_DN2_c0_g1	0.00	0.00
+TRINITY_DN3_c2_g1	1.00	5.00
+TRINITY_DN3_c1_g1	5.00	1.00
+TRINITY_DN3_c3_g1	0.00	0.00
diff -r 0067c78f49dc -r de0af39266ef test-data/count/matrix_rsem_bowtie2/matrix.TMM.EXPR.matrix
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/matrix_rsem_bowtie2/matrix.TMM.EXPR.matrix	Mon Apr 25 10:02:37 2016 -0400
@@ -0,0 +1,8 @@
+	sample_A.tsv	sample_B.tsv
+TRINITY_DN3_c0_g1	0	0
+TRINITY_DN2_c2_g1	529174.03	161779.66
+TRINITY_DN2_c3_g1	0	0
+TRINITY_DN0_c0_g1	309046.31	309046.31
+TRINITY_DN2_c0_g1	0	0
+TRINITY_DN1_c0_g1	0	0
+TRINITY_DN2_c1_g1	161779.66	529174.03
diff -r 0067c78f49dc -r de0af39266ef test-data/count/matrix_rsem_bowtie2/matrix.TPM.not_cross_norm
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/matrix_rsem_bowtie2/matrix.TPM.not_cross_norm	Mon Apr 25 10:02:37 2016 -0400
@@ -0,0 +1,8 @@
+	sample_A.tsv	sample_B.tsv
+TRINITY_DN3_c0_g1	0	0
+TRINITY_DN2_c2_g1	529174.03	161779.66
+TRINITY_DN2_c3_g1	0	0
+TRINITY_DN0_c0_g1	309046.31	309046.31
+TRINITY_DN2_c0_g1	0	0
+TRINITY_DN1_c0_g1	0	0
+TRINITY_DN2_c1_g1	161779.66	529174.03
diff -r 0067c78f49dc -r de0af39266ef test-data/count/matrix_rsem_bowtie2/matrix.counts.matrix
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/matrix_rsem_bowtie2/matrix.counts.matrix	Mon Apr 25 10:02:37 2016 -0400
@@ -0,0 +1,8 @@
+	sample_A.tsv	sample_B.tsv
+TRINITY_DN3_c0_g1	0.00	0.00
+TRINITY_DN2_c2_g1	1.00	6.00
+TRINITY_DN2_c3_g1	0.00	0.00
+TRINITY_DN0_c0_g1	5.00	5.00
+TRINITY_DN2_c0_g1	0.00	0.00
+TRINITY_DN1_c0_g1	0.00	0.00
+TRINITY_DN2_c1_g1	6.00	1.00
diff -r 0067c78f49dc -r de0af39266ef test-data/count/matrix_rsem_bowtie_UpperQuartile/matrix.TPM.not_cross_norm
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/matrix_rsem_bowtie_UpperQuartile/matrix.TPM.not_cross_norm	Mon Apr 25 10:02:37 2016 -0400
@@ -0,0 +1,8 @@
+	sample_A.tsv	sample_B.tsv
+TRINITY_DN3_c0_g1	0	0
+TRINITY_DN4_c0_g1	0	0
+TRINITY_DN0_c0_g1	331152.79	331152.79
+TRINITY_DN2_c0_g1	0	0
+TRINITY_DN3_c2_g1	524034.76	144812.45
+TRINITY_DN3_c1_g1	144812.45	524034.76
+TRINITY_DN3_c3_g1	0	0
diff -r 0067c78f49dc -r de0af39266ef test-data/count/matrix_rsem_bowtie_UpperQuartile/matrix.TPM.not_cross_norm.upper_quartile_norm.matrix
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/matrix_rsem_bowtie_UpperQuartile/matrix.TPM.not_cross_norm.upper_quartile_norm.matrix	Mon Apr 25 10:02:37 2016 -0400
@@ -0,0 +1,8 @@
+RSEM	RSEM.isoforms_B.results
+TRINITY_DN3_c2_g1_i1	524034.76	144812.45
+TRINITY_DN4_c0_g1_i1	0	0
+TRINITY_DN3_c3_g1_i1	0	0
+TRINITY_DN3_c1_g1_i1	144812.45	524034.76
+TRINITY_DN2_c0_g1_i1	0	0
+TRINITY_DN3_c0_g1_i1	0	0
+TRINITY_DN0_c0_g1_i1	331152.79	331152.79
diff -r 0067c78f49dc -r de0af39266ef test-data/count/matrix_rsem_bowtie_UpperQuartile/matrix.UpperQuartile.EXPR.matrix
diff -r 0067c78f49dc -r de0af39266ef test-data/count/matrix_rsem_bowtie_UpperQuartile/matrix.counts.matrix
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/matrix_rsem_bowtie_UpperQuartile/matrix.counts.matrix	Mon Apr 25 10:02:37 2016 -0400
@@ -0,0 +1,8 @@
+	sample_A.tsv	sample_B.tsv
+TRINITY_DN3_c0_g1	0.00	0.00
+TRINITY_DN4_c0_g1	0.00	0.00
+TRINITY_DN0_c0_g1	5.00	5.00
+TRINITY_DN2_c0_g1	0.00	0.00
+TRINITY_DN3_c2_g1	1.00	5.00
+TRINITY_DN3_c1_g1	5.00	1.00
+TRINITY_DN3_c3_g1	0.00	0.00
diff -r 0067c78f49dc -r de0af39266ef test-data/count/matrix_rsem_bowtie_none/matrix.TPM.not_cross_norm
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/matrix_rsem_bowtie_none/matrix.TPM.not_cross_norm	Mon Apr 25 10:02:37 2016 -0400
@@ -0,0 +1,8 @@
+	sample_A.tsv	sample_B.tsv
+TRINITY_DN3_c0_g1	0	0
+TRINITY_DN4_c0_g1	0	0
