# HG changeset patch
# User iuc
# Date 1470076975 14400
# Node ID 831abd20e690cfa4ecf5401f5f95006fb2d61488
# Parent  8bd817614cc854ae2a1e99fc78f17b2f16ff0fb2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214

diff -r 8bd817614cc8 -r 831abd20e690 abundance_estimates_to_matrix.xml
--- a/abundance_estimates_to_matrix.xml	Tue Jul 12 11:36:37 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,202 +0,0 @@
-<tool id="abundance_estimates_to_matrix" name="Build expression matrix" version="2.1.1.1">
-    <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="3.14.0">bioconductor-edger</requirement>
-    </requirements>
-    <stdio>
-        <exit_code range="1:"/>
-    </stdio>
-    <command><![CDATA[
-        #for $entry in $samples:
-            ln -s "${entry.file}" "${entry.sample_name}" &&
-        #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}"
-        #end for
-    ]]></command>
-    <inputs>
-        <repeat name="samples" title="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">10.1038/nbt.1883</citation>
-    </citations>
-</tool>
-
diff -r 8bd817614cc8 -r 831abd20e690 align_and_estimate_abundance.xml
--- a/align_and_estimate_abundance.xml	Tue Jul 12 11:36:37 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,260 +0,0 @@
-<tool id="align_and_estimate_abundance" name="Align reads and estimate abundance" version="2.1.1.1">
-    <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
-
-            --max_ins_size $inputs.paired_fragment_length
-
-        #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
-
-        ## Additional parameters.
-        #if $additional_params.gene_map.has_gene_map == "no":
-            --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="yes">Yes</option>
-                    <option value="no">No</option>
-                </param>
-                <when value="yes">
-                </when>
-                <when value="no">
-                    <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="yes"/>
-            <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="yes"/>
-            <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="yes"/>
-            <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">10.1038/nbt.1883</citation>
-    </citations>
-</tool>
-
diff -r 8bd817614cc8 -r 831abd20e690 macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Mon Aug 01 14:42:55 2016 -0400
@@ -0,0 +1,23 @@
+<?xml version="1.0"?>
+<macros>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="2.2.0">trinity</requirement>
+            <yield/>
+        </requirements>
+    </xml>
+
+    <token name="@WRAPPER_VERSION@">2.2.0</token>
+
+    <xml name="stdio">
+        <stdio>
+            <exit_code range="1:" level="fatal" description="Error in Trinity execution" />
+        </stdio>
+    </xml>
+
+    <xml name="citation">
+        <citations>
+            <citation type="doi">10.1038/nbt.1883</citation>
+        </citations>
+    </xml>
+</macros>
diff -r 8bd817614cc8 -r 831abd20e690 run_DE_analysis.xml
--- a/run_DE_analysis.xml	Tue Jul 12 11:36:37 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,144 +0,0 @@
-<tool id="run_DE_analysis" name="Differential expression analysis" version="2.1.1.1">
-    <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="3.14.0">bioconductor-edger</requirement>
-        <requirement type="package" version="3.28.10">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" />
-        </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" />
-        </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">10.1038/nbt.1883</citation>
-    </citations>
-</tool>
-
diff -r 8bd817614cc8 -r 831abd20e690 samples_qccheck.xml
--- a/samples_qccheck.xml	Tue Jul 12 11:36:37 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,114 +0,0 @@