+TRINITY_DN0_c0_g1	331152.79	331152.79
+TRINITY_DN2_c0_g1	0	0
+TRINITY_DN3_c2_g1	524034.76	144812.45
+TRINITY_DN3_c1_g1	144812.45	524034.76
+TRINITY_DN3_c3_g1	0	0
diff -r 0067c78f49dc -r de0af39266ef test-data/count/matrix_rsem_bowtie_none/matrix.counts.matrix
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/matrix_rsem_bowtie_none/matrix.counts.matrix	Mon Apr 25 10:02:37 2016 -0400
@@ -0,0 +1,8 @@
+	sample_A.tsv	sample_B.tsv
+TRINITY_DN3_c0_g1	0.00	0.00
+TRINITY_DN4_c0_g1	0.00	0.00
+TRINITY_DN0_c0_g1	5.00	5.00
+TRINITY_DN2_c0_g1	0.00	0.00
+TRINITY_DN3_c2_g1	1.00	5.00
+TRINITY_DN3_c1_g1	5.00	1.00
+TRINITY_DN3_c3_g1	0.00	0.00
diff -r 0067c78f49dc -r de0af39266ef test-data/count/qcheck/matrix.counts.matrix
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/qcheck/matrix.counts.matrix	Mon Apr 25 10:02:37 2016 -0400
@@ -0,0 +1,41 @@
+	wt_37_2	wt_37_3	wt_37_1	wt_GSNO_3	wt_GSNO_1	wt_GSNO_2	wt_ph8_3	wt_ph8_1	wt_ph8_2
+TR24|c0_g1_i1	90.00	67.00	85.00	36.00	35.00	34.00	222.00	196.00	201.00
+TR2779|c0_g1_i1	186.00	137.00	217.00	147.00	186.00	197.00	1088.00	1094.00	1086.00
+TR127|c1_g1_i1	9.00	23.00	16.00	2.00	0.00	1.00	3.00	1.00	1.00
+TR2107|c1_g1_i1	59.00	65.00	47.00	6.00	6.00	7.00	3.00	1.00	2.00
+TR2011|c5_g1_i1	11.00	4.00	4.00	8.00	5.00	7.00	3.00	4.00	8.00
+TR4163|c0_g1_i1	368.00	422.00	425.00	172.00	216.00	210.00	234.00	254.00	212.00
+TR5055|c0_g2_i1	36.00	17.00	27.00	4.00	7.00	3.00	4.00	4.00	11.00
+TR1449|c0_g1_i1	196.00	230.00	207.00	66.00	113.00	91.00	124.00	130.00	107.00
+TR1982|c2_g1_i1	7.00	7.00	6.00	4.00	3.00	8.00	16.00	9.00	11.00
+TR1859|c3_g1_i1	0.00	0.00	1.00	0.00	0.00	0.00	1.00	2.00	4.00
+TR1492|c0_g1_i2	1895.00	1906.00	1921.00	1104.00	1263.00	1319.00	899.00	929.00	922.00
+TR1122|c0_g1_i1	2.00	3.00	0.00	3.00	0.00	0.00	1.00	1.00	0.00
+TR2278|c0_g1_i1	497.00	610.00	598.00	333.00	406.00	413.00	323.00	409.00	337.00
+TR4084|c0_g1_i1	95.00	148.00	86.00	77.00	111.00	127.00	175.00	201.00	158.00
+TR4761|c0_g1_i1	2089.00	1746.00	1875.00	155.00	174.00	165.00	394.00	389.00	406.00
+TR3638|c0_g1_i1	647.00	676.00	712.00	117.00	184.00	174.00	324.00	344.00	338.00
+TR2090|c0_g1_i1	0.00	0.00	0.00	22.00	0.00	0.02	10.33	0.00	9.09
+TR3854|c0_g1_i1	1878.00	1734.00	1864.00	1775.00	2173.00	2151.00	2216.00	2142.00	2155.00
+TR131|c0_g1_i1	32.00	28.00	31.00	1001.00	1233.00	1208.00	1486.00	1492.00	1457.00
+TR5075|c0_g1_i1	13.00	22.00	21.00	6.00	8.00	10.00	163.00	121.00	142.00
+TR2182|c3_g2_i6	1.44	2.70	3.84	3.35	0.00	0.00	1.22	2.18	2.63
+TR3788|c0_g1_i1	17.00	30.00	22.00	91.00	132.00	125.00	32.00	22.00	27.00
+TR4859|c0_g1_i1	6.00	12.00	8.00	4.00	1.00	3.00	1.00	1.00	2.00
+TR2487|c0_g1_i1	386.00	383.00	424.00	689.00	866.00	806.00	963.00	989.00	1032.00
+TR2122|c0_g2_i2	145.00	135.00	136.00	155.00	157.00	201.00	369.00	398.00	344.00
+TR4277|c0_g1_i1	4466.00	4701.00	4284.00	118.00	134.00	164.00	172.00	162.00	170.00
+TR4669|c0_g2_i1	0.00	0.00	0.00	209.00	0.00	217.50	0.14	0.06	0.18
+TR3091|c0_g1_i1	22.00	17.00	19.00	250.00	308.00	284.00	333.00	343.00	316.00
+TR2130|c1_g3_i1	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00
+TR3807|c0_g1_i1	6.00	4.00	2.00	0.00	0.00	1.00	0.00	1.00	0.00
+TR1894|c2_g1_i1	21.00	14.00	11.00	1.00	2.00	5.00	1.00	3.00	1.00
+TR5212|c0_g1_i1	64.00	89.00	78.00	73.00	98.00	108.00	103.00	105.00	84.00
+TR939|c0_g1_i1	96.00	99.00	99.00	72.00	89.00	88.00	107.00	103.00	108.00
+TR1891|c0_g1_i1	115.00	137.96	124.00	96.53	139.00	110.94	364.77	411.00	384.00
+TR2672|c0_g1_i1	14.00	29.00	22.00	0.00	4.00	2.00	14.00	4.00	7.00
+TR2844|c0_g1_i1	166.00	211.00	178.00	161.00	214.00	223.00	199.00	245.00	213.00
+TR1837|c2_g1_i1	1.00	0.00	0.00	1.00	1.00	4.00	0.00	3.00	2.00
+TR1678|c0_g1_i1	1.00	0.00	1.00	0.00	0.00	2.00	8.00	10.00	6.00
+TR3249|c0_g1_i1	1.00	2.00	1.00	4.00	1.00	0.00	6.00	1.00	7.00
+TR1479|c0_g1_i1	136.00	178.00	141.00	277.00	324.00	354.00	367.00	363.00	302.00
diff -r 0067c78f49dc -r de0af39266ef test-data/count/qcheck/matrix.counts.matrix.minCol10.minRow10.CPM.log2.principal_components.pdf
Binary file test-data/count/qcheck/matrix.counts.matrix.minCol10.minRow10.CPM.log2.principal_components.pdf has changed
diff -r 0067c78f49dc -r de0af39266ef test-data/count/qcheck/matrix.counts.matrix.minCol10.minRow10.CPM.log2.sample_cor_matrix.pdf
Binary file test-data/count/qcheck/matrix.counts.matrix.minCol10.minRow10.CPM.log2.sample_cor_matrix.pdf has changed
diff -r 0067c78f49dc -r de0af39266ef test-data/count/qcheck/wt_37.rep_compare.pdf
Binary file test-data/count/qcheck/wt_37.rep_compare.pdf has changed
diff -r 0067c78f49dc -r de0af39266ef test-data/count/qcheck/wt_GSNO.rep_compare.pdf
Binary file test-data/count/qcheck/wt_GSNO.rep_compare.pdf has changed
diff -r 0067c78f49dc -r de0af39266ef test-data/count/qcheck/wt_ph8.rep_compare.pdf
Binary file test-data/count/qcheck/wt_ph8.rep_compare.pdf has changed
diff -r 0067c78f49dc -r de0af39266ef test-data/count/rsem_bowtie/RSEM.genes.results
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/rsem_bowtie/RSEM.genes.results	Mon Apr 25 10:02:37 2016 -0400
@@ -0,0 +1,8 @@
+gene_id	transcript_id(s)	length	effective_length	expected_count	TPM	FPKM
+TRINITY_DN0_c0_g1	TRINITY_DN0_c0_g1_i1	229.00	11.55	0.00	0.00	0.00
+TRINITY_DN1_c0_g1	TRINITY_DN1_c0_g1_i1	380.00	123.91	5.00	329523.81	3668378.58
+TRINITY_DN2_c0_g1	TRINITY_DN2_c0_g1_i1	279.00	35.45	0.00	0.00	0.00
+TRINITY_DN2_c1_g1	TRINITY_DN2_c1_g1_i1	541.00	281.27	5.00	145165.14	1616031.03
+TRINITY_DN2_c2_g1	TRINITY_DN2_c2_g1_i1	240.00	15.55	1.00	525311.05	5847953.22
+TRINITY_DN2_c3_g1	TRINITY_DN2_c3_g1_i1	202.00	3.45	0.00	0.00	0.00
+TRINITY_DN3_c0_g1	TRINITY_DN3_c0_g1_i1	216.00	6.82	0.00	0.00	0.00
diff -r 0067c78f49dc -r de0af39266ef test-data/count/rsem_bowtie/RSEM.genes_B.results
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/rsem_bowtie/RSEM.genes_B.results	Mon Apr 25 10:02:37 2016 -0400
@@ -0,0 +1,8 @@
+gene_id	transcript_id(s)	length	effective_length	expected_count	TPM	FPKM
+TRINITY_DN0_c0_g1	TRINITY_DN0_c0_g1_i1	229.00	11.55	0.00	0.00	0.00
+TRINITY_DN1_c0_g1	TRINITY_DN1_c0_g1_i1	380.00	123.91	5.00	329523.81	3668378.58
+TRINITY_DN2_c0_g1	TRINITY_DN2_c0_g1_i1	279.00	35.45	0.00	0.00	0.00
+TRINITY_DN2_c2_g1	TRINITY_DN2_c2_g1_i1	541.00	281.27	5.00	145165.14	1616031.03
+TRINITY_DN2_c1_g1	TRINITY_DN2_c1_g1_i1	240.00	15.55	1.00	525311.05	5847953.22
+TRINITY_DN2_c3_g1	TRINITY_DN2_c3_g1_i1	202.00	3.45	0.00	0.00	0.00
+TRINITY_DN3_c0_g1	TRINITY_DN3_c0_g1_i1	216.00	6.82	0.00	0.00	0.00
diff -r 0067c78f49dc -r de0af39266ef test-data/count/rsem_bowtie/RSEM.isoforms.results
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/rsem_bowtie/RSEM.isoforms.results	Mon Apr 25 10:02:37 2016 -0400
@@ -0,0 +1,8 @@
+transcript_id	gene_id	length	effective_length	expected_count	TPM	FPKM	IsoPct
+TRINITY_DN0_c0_g1_i1	TRINITY_DN0_c0_g1	229	11.55	0.00	0.00	0.00	0.00
+TRINITY_DN1_c0_g1_i1	TRINITY_DN1_c0_g1	380	123.91	5.00	329523.81	3668378.58	100.00
+TRINITY_DN2_c0_g1_i1	TRINITY_DN2_c0_g1	279	35.45	0.00	0.00	0.00	0.00
+TRINITY_DN2_c1_g1_i1	TRINITY_DN2_c1_g1	541	281.27	5.00	145165.14	1616031.03	100.00
+TRINITY_DN2_c2_g1_i1	TRINITY_DN2_c2_g1	240	15.55	1.00	525311.05	5847953.22	100.00
+TRINITY_DN2_c3_g1_i1	TRINITY_DN2_c3_g1	202	3.45	0.00	0.00	0.00	0.00