-<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" />
-        </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">10.1038/nbt.1883</citation>
-    </citations>
-</tool>
-
diff -r 8bd817614cc8 -r 831abd20e690 test-data/count/exp_diff/input.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/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results	Mon Aug 01 14:42:55 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 8bd817614cc8 -r 831abd20e690 test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.MA_n_Volcano.pdf
Binary file test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.MA_n_Volcano.pdf has changed
diff -r 8bd817614cc8 -r 831abd20e690 test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.edgeR.DE_results
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.edgeR.DE_results	Mon Aug 01 14:42:55 2016 -0400
@@ -0,0 +1,39 @@
+logFC	logCPM	PValue	FDR
+TR131|c0_g1_i1	5.8364197685119	16.0402624962907	0	0
+TR4277|c0_g1_i1	-4.41329137350676	17.4523259866001	0	0
+TR3091|c0_g1_i1	4.45193883524837	14.0450613692144	2.75977672027703e-191	3.0023764016608e-190
+TR4761|c0_g1_i1	-2.92753980838104	16.3343761538543	3.16039621227453e-191	3.0023764016608e-190
+TR2487|c0_g1_i1	1.58705373680526	15.8895982491351	1.69098562804069e-123	1.28514907731092e-122
+TR1479|c0_g1_i1	1.67068054401246	14.5625418524933	4.82942248775202e-81	3.05863424224295e-80
+TR3638|c0_g1_i1	-1.49936398500381	15.1049693447894	1.31792237756209e-64	7.15443576390849e-64
+TR3854|c0_g1_i1	0.756865722480515	17.5147652035186	8.35417282711821e-40	3.96823209288115e-39
+TR2122|c0_g2_i2	0.903942128151819	13.8996874045924	3.62505920095794e-13	1.53058055151558e-12
+TR2844|c0_g1_i1	0.707836713891037	14.1854217777842	1.87464339893047e-12	7.1236449159358e-12
+TR3788|c0_g1_i1	2.92403132462783	12.8779140660683	1.50355808369265e-09	5.19410974366551e-09
+TR4669|c0_g2_i1	10.5374101870061	13.0322839834498	3.83881845042015e-08	1.21562584263305e-07
+TR2672|c0_g1_i1	-2.77697626464917	10.2324144831548	6.6653206315345e-08	1.9483244922947e-07
+TR4163|c0_g1_i1	-0.420124679057253	14.7293558096347	2.6407759845512e-06	7.16782052949613e-06
+TR2107|c1_g1_i1	-2.54740509831049	11.4796217709789	1.31520100526586e-05	3.33184254667352e-05
+TR2779|c0_g1_i1	0.57151150266807	14.0680960027645	7.44562831370785e-05	0.000176833672450561
+TR127|c1_g1_i1	-3.25307512484374	9.84850588284066	0.000331345441643876	0.000740654516615722
+TR1894|c2_g1_i1	-1.90241917506329	9.93135664117576	0.00432077639530722	0.00912163905675968
+TR5055|c0_g2_i1	-1.8950478385132	10.598211984773	0.00591755208579545	0.0118351041715909
+TR2090|c0_g1_i1	6.41050251489574	9.11635750687386	0.0113096900461153	0.021488411087619
+TR5212|c0_g1_i1	0.867439938079617	13.0331405503531	0.0317111501604761	0.0573820812427663
+TR3807|c0_g1_i1	-2.67963301995355	8.56046890206839	0.0557212159288941	0.0962457366044534
+TR1449|c0_g1_i1	-0.636836241811875	13.7146214195087	0.0845994280568489	0.139772968093924
+TR4084|c0_g1_i1	0.527023803952886	13.333880353991	0.19596368831627	0.301997237380275
+TR1891|c0_g1_i1	0.481345196849859	13.5019985083809	0.198682393013339	0.301997237380275
+TR24|c0_g1_i1	-0.590671163985234	12.3854267629296	0.21115333494008	0.308608720297039
+TR1837|c2_g1_i1	2.67943439258847	8.19914223144978	0.242162966500684	0.336820885113627
+TR4859|c0_g1_i1	-1.04273446956489	9.43870802835889	0.248183810083725	0.336820885113627
+TR939|c0_g1_i1	0.361607908864682	13.0838256643577	0.341542524228359	0.447538480023367
+TR2011|c5_g1_i1	0.672074276530526	9.63297397547156	0.357699118838244	0.453085550528442
+TR5075|c0_g1_i1	-0.617596452044795	10.4317228965746	0.378826401739151	0.464367847293153
+TR3249|c0_g1_i1	0.936067544593607	8.34110243846743	0.532174466327564	0.631957178763983
+TR1492|c0_g1_i2	-0.0311770185465736	17.1360846492483	0.562063331952301	0.647224442854165
+TR2278|c0_g1_i1	0.0373157391528861	15.4251088322423	0.63557189922311	0.710345063837593
+TR2182|c3_g2_i6	-0.665499179094881	8.45651702709919	0.835363486459349	0.906966071013008
+TR1982|c2_g1_i1	0.176241441184615	9.49445846907393	0.904611213246767	0.954867391760477
+TR1678|c0_g1_i1	0.476522568809639	7.93710096737952	1	1
+TR1122|c0_g1_i1	-0.015204817268041	8.26206767263358	1	1
diff -r 8bd817614cc8 -r 831abd20e690 test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.edgeR.DE_results.MA_n_Volcano.pdf
Binary file test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.edgeR.DE_results.MA_n_Volcano.pdf has changed
diff -r 8bd817614cc8 -r 831abd20e690 test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.voom.DE_results
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.voom.DE_results	Mon Aug 01 14:42:55 2016 -0400
@@ -0,0 +1,39 @@
+logFC	logCPM	PValue	FDR
+TR131|c0_g1_i1	5.8235943392439	16.1127963113785	7.14846919291531e-10	2.71641829330782e-08
+TR4277|c0_g1_i1	-4.41182125975734	17.3835558041266	1.56187740933885e-09	2.96756707774382e-08
+TR3091|c0_g1_i1	4.43711915085412	14.1189484156579	4.80332538807657e-08	5.96619459206176e-07
+TR2487|c0_g1_i1	1.58597331690052	15.926957585609	6.28020483374923e-08	5.96619459206176e-07
+TR4761|c0_g1_i1	-2.92047098366841	16.2714320125634	5.50582910815067e-07	4.18443012219451e-06
+TR1479|c0_g1_i1	1.67737907773679	14.6004783880878	9.51214752241748e-07	5.52604916020242e-06
+TR3638|c0_g1_i1	-1.50273266496817	15.0596817330556	1.02518921423282e-06	5.52604916020242e-06
+TR3788|c0_g1_i1	2.93902285611693	12.9382150715361	2.41689084349911e-06	1.02046502281074e-05
+TR3854|c0_g1_i1	0.759398996973938	17.5343629610585	1.16337877056893e-06	5.52604916020242e-06
+TR2107|c1_g1_i1	-2.46238704341773	11.2600018185657	0.000160625103091043	0.000554886719769058
+TR2122|c0_g2_i2	0.898555189960494	13.9141616710754	0.000116065228333624	0.000441047867667773
+TR2844|c0_g1_i1	0.712285451514242	14.1964395706942	0.000226456956836179	0.0007171136966479
+TR5212|c0_g1_i1	0.877383155201317	13.0382243238454	0.00044264831250554	0.00129389506732389
+TR4163|c0_g1_i1	-0.417753044994067	14.7100536369854	0.00073550773195026	0.00199637812957928
+TR1449|c0_g1_i1	-0.639430683731338	13.6750299459863	0.0021688744394372	0.00549448191324091
+TR2672|c0_g1_i1	-2.89090970573392	9.81450205355949	0.0110308904582196	0.0220617809164392
+TR127|c1_g1_i1	-3.10441694967501	9.33201892428652	0.0147505107490706	0.0271381068158418
+TR939|c0_g1_i1	0.363392391144623	13.0700139113805	0.00528218330196852	0.0125451853421752
+TR5055|c0_g2_i1	-1.80082179647401	10.290740057161	0.014997374819281	0.0271381068158418
+TR1894|c2_g1_i1	-1.81920882927282	9.4761161835092	0.0211021355265418	0.0348643978264604
+TR1891|c0_g1_i1	0.477106166889499	13.4994625375761	0.00640932243854848	0.0143267207449907
+TR1837|c2_g1_i1	2.21852868850051	7.02301103616459	0.041457300582048	0.063015096884713
+TR3807|c0_g1_i1	-1.9168529396959	7.35599058475032	0.0566225608328877	0.0827560504480666
+TR2779|c0_g1_i1	0.600059279980753	14.0739938889057	0.00964636468216327	0.0203645476623447
+TR24|c0_g1_i1	-0.588697529952342	12.3096839182028	0.0194904179372949	0.0336652673462366
+TR4859|c0_g1_i1	-1.06821251099455	8.91301871295058	0.111617387620425	0.157091138132451
+TR2090|c0_g1_i1	2.22339391910091	8.98366602727699	0.254495907488744	0.322361482819076
+TR4084|c0_g1_i1	0.567566096899832	13.3297126444574	0.036433281659912	0.0576860292948607
+TR2182|c3_g2_i6	-1.0316496616205	7.37334712818428	0.34572838664377	0.423796086853654
+TR2011|c5_g1_i1	0.791574287810665	9.32879226678442	0.161547389819689	0.211682786660282
+TR5075|c0_g1_i1	-0.550289601556128	10.1785868671389	0.12853444928267	0.174439609740767
+TR1678|c0_g1_i1	0.331221243897688	5.95523974949609	0.7547763751788	0.806418050624271