+TRINITY_DN3_c0_g1_i1	TRINITY_DN3_c0_g1	216	6.82	0.00	0.00	0.00	0.00
diff -r 0067c78f49dc -r de0af39266ef test-data/count/rsem_bowtie/RSEM.isoforms_B.results
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/rsem_bowtie/RSEM.isoforms_B.results	Mon Apr 25 10:02:37 2016 -0400
@@ -0,0 +1,8 @@
+transcript_id	gene_id	length	effective_length	expected_count	TPM	FPKM	IsoPct
+TRINITY_DN0_c0_g1_i1	TRINITY_DN0_c0_g1	229	11.55	0.00	0.00	0.00	0.00
+TRINITY_DN1_c0_g1_i1	TRINITY_DN1_c0_g1	380	123.91	5.00	329523.81	3668378.58	100.00
+TRINITY_DN2_c0_g1_i1	TRINITY_DN2_c0_g1	279	35.45	0.00	0.00	0.00	0.00
+TRINITY_DN2_c2_g1_i1	TRINITY_DN2_c2_g1	541	281.27	5.00	145165.14	1616031.03	100.00
+TRINITY_DN2_c1_g1_i1	TRINITY_DN2_c1_g1	240	15.55	1.00	525311.05	5847953.22	100.00
+TRINITY_DN2_c3_g1_i1	TRINITY_DN2_c3_g1	202	3.45	0.00	0.00	0.00	0.00
+TRINITY_DN3_c0_g1_i1	TRINITY_DN3_c0_g1	216	6.82	0.00	0.00	0.00	0.00
diff -r 0067c78f49dc -r de0af39266ef test-data/count/rsem_bowtie2/RSEM.genes.results
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/rsem_bowtie2/RSEM.genes.results	Mon Apr 25 10:02:37 2016 -0400
@@ -0,0 +1,8 @@
+gene_id	transcript_id(s)	length	effective_length	expected_count	TPM	FPKM
+TRINITY_DN0_c0_g1	TRINITY_DN0_c0_g1_i1	229.00	10.58	0.00	0.00	0.00
+TRINITY_DN1_c0_g1	TRINITY_DN1_c0_g1_i1	380.00	122.00	5.00	309046.31	3415300.55
+TRINITY_DN2_c0_g1	TRINITY_DN2_c0_g1_i1	279.00	32.50	0.00	0.00	0.00
+TRINITY_DN2_c1_g1	TRINITY_DN2_c1_g1_i1	541.00	279.67	6.00	161779.66	1787842.67
+TRINITY_DN2_c2_g1	TRINITY_DN2_c2_g1_i1	240.00	14.25	1.00	529174.03	5847953.22
+TRINITY_DN2_c3_g1	TRINITY_DN2_c3_g1_i1	202.00	3.17	0.00	0.00	0.00
+TRINITY_DN3_c0_g1	TRINITY_DN3_c0_g1_i1	216.00	6.25	0.00	0.00	0.00
diff -r 0067c78f49dc -r de0af39266ef test-data/count/rsem_bowtie2/RSEM.genes_B.results
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/rsem_bowtie2/RSEM.genes_B.results	Mon Apr 25 10:02:37 2016 -0400
@@ -0,0 +1,8 @@
+gene_id	transcript_id(s)	length	effective_length	expected_count	TPM	FPKM
+TRINITY_DN0_c0_g1	TRINITY_DN0_c0_g1_i1	380.00	122.00	5.00	309046.31	3415300.55
+TRINITY_DN1_c0_g1	TRINITY_DN1_c0_g1_i1	229.00	10.58	0.00	0.00	0.00
+TRINITY_DN2_c0_g1	TRINITY_DN2_c0_g1_i1	279.00	32.50	0.00	0.00	0.00
+TRINITY_DN2_c2_g1	TRINITY_DN2_c2_g1_i1	541.00	279.67	6.00	161779.66	1787842.67
+TRINITY_DN2_c1_g1	TRINITY_DN2_c1_g1_i1	240.00	14.25	1.00	529174.03	5847953.22
+TRINITY_DN2_c3_g1	TRINITY_DN2_c3_g1_i1	202.00	3.17	0.00	0.00	0.00
+TRINITY_DN3_c0_g1	TRINITY_DN3_c0_g1_i1	216.00	6.25	0.00	0.00	0.00
diff -r 0067c78f49dc -r de0af39266ef test-data/count/rsem_bowtie2/RSEM.isoforms.results
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/rsem_bowtie2/RSEM.isoforms.results	Mon Apr 25 10:02:37 2016 -0400
@@ -0,0 +1,8 @@
+transcript_id	gene_id	length	effective_length	expected_count	TPM	FPKM	IsoPct
+TRINITY_DN0_c0_g1_i1	TRINITY_DN0_c0_g1	229	10.58	0.00	0.00	0.00	0.00
+TRINITY_DN1_c0_g1_i1	TRINITY_DN1_c0_g1	380	122.00	5.00	309046.31	3415300.55	100.00
+TRINITY_DN2_c0_g1_i1	TRINITY_DN2_c0_g1	279	32.50	0.00	0.00	0.00	0.00
+TRINITY_DN2_c1_g1_i1	TRINITY_DN2_c1_g1	541	279.67	6.00	161779.66	1787842.67	100.00
+TRINITY_DN2_c2_g1_i1	TRINITY_DN2_c2_g1	240	14.25	1.00	529174.03	5847953.22	100.00
+TRINITY_DN2_c3_g1_i1	TRINITY_DN2_c3_g1	202	3.17	0.00	0.00	0.00	0.00
+TRINITY_DN3_c0_g1_i1	TRINITY_DN3_c0_g1	216	6.25	0.00	0.00	0.00	0.00
diff -r 0067c78f49dc -r de0af39266ef test-data/count/rsem_bowtie2/RSEM.isoforms_B.results
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/rsem_bowtie2/RSEM.isoforms_B.results	Mon Apr 25 10:02:37 2016 -0400