+TR4669|c0_g2_i1	6.27373933776222	13.1239272719772	0.48073138273468	0.553569471027814
+TR1122|c0_g1_i1	-0.199192308627843	7.01379133029712	0.87736931102229	0.87736931102229
+TR3249|c0_g1_i1	0.258869539778469	7.31927198802943	0.798677928444158	0.820263818402108
+TR1982|c2_g1_i1	0.132112224684827	9.08491674138301	0.763974995328257	0.806418050624271
+TR2278|c0_g1_i1	0.0407550618622219	15.423513715505	0.613273487399665	0.685423309446684
+TR1492|c0_g1_i2	-0.0324123498367541	17.1356104672946	0.389074079094509	0.462025468924729
diff -r 8bd817614cc8 -r 831abd20e690 test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.voom.DE_results.MA_n_Volcano.pdf
Binary file test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.voom.DE_results.MA_n_Volcano.pdf has changed
diff -r 8bd817614cc8 -r 831abd20e690 test-data/count/exp_diff/input.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/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results	Mon Aug 01 14:42:55 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 8bd817614cc8 -r 831abd20e690 test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano.pdf
Binary file test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano.pdf has changed
diff -r 8bd817614cc8 -r 831abd20e690 test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.edgeR.DE_results
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.edgeR.DE_results	Mon Aug 01 14:42:55 2016 -0400
@@ -0,0 +1,39 @@
+logFC	logCPM	PValue	FDR
+TR131|c0_g1_i1	5.83867709149149	16.0447742820606	3.67956255674e-64	1.3982337715612e-62
+TR3091|c0_g1_i1	4.35104356420213	13.9337836495047	7.47918124727105e-59	1.4210444369815e-57
+TR4277|c0_g1_i1	-4.51249642920563	17.4585638169146	1.30305812944242e-53	1.65054029729373e-52
+TR5075|c0_g1_i1	3.18286810352713	12.8084040893566	8.25600206225396e-24	7.84320195914126e-23
+TR2107|c1_g1_i1	-4.48477961203985	11.2510359028096	1.80754966502889e-22	1.37373774542196e-21
+TR2779|c0_g1_i1	2.75442228103487	15.7797198210508	8.23352696880425e-15	5.21456708024269e-14
+TR1891|c0_g1_i1	1.85607282303223	14.4424161372431	4.82341414399837e-12	2.61842482102769e-11
+TR4761|c0_g1_i1	-2.05815692521639	16.4916266891202	6.53530817860542e-12	3.10427138483757e-11
+TR1479|c0_g1_i1	1.43256512308186	14.3771181295432	1.13197856555697e-09	4.77946505457389e-09
+TR2122|c0_g2_i2	1.63807722824331	14.4300672231344	2.54380104198531e-09	9.66644395954419e-09
+TR24|c0_g1_i1	1.56169455062581	13.613754007054	1.01137959952142e-08	3.49385679834671e-08
+TR2487|c0_g1_i1	1.52157644373511	15.8810635663776	2.37540305111961e-07	7.52210966187877e-07
+TR4084|c0_g1_i1	0.991060679215133	13.5661427311877	4.21767858359174e-07	1.23285989366528e-06
+TR1678|c0_g1_i1	3.62458577193226	9.02581543875671	1.43837087677047e-05	3.90414952266271e-05
+TR127|c1_g1_i1	-2.90111481011278	9.73961125813442	2.21824302925283e-05	5.61954900744051e-05
+TR1894|c2_g1_i1	-2.85359093751189	9.70265145133598	3.82707393478771e-05	9.08930059512081e-05
+TR5055|c0_g2_i1	-1.8545312748531	10.5508309427169	0.000561739096452478	0.0012556520979526
+TR2090|c0_g1_i1	5.85461418677349	8.72713197001274	0.000625444406369261	0.00132038263566844
+TR4859|c0_g1_i1	-2.31469487039419	9.12085022188999	0.00236706272759891	0.00473412545519782
+TR1492|c0_g1_i2	-0.847097868783511	16.8160271449712	0.00265383515294934	0.00504228679060374
+TR3638|c0_g1_i1	-0.812580107843708	15.3469752226999	0.00403607816905259	0.00730337954399992
+TR3807|c0_g1_i1	-2.92018331334326	8.37863764275674	0.0119536481076316	0.0206472103677272
+TR1449|c0_g1_i1	-0.576747771663695	13.7363876885022	0.0130185393324759	0.0215088910710471
+TR1982|c2_g1_i1	1.11743546508384	9.86122459596308	0.024471659211255	0.0382656346855499
+TR2672|c0_g1_i1	-1.09825528852042	10.4080374441724	0.025174759661546	0.0382656346855499
+TR3249|c0_g1_i1	2.00776956676821	8.66772655901099	0.0275363688345113	0.0402454621427472
+TR5212|c0_g1_i1	0.582012857882519	12.8600915149255	0.0318599127004672	0.0448398771339909
+TR4163|c0_g1_i1	-0.585935901552979	14.6858409740027	0.0333717283041774	0.0452902026985264
+TR2844|c0_g1_i1	0.484938504762758	14.0537413817093	0.0410237194953782	0.0537552186491163
+TR1859|c3_g1_i1	2.64648031785777	8.0811923384908	0.0677782555815868	0.0858524570700099
+TR2278|c0_g1_i1	-0.462893051132405	15.2205527935145	0.0990317248813937	0.121393727273966
+TR3854|c0_g1_i1	0.45233145936844	17.3656486469949	0.115995274036176	0.13774438791796
+TR3788|c0_g1_i1	0.512277745155381	11.1125640718165	0.129462204245195	0.149077689736891
+TR939|c0_g1_i1	0.343195417039388	13.0829763503018	0.196684960972624	0.219824368145874
+TR1837|c2_g1_i1	2.21076601464763	7.9226544260522	0.248563909756302	0.269869387735413
+TR1122|c0_g1_i1	-0.860567840252952	7.98418712954456	0.72405804618472	0.764283493194982
+TR2011|c5_g1_i1	-0.075980865610854	9.27931055760989	0.901508002533997	0.925873083683564
+TR2182|c3_g2_i6	-0.147124070779728	8.45393312498213	1	1
diff -r 8bd817614cc8 -r 831abd20e690 test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.edgeR.DE_results.MA_n_Volcano.pdf
Binary file test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.edgeR.DE_results.MA_n_Volcano.pdf has changed
diff -r 8bd817614cc8 -r 831abd20e690 test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.voom.DE_results
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.voom.DE_results	Mon Aug 01 14:42:55 2016 -0400
@@ -0,0 +1,39 @@
+logFC	logCPM	PValue	FDR
+TR131|c0_g1_i1	5.89108692370307	16.0946870940125	4.52958285205525e-36	1.721241483781e-34
+TR4277|c0_g1_i1	-4.47812345668175	17.3786096664403	1.7008141018303e-32	3.23154679347758e-31
+TR3091|c0_g1_i1	4.37454375877296	13.9751350003907	7.58044859691792e-23	9.60190155609603e-22
+TR2779|c0_g1_i1	2.89398117484377	15.8061264352363	3.97828335136821e-18	3.7793691837998e-17
+TR5075|c0_g1_i1	3.21512246000432	12.8334153580766	2.0588784190888e-14	1.56474759850749e-13
+TR2107|c1_g1_i1	-4.32040270723487	11.0762608486921	9.69490500265428e-11	6.14010650168104e-10
+TR4761|c0_g1_i1	-2.00464775189483	16.4172477083723	2.27235196662378e-10	1.23356249616719e-09
+TR1891|c0_g1_i1	1.89490003648365	14.4620196202787	1.18363400337593e-09	5.62226151603565e-09
+TR2122|c0_g2_i2	1.68823123696301	14.4430864744705	3.40183177422869e-08	1.436328971341e-07
+TR24|c0_g1_i1	1.665273448047	13.6146325155501	1.25297628243395e-07	4.76130987324901e-07
+TR2487|c0_g1_i1	1.57111929409713	15.8914511338271	3.01913153313087e-07	1.04297271144521e-06
+TR1479|c0_g1_i1	1.45195340320994	14.3929474544484	1.34694977997748e-06	4.2653409699287e-06
+TR1678|c0_g1_i1	3.32711159096413	8.62991286220581	4.44668660347576e-05	0.000129980069947753
+TR127|c1_g1_i1	-2.68488776770857	9.36026180000128	0.000136507461427459	0.00037052025244596
+TR1894|c2_g1_i1	-2.65840371977461	9.30640094015976	0.000158988679158599	0.000402771320535117
+TR2090|c0_g1_i1	3.12073361486577	8.21515298661506	0.000414922023762837	0.000985439806436737
+TR5055|c0_g2_i1	-1.75449782198233	10.3047459168783	0.000987360143376457	0.0020844269693503
+TR4084|c0_g1_i1	0.990738086664283	13.5812840323914	0.000929878324478984	0.00207855154883538
+TR4859|c0_g1_i1	-2.03844841522755	8.5557148387818	0.00574511253124233	0.0114902250624847
+TR3807|c0_g1_i1	-2.27805436961797	7.32408068149202	0.00831980659467625	0.0150548881236999
+TR1859|c3_g1_i1	2.08358066039446	6.92308482511994	0.0216139227266133	0.0357099592874481
+TR1492|c0_g1_i2	-0.80292474159496	16.7717103141256	0.00797659176853916	0.0150548881236999
+TR3638|c0_g1_i1	-0.765536214533451	15.2959378061905	0.00929698340782949	0.0160584258862509
+TR2672|c0_g1_i1	-1.15555384827173	10.1973122527932	0.0235572978271919	0.0372990548930539