@@ -0,0 +1,8 @@
+transcript_id	gene_id	length	effective_length	expected_count	TPM	FPKM	IsoPct
+TRINITY_DN0_c0_g1_i1	TRINITY_DN0_c0_g1	380	122.00	5.00	309046.31	3415300.55	100.00
+TRINITY_DN1_c0_g1_i1	TRINITY_DN1_c0_g1	229	10.58	0.00	0.00	0.00	0.00
+TRINITY_DN2_c0_g1_i1	TRINITY_DN2_c0_g1	279	32.50	0.00	0.00	0.00	0.00
+TRINITY_DN2_c2_g1_i1	TRINITY_DN2_c2_g1	541	279.67	6.00	161779.66	1787842.67	100.00
+TRINITY_DN2_c1_g1_i1	TRINITY_DN2_c1_g1	240	14.25	1.00	529174.03	5847953.22	100.00
+TRINITY_DN2_c3_g1_i1	TRINITY_DN2_c3_g1	202	3.17	0.00	0.00	0.00	0.00
+TRINITY_DN3_c0_g1_i1	TRINITY_DN3_c0_g1	216	6.25	0.00	0.00	0.00	0.00
diff -r 0067c78f49dc -r de0af39266ef test-data/count/samples.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/samples.txt	Mon Apr 25 10:02:37 2016 -0400
@@ -0,0 +1,9 @@
+wt_37	wt_37_1	/broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_37_1-SRX707647-SRR1582649_1.fastq	/broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_37_1-SRX707647-SRR1582649_2.fastq
+wt_37	wt_37_2	/broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_37_2-SRX707648-SRR1582650_1.fastq	/broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_37_2-SRX707648-SRR1582650_2.fastq
+wt_37	wt_37_3	/broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_37_3-SRX707649-SRR1582651_1.fastq	/broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_37_3-SRX707649-SRR1582651_2.fastq
+wt_GSNO	wt_GSNO_1	/broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_GSNO_1-SRX707644-SRR1582646_1.fastq	/broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_GSNO_1-SRX707644-SRR1582646_2.fastq
+wt_GSNO	wt_GSNO_2	/broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_GSNO_2-SRX707645-SRR1582647_1.fastq	/broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_GSNO_2-SRX707645-SRR1582647_2.fastq
+wt_GSNO	wt_GSNO_3	/broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_GSNO_3-SRX707646-SRR1582648_1.fastq	/broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_GSNO_3-SRX707646-SRR1582648_2.fastq
+wt_ph8	wt_ph8_1	/broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_ph8_1-SRX707641-SRR1582643_1.fastq	/broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_ph8_1-SRX707641-SRR1582643_2.fastq
+wt_ph8	wt_ph8_2	/broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_ph8_2-SRX707642-SRR1582644_1.fastq	/broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_ph8_2-SRX707642-SRR1582644_2.fastq
+wt_ph8	wt_ph8_3	/broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_ph8_3-SRX707643-SRR1582645_1.fastq	/broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_ph8_3-SRX707643-SRR1582645_2.fastq
diff -r 0067c78f49dc -r de0af39266ef test-data/norm/Trinity.fasta
--- a/test-data/norm/Trinity.fasta	Wed Dec 09 07:19:52 2015 -0500
+++ b/test-data/norm/Trinity.fasta	Mon Apr 25 10:02:37 2016 -0400
@@ -1,10 +1,23 @@
->TR1|c0_g1_i1 len=279 path=[257:0-278] [-1, 257, -2]
+>TRINITY_DN1_c0_g1_i1 len=229 path=[207:0-228] [-1, 207, -2]
+AAATATCACAACCACCTGAACAGGAACTTGGGATAAACAGGCAATGATGAGAGCCGATGT
+TTTTCTGTTGGTGTTTACATTGCTCTGCTCTGTGAAAGGATCCTGCAGCAGAGGCTTCCT
+ACCTGAAAAATGTTTCTCTCAATTGTAGTGTGTGAGTTACTGGTAAGACGCTTACACCTA
+TAACTCAAGGTCGGAATAGTCCCTCCAGTCCCTTTAGTAACCCAGTGGC
+>TRINITY_DN0_c0_g1_i1 len=380 path=[358:0-379] [-1, 358, -2]
+CCAAGGTAGAAAACATCCCTGCTGACAAGACCTACCTGTGACATACTCACTCTCTTAGGG
+CTTTTAAAGACAAGCCATTAAAATAGATGACCTTTCACAGACTGAAACTTGAATCACTGC
+AAAATGAATCTAGGTTGCTGTCACTTTTTCTTTTGGGTGGCGGGGCTTGATGTAGATTTT
+ATTCTATGTACAGAATTTAATGTTGAATATATTAAAAATAACAAACCTGGCATGGTTTTG
+GGAGGTTAGATTTACTGGAAATGTATTCATACTGTGAACTGTGCTCTGATGGTTAGAATG