+TR3249|c0_g1_i1	1.48866796495104	8.06119288435276	0.0588654345124954	0.0794847966327657
+TR1982|c2_g1_i1	1.06368641289493	9.64628067316551	0.0510418091524593	0.0745995672228252
+TR1837|c2_g1_i1	1.43890969571076	6.48444225997254	0.130037630852572	0.154419686637429
+TR5212|c0_g1_i1	0.63168831011067	12.8380836623566	0.0456316928604782	0.0693601731479268
+TR4163|c0_g1_i1	-0.545743678134199	14.6411189904126	0.0582697662607788	0.0794847966327657
+TR1449|c0_g1_i1	-0.549932747054717	13.6939664483469	0.0606594500618475	0.0794847966327657
+TR2844|c0_g1_i1	0.508967050135572	14.0451022220879	0.0750763100520493	0.0950966593992624
+TR3854|c0_g1_i1	0.504473372285636	17.3527799714624	0.0956174473541405	0.117208483853463
+TR1122|c0_g1_i1	-0.501746583160273	6.50836597017328	0.595453777887275	0.628534543325457
+TR3788|c0_g1_i1	0.524753873079964	11.0311382344715	0.215975804877357	0.234488016723988
+TR2278|c0_g1_i1	-0.424377145183038	15.1829447141358	0.145500439954072	0.167545961159234
+TR2182|c3_g2_i6	0.0429471548350905	7.57134083040984	0.956400717774849	0.956400717774849
+TR939|c0_g1_i1	0.398499350568058	13.0523653134109	0.192129988432482	0.214733516483362
+TR2011|c5_g1_i1	0.0410416962762211	8.85697121679121	0.9477445647389	0.956400717774849
diff -r 8bd817614cc8 -r 831abd20e690 test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.voom.DE_results.MA_n_Volcano.pdf
Binary file test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.voom.DE_results.MA_n_Volcano.pdf has changed
diff -r 8bd817614cc8 -r 831abd20e690 test-data/count/exp_diff/input.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/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results	Mon Aug 01 14:42:55 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 8bd817614cc8 -r 831abd20e690 test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano.pdf
Binary file test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano.pdf has changed
diff -r 8bd817614cc8 -r 831abd20e690 test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.edgeR.DE_results
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.edgeR.DE_results	Mon Aug 01 14:42:55 2016 -0400
@@ -0,0 +1,40 @@
+logFC	logCPM	PValue	FDR
+TR2779|c0_g1_i1	2.23948335958727	15.9163308249372	1.20766376889896e-237	4.70988869870595e-236
+TR1492|c0_g1_i2	-0.807859120941235	16.8439348559211	2.37986391219743e-61	4.64073462878498e-60
+TR1891|c0_g1_i1	1.35697452203657	14.6311197032228	1.60645028176433e-35	2.08838536629363e-34
+TR4761|c0_g1_i1	0.880921757190946	14.8138260614735	1.59143301924913e-24	1.5516471937679e-23
+TR2122|c0_g2_i2	0.729785350305026	14.7699678361852	6.52776857951534e-13	5.09165949202196e-12
+TR3854|c0_g1_i1	-0.289859344737128	17.7786469452325	6.1302236270955e-12	3.98464535761207e-11
+TR3638|c0_g1_i1	0.702510801497461	14.6355179638282	5.62335492840333e-11	3.133012031539e-10
+TR2278|c0_g1_i1	-0.490901034745758	15.2921454021456	1.53296499052609e-09	7.47320432881468e-09
+TR24|c0_g1_i1	2.16007337608378	13.5636496776551	8.67157466173412e-09	3.75768235341812e-08
+TR5075|c0_g1_i1	3.7524485458028	12.8683202800317	5.50095216588421e-08	2.14537134469484e-07
+TR4669|c0_g2_i1	-10.4044948993067	13.1110475123695	1.35189372056785e-06	4.79307773655872e-06
+TR3788|c0_g1_i1	-2.47698512550917	13.0240883091698	1.80487840553907e-05	5.86585481800198e-05
+TR1479|c0_g1_i1	-0.272661827455658	15.1172528121102	0.000483095512098729	0.00144928653629619
+TR1678|c0_g1_i1	3.02812287247775	9.36059212330112	0.0074853976481696	0.0208521791627582
+TR2107|c1_g1_i1	-1.98032359155541	9.36544178725855	0.0305238827180189	0.0756824353198294
+TR2844|c0_g1_i1	-0.244755727600329	14.4560017424587	0.0310492042337762	0.0756824353198294
+TR1859|c3_g1_i1	4.12978123132011	8.37588761488442	0.0428877609330621	0.0983895691993777
+TR3091|c0_g1_i1	-0.148576217250104	14.9963238698071	0.0547318692708507	0.11858571675351
+TR2672|c0_g1_i1	1.64029381826409	9.53984158811941	0.100507062957769	0.206303971334369
+TR4163|c0_g1_i1	-0.156926020788278	14.5006265631178	0.113620071038851	0.22155913852576
+TR4859|c0_g1_i1	-1.3062724221166	8.73091245897321	0.181160758857669	0.3364414093071
+TR4084|c0_g1_i1	0.390578563212142	13.8603174460746	0.270419882900116	0.479380701504752
+TR1982|c2_g1_i1	0.866592651710305	10.0958159836705	0.312186869456376	0.515984430920105
+TR1894|c2_g1_i1	-0.989932992780787	8.78384403630691	0.317528880566218	0.515984430920105
+TR4277|c0_g1_i1	-0.107189584823599	14.0046148411409	0.347278576725125	0.541754579691195
+TR2487|c0_g1_i1	-0.0467513454249246	16.526653433485	0.376403968202147	0.560230359736405
+TR3249|c0_g1_i1	1.00369455926223	9.08504250192555	0.387851787509819	0.560230359736405
+TR5212|c0_g1_i1	-0.310409394484433	13.3365591825697	0.416163942507532	0.572783249883747
+TR2011|c5_g1_i1	-0.799376994792807	9.70509536731836	0.425915749913555	0.572783249883747
+TR1837|c2_g1_i1	-0.59484087321072	8.66193471010726	0.588495494688377	0.76504414309489
+TR2090|c0_g1_i1	-0.766971023107968	9.89421471118339	0.638322407555079	0.8030507707951
+TR131|c0_g1_i1	-0.0187996511046741	17.0827735361623	0.697507705031756	0.850087515507453
+TR1122|c0_g1_i1	-0.908051089281089	8.22928258978683	0.753364106379395	0.890339398448377
+TR1449|c0_g1_i1	0.0452741219590205	13.4583026590017	0.919111339143084	1
+TR939|c0_g1_i1	-0.0309689709592036	13.3146949564453	0.956245904999637	1
+TR5055|c0_g2_i1	0.0548476287872344	9.62768102188797	0.999999999999985	1
+TR2182|c3_g2_i6	0.517423422896207	8.5297276065799	1	1
+TR127|c1_g1_i1	0.299043611515333	8.4576897025083	1	1
+TR3807|c0_g1_i1	-0.266132577378544	7.94319410024963	1	1
diff -r 8bd817614cc8 -r 831abd20e690 test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.edgeR.DE_results.MA_n_Volcano.pdf
Binary file test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.edgeR.DE_results.MA_n_Volcano.pdf has changed
diff -r 8bd817614cc8 -r 831abd20e690 test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.voom.DE_results
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.voom.DE_results	Mon Aug 01 14:42:55 2016 -0400
@@ -0,0 +1,40 @@
+logFC	logCPM	PValue	FDR
+TR2779|c0_g1_i1	2.23795519272237	15.9076254017254	2.92187316761645e-09	1.13953053537042e-07
+TR1492|c0_g1_i2	-0.807554446371668	16.8426446227048	5.58321346448906e-08	1.08872662557537e-06
+TR24|c0_g1_i1	2.16839334936064	13.5222768601527	3.73856822091501e-07	4.86013868718952e-06
+TR3788|c0_g1_i1	-2.47096654484901	13.0144557887788	1.245732049043e-06	9.71670998253539e-06
+TR5075|c0_g1_i1	3.68481140303272	12.7944067233298	3.44359702134355e-06	2.23833806387331e-05
+TR3854|c0_g1_i1	-0.290746293924475	17.7782076349597	5.25322144866517e-07	5.12189091244854e-06
+TR1891|c0_g1_i1	1.35768165107067	14.6117632515968	5.28666359293828e-06	2.79053243123467e-05
+TR4761|c0_g1_i1	0.878920056028248	14.8002262876656	5.72416908971214e-06	2.79053243123467e-05
+TR2122|c0_g2_i2	0.730166040402744	14.7551588447381	0.000213340170514583	0.000924474072229861
+TR3638|c0_g1_i1	0.708321413581678	14.6195575978943	0.000258928735946659	0.00100982207019197
+TR2107|c1_g1_i1	-1.90861736829884	8.90712643491077	0.00457979737107378	0.0148843414559898
+TR1678|c0_g1_i1	2.86408187112217	8.67828416118206	0.00614682516189	0.01844047548567
+TR2278|c0_g1_i1	-0.503051556783977	15.2850549214884	0.00155857674629228	0.00552586300958173
+TR1859|c3_g1_i1	1.96144637998691	6.77065030795652	0.0428269385052548	0.0982500353944082
+TR2672|c0_g1_i1	1.69730734417424	8.97832173338033	0.0866262290356731	0.160877282494822
+TR1479|c0_g1_i1	-0.277933522953326	15.1098597149167	0.0157877120065803	0.0439800548754737