+AAAAGCTTATCAAGCATTCCATATAACAGTGGATGTAGAAAATGTTTTCAGGTGGATATG
+TATATGGTACAGATGTAAAG
+>TRINITY_DN2_c0_g1_i1 len=279 path=[257:0-278] [-1, 257, -2]
 TCCAGACCATCGACAACATTGTCTTCTTCCCAGCCACAAGCAAGAAGGAGGATGCAGAGA
 ACTTAGCTGCAGCCCAGAGAGATGCAGTAGACTTCGATGTTCGAGTTGATACTCAAGACC
 AAGGAATGTACCGCTTTTTAACATCACAACAACTGTTCAAGCTACTGGACTGCTTATTAG
 AGTCGCATAGATTTGCAAAAGCATTTAATTCCAACAATGAACAGAGGACTGCTCTGTGGA
 AAGCAGGCTTCAAAGGCAAGTCCAAGCCCAATCTTCTAA
->TR1|c1_g1_i1 len=541 path=[519:0-540] [-1, 519, -2]
+>TRINITY_DN2_c1_g1_i1 len=541 path=[519:0-540] [-1, 519, -2]
 GTCTGAATTCGCATGTAATGCAGCTTTCCCAGACACAAGTATGGAAGCAATCCGACTTAT
 TCGCCATTGTGCAAAATATGTGTCTGATAGACCGCAGGCTTTCAAGGAGTACACAAGTGA
 TGACATGAGCGTGGCACCTGAAGACAGGGTGTGGGTGAGAGGGTGGTTCCCGATCCTCTT
@@ -15,21 +28,19 @@
 CCAGTATTTAGAAGTTCTCAGCGATGTACTTTTGGATGATATTTTTGCCCAGCTTTACTG
 GTGTGTACAACAAGACAATGAGCAGTTAGCACGATCTGGTACAAACTGCTTAGAAAACGT
 G
->TR1|c2_g1_i1 len=240 path=[218:0-239] [-1, 218, -2]
+>TRINITY_DN2_c2_g1_i1 len=240 path=[218:0-239] [-1, 218, -2]
 ACAAGCAGCCTGGCGTGTGGGCTGCGCATTCTCTTCCGGATGTACATGGACGAGAGCAGA
 GTCAGTGCCTGGGAAGAAGTCCAGCAGAGGCTTTTAAACGTCTGCAGGGAAGCGCTGAGC
 TACTTCCTCACTCTAACATCCGAAAGTCACCGGGAAGCCTGGACTAACTTACTGTTACTG
 TTCCTCACTAAAGTTCTGAAGATCAGTGACAGCAGGTTTAAAGCTCACGCATCATTCTAC
->TR2|c0_g1_i1 len=380 path=[358:0-379] [-1, 358, -2]
-CCAAGGTAGAAAACATCCCTGCTGACAAGACCTACCTGTGACATACTCACTCTCTTAGGG
-CTTTTAAAGACAAGCCATTAAAATAGATGACCTTTCACAGACTGAAACTTGAATCACTGC
-AAAATGAATCTAGGTTGCTGTCACTTTTTCTTTTGGGTGGCGGGGCTTGATGTAGATTTT
-ATTCTATGTACAGAATTTAATGTTGAATATATTAAAAATAACAAACCTGGCATGGTTTTG
-GGAGGTTAGATTTACTGGAAATGTATTCATACTGTGAACTGTGCTCTGATGGTTAGAATG
-AAAAGCTTATCAAGCATTCCATATAACAGTGGATGTAGAAAATGTTTTCAGGTGGATATG
-TATATGGTACAGATGTAAAG
->TR3|c0_g1_i1 len=229 path=[207:0-228] [-1, 207, -2]
-AAATATCACAACCACCTGAACAGGAACTTGGGATAAACAGGCAATGATGAGAGCCGATGT
-TTTTCTGTTGGTGTTTACATTGCTCTGCTCTGTGAAAGGATCCTGCAGCAGAGGCTTCCT
-ACCTGAAAAATGTTTCTCTCAATTGTAGTGTGTGAGTTACTGGTAAGACGCTTACACCTA
-TAACTCAAGGTCGGAATAGTCCCTCCAGTCCCTTTAGTAACCCAGTGGC
+>TRINITY_DN2_c3_g1_i1 len=202 path=[180:0-201] [-1, 180, -2]
+GGTGAAAAGTTTACTCTTGAAATCTGGGATAAAACGTGTAACTGCACCCTGGATATCTTC
+AAAACCACAATTCCTCACGCGCTTCTGACTTGGCGTCCCACCTCTGGCGAGGCCGAACCC
+CCATCTCCATCAGCTGTGAGTGAAAAGCCGTTGGATGCAATATCACAAAAATCTGTAGAC
+ATACATGATTCTATTCAACCAA
+>TRINITY_DN3_c0_g1_i1 len=216 path=[194:0-215] [-1, 194, -2]
+ATTGATTTATTTAATAAGAAACCAAAGAGAGGAATACAATACCTCCAAGAACAAGGGATG
+CTTGGCACCACACCCGAAGATATAGCTCAGTTCTTACATCAAGAAGAAAGATTAGACTCT
+ACTCAGGTGGGTGAGTTCCTGGGAGATAATGATAAATTCAATAAAGAAGTCATGTATGCA
+TATGTAGACCAACATGACTTTTCAGGAAAAGACTTT
+
diff -r 0067c78f49dc -r de0af39266ef test-data/raw/Trinity.fasta
--- a/test-data/raw/Trinity.fasta	Wed Dec 09 07:19:52 2015 -0500
+++ b/test-data/raw/Trinity.fasta	Mon Apr 25 10:02:37 2016 -0400
@@ -1,10 +1,23 @@
->TR1|c0_g1_i1 len=279 path=[257:0-278] [-1, 257, -2]
+>TRINITY_DN1_c0_g1_i1 len=380 path=[358:0-379] [-1, 358, -2]
+CCAAGGTAGAAAACATCCCTGCTGACAAGACCTACCTGTGACATACTCACTCTCTTAGGG
+CTTTTAAAGACAAGCCATTAAAATAGATGACCTTTCACAGACTGAAACTTGAATCACTGC
+AAAATGAATCTAGGTTGCTGTCACTTTTTCTTTTGGGTGGCGGGGCTTGATGTAGATTTT
+ATTCTATGTACAGAATTTAATGTTGAATATATTAAAAATAACAAACCTGGCATGGTTTTG
+GGAGGTTAGATTTACTGGAAATGTATTCATACTGTGAACTGTGCTCTGATGGTTAGAATG
+AAAAGCTTATCAAGCATTCCATATAACAGTGGATGTAGAAAATGTTTTCAGGTGGATATG
+TATATGGTACAGATGTAAAG
+>TRINITY_DN0_c0_g1_i1 len=229 path=[207:0-228] [-1, 207, -2]
+AAATATCACAACCACCTGAACAGGAACTTGGGATAAACAGGCAATGATGAGAGCCGATGT
+TTTTCTGTTGGTGTTTACATTGCTCTGCTCTGTGAAAGGATCCTGCAGCAGAGGCTTCCT
+ACCTGAAAAATGTTTCTCTCAATTGTAGTGTGTGAGTTACTGGTAAGACGCTTACACCTA
+TAACTCAAGGTCGGAATAGTCCCTCCAGTCCCTTTAGTAACCCAGTGGC
+>TRINITY_DN2_c0_g1_i1 len=279 path=[257:0-278] [-1, 257, -2]
 TCCAGACCATCGACAACATTGTCTTCTTCCCAGCCACAAGCAAGAAGGAGGATGCAGAGA
 ACTTAGCTGCAGCCCAGAGAGATGCAGTAGACTTCGATGTTCGAGTTGATACTCAAGACC
 AAGGAATGTACCGCTTTTTAACATCACAACAACTGTTCAAGCTACTGGACTGCTTATTAG
 AGTCGCATAGATTTGCAAAAGCATTTAATTCCAACAATGAACAGAGGACTGCTCTGTGGA
 AAGCAGGCTTCAAAGGCAAGTCCAAGCCCAATCTTCTAA
->TR1|c1_g1_i1 len=541 path=[519:0-540] [-1, 519, -2]
+>TRINITY_DN2_c1_g1_i1 len=541 path=[519:0-540] [-1, 519, -2]
 GTCTGAATTCGCATGTAATGCAGCTTTCCCAGACACAAGTATGGAAGCAATCCGACTTAT
 TCGCCATTGTGCAAAATATGTGTCTGATAGACCGCAGGCTTTCAAGGAGTACACAAGTGA
 TGACATGAGCGTGGCACCTGAAGACAGGGTGTGGGTGAGAGGGTGGTTCCCGATCCTCTT
@@ -15,21 +28,19 @@
 CCAGTATTTAGAAGTTCTCAGCGATGTACTTTTGGATGATATTTTTGCCCAGCTTTACTG
 GTGTGTACAACAAGACAATGAGCAGTTAGCACGATCTGGTACAAACTGCTTAGAAAACGT
 G
->TR1|c2_g1_i1 len=240 path=[218:0-239] [-1, 218, -2]
+>TRINITY_DN2_c2_g1_i1 len=240 path=[218:0-239] [-1, 218, -2]
 ACAAGCAGCCTGGCGTGTGGGCTGCGCATTCTCTTCCGGATGTACATGGACGAGAGCAGA
 GTCAGTGCCTGGGAAGAAGTCCAGCAGAGGCTTTTAAACGTCTGCAGGGAAGCGCTGAGC
 TACTTCCTCACTCTAACATCCGAAAGTCACCGGGAAGCCTGGACTAACTTACTGTTACTG
 TTCCTCACTAAAGTTCTGAAGATCAGTGACAGCAGGTTTAAAGCTCACGCATCATTCTAC
->TR2|c0_g1_i1 len=380 path=[358:0-379] [-1, 358, -2]
-CCAAGGTAGAAAACATCCCTGCTGACAAGACCTACCTGTGACATACTCACTCTCTTAGGG
-CTTTTAAAGACAAGCCATTAAAATAGATGACCTTTCACAGACTGAAACTTGAATCACTGC
-AAAATGAATCTAGGTTGCTGTCACTTTTTCTTTTGGGTGGCGGGGCTTGATGTAGATTTT
-ATTCTATGTACAGAATTTAATGTTGAATATATTAAAAATAACAAACCTGGCATGGTTTTG
-GGAGGTTAGATTTACTGGAAATGTATTCATACTGTGAACTGTGCTCTGATGGTTAGAATG
-AAAAGCTTATCAAGCATTCCATATAACAGTGGATGTAGAAAATGTTTTCAGGTGGATATG
-TATATGGTACAGATGTAAAG
->TR3|c0_g1_i1 len=229 path=[207:0-228] [-1, 207, -2]
-AAATATCACAACCACCTGAACAGGAACTTGGGATAAACAGGCAATGATGAGAGCCGATGT
-TTTTCTGTTGGTGTTTACATTGCTCTGCTCTGTGAAAGGATCCTGCAGCAGAGGCTTCCT
-ACCTGAAAAATGTTTCTCTCAATTGTAGTGTGTGAGTTACTGGTAAGACGCTTACACCTA
-TAACTCAAGGTCGGAATAGTCCCTCCAGTCCCTTTAGTAACCCAGTGGC
+>TRINITY_DN2_c3_g1_i1 len=202 path=[180:0-201] [-1, 180, -2]
+GGTGAAAAGTTTACTCTTGAAATCTGGGATAAAACGTGTAACTGCACCCTGGATATCTTC
+AAAACCACAATTCCTCACGCGCTTCTGACTTGGCGTCCCACCTCTGGCGAGGCCGAACCC
+CCATCTCCATCAGCTGTGAGTGAAAAGCCGTTGGATGCAATATCACAAAAATCTGTAGAC
+ATACATGATTCTATTCAACCAA
+>TRINITY_DN3_c0_g1_i1 len=216 path=[194:0-215] [-1, 194, -2]
+ATTGATTTATTTAATAAGAAACCAAAGAGAGGAATACAATACCTCCAAGAACAAGGGATG
+CTTGGCACCACACCCGAAGATATAGCTCAGTTCTTACATCAAGAAGAAAGATTAGACTCT
+ACTCAGGTGGGTGAGTTCCTGGGAGATAATGATAAATTCAATAAAGAAGTCATGTATGCA
+TATGTAGACCAACATGACTTTTCAGGAAAAGACTTT
+
diff -r 0067c78f49dc -r de0af39266ef tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Dec 09 07:19:52 2015 -0500
+++ b/tool_dependencies.xml	Mon Apr 25 10:02:37 2016 -0400
@@ -1,14 +1,32 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="trinity" version="2.0.6">
-        <repository changeset_revision="e65cf857feb6" name="package_trinity_2_0_6" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    <package name="trinity" version="2.1.1">
+        <repository changeset_revision="b66b28a11557" name="package_trinity_2_1_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
     <package name="bowtie" version="1.1.2">
         <repository changeset_revision="a1c1a92e13a6" name="package_bowtie_1_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
+    <package name="bowtie2" version="2.2.6">
+        <repository changeset_revision="0d9cd7487cc9" name="package_bowtie_2_2_6" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
     <package name="samtools" version="1.2">
         <repository changeset_revision="f6ae3ba3f3c1" name="package_samtools_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
+    <package name="edger" version="3.12.0">
+        <repository changeset_revision="5c1431123155" name="package_r_edger_3_12_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="rsem" version="1.2.28">
+        <repository changeset_revision="4567331d510a" name="package_rsem_1_2_28" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="express" version="1.5.1">
+        <repository changeset_revision="93017e8743e5" name="package_express_1_5_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="limma" version="3.27.4">
+        <repository changeset_revision="7c305aa20292" name="package_r_limma_3_27_4" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="deseq2" version="1.10.0">
+       <repository changeset_revision="362a2224b1d2" name="package_deseq2_1_10_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
     <set_environment version="1.0">
         <environment_variable action="set_to" name="TRINITY_MEM_OPTIONS">--max_memory 30G --bflyHeapSpaceMax 30G</environment_variable>
     </set_environment>
diff -r 0067c78f49dc -r de0af39266ef trinity.xml
--- a/trinity.xml	Wed Dec 09 07:19:52 2015 -0500
+++ b/trinity.xml	Mon Apr 25 10:02:37 2016 -0400
@@ -1,7 +1,7 @@
-<tool id="trinity" name="Trinity" version="2.0.6.1">
+<tool id="trinity" name="Trinity" version="2.1.1">
     <description>de novo assembly of RNA-Seq data</description>
     <requirements>
-        <requirement type="package" version="2.0.6">trinity</requirement>
+        <requirement type="package" version="2.1.1">trinity</requirement>
         <requirement type="package" version="1.1.2">bowtie</requirement>
         <requirement type="package" version="1.2">samtools</requirement>
         <requirement type="set_environment">TRINITY_MEM_OPTIONS</requirement>
@@ -62,9 +62,9 @@
         #end if
 
         ## CPU and butterfly options.
-        --CPU \${GALAXY_SLOTS:-4} \${TRINITY_MEM_OPTIONS} --bfly_opts "-V 10 --stderr"
+        --CPU \${GALAXY_SLOTS:-4} \${TRINITY_MEM_OPTIONS:---max_memory 1G} --bfly_opts "-V 10 --stderr"
         
-         > $trinity_log 2>&1
+        ## > $trinity_log 2>&1
 
     ]]></command>
     <inputs>
@@ -87,11 +87,10 @@
                         </param>
                     </when>
                 </conditional>
-                <param name="paired_fragment_length" type="integer" value="300" min="1" label="Paired Fragment Length" help="Maximum length expected between fragment pairs"/>
                 <param name="jaccard_clip" type="boolean" truevalue="--jaccard_clip" falsevalue="" checked="false" label="Jaccard Clip options" help="set if you expect high gene density with UTR overlap"/>
             </when>
             <when value="single">
-                <param format="fasta,fastq" name="input" type="data" label="Single-end reads" help=""/>
+                <param format="fasta,fastqsanger" name="input" type="data" label="Single-end reads" help=""/>
                 <conditional name="strand">
                     <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/>
                     <when value="false">
@@ -130,7 +129,7 @@
         </section>
     </inputs>
     <outputs>
-        <data format="txt" name="trinity_log" label="${tool.name} on ${on_string}: log" />
+        <!--data format="txt" name="trinity_log" label="${tool.name} on ${on_string}: log" /-->
         <data format="fasta" name="assembled_transcripts" label="${tool.name} on ${on_string}: Assembled Transcripts" from_work_dir="trinity_out_dir/Trinity.fasta"/>
     </outputs>
     <tests>