+TR1982|c2_g1_i1	0.859948395691952	9.74982883974683	0.0845253825418736	0.160877282494822
+TR4859|c0_g1_i1	-1.04376243585308	7.84838377560073	0.178339170085147	0.289801151388364
+TR2011|c5_g1_i1	-0.835627288758852	9.33803398810951	0.117576176969539	0.20843049553691
+TR4084|c0_g1_i1	0.383433512314591	13.8345091917852	0.0320674039619619	0.083375250301101
+TR1894|c2_g1_i1	-0.899367664455804	7.86698528437277	0.236693956821629	0.369242572641742
+TR5212|c0_g1_i1	-0.317453614519532	13.3093804544918	0.0408068910563242	0.0982500353944082
+TR2182|c3_g2_i6	0.988859576038597	7.34392475064937	0.332144974966109	0.462630500845651
+TR3249|c0_g1_i1	1.18548803762213	8.36747688877935	0.296376188714782	0.444564283072173
+TR1837|c2_g1_i1	-0.83411458992077	7.6102620160458	0.393260306376011	0.528867308574635
+TR3807|c0_g1_i1	-0.40219136988549	5.09566487188118	0.681998347783062	0.765740423023185
+TR4669|c0_g2_i1	-6.05037553674292	13.1239272719772	0.480074268471172	0.603964402270185
+TR1122|c0_g1_i1	-0.184244267394782	6.64199260311611	0.869699168726351	0.892585988955992
+TR127|c1_g1_i1	0.354388761220407	7.15556768591471	0.687202943738756	0.765740423023185
+TR2844|c0_g1_i1	-0.251980888130202	14.4425124782726	0.0594765231313145	0.128865800117848
+TR2090|c0_g1_i1	0.862128177746631	9.64998833298881	0.646749723219784	0.764340581987017
+TR3091|c0_g1_i1	-0.148831558112849	14.9878570236746	0.0841354210369957	0.160877282494822
+TR5055|c0_g2_i1	-0.0583511298028353	9.18288041060754	0.918331019801174	0.918331019801174
+TR4163|c0_g1_i1	-0.161834057105857	14.4879250602579	0.126768900432688	0.214955961603254
+TR4277|c0_g1_i1	-0.103273026252208	13.9874746529507	0.30829078508145	0.445308911784317
+TR939|c0_g1_i1	-0.0333503331526365	13.2856573711711	0.715260879184748	0.774865952450143
+TR1449|c0_g1_i1	0.049884213852527	13.4293306544833	0.75234222467997	0.793009371959969
+TR2487|c0_g1_i1	-0.0480185034754555	16.5239765307922	0.407818984620182	0.530164680006236
+TR131|c0_g1_i1	-0.0203187870937255	17.0810493411762	0.539920494505425	0.658028102678487
diff -r 8bd817614cc8 -r 831abd20e690 test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.voom.DE_results.MA_n_Volcano.pdf
Binary file test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.voom.DE_results.MA_n_Volcano.pdf has changed
diff -r 8bd817614cc8 -r 831abd20e690 test-data/count/exp_diff/matrix.counts.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results
--- a/test-data/count/exp_diff/matrix.counts.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results	Tue Jul 12 11:36:37 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,39 +0,0 @@
-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 8bd817614cc8 -r 831abd20e690 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 8bd817614cc8 -r 831abd20e690 test-data/count/exp_diff/matrix.counts.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results
--- a/test-data/count/exp_diff/matrix.counts.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results	Tue Jul 12 11:36:37 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,39 +0,0 @@
-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 8bd817614cc8 -r 831abd20e690 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 8bd817614cc8 -r 831abd20e690 test-data/count/exp_diff/matrix.counts.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results
--- a/test-data/count/exp_diff/matrix.counts.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results	Tue Jul 12 11:36:37 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,40 +0,0 @@
-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 8bd817614cc8 -r 831abd20e690 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 8bd817614cc8 -r 831abd20e690 test-data/count/matrix_rsem_bowtie_UpperQuartile/matrix.UpperQuartile.EXPR.matrix
--- a/test-data/count/matrix_rsem_bowtie_UpperQuartile/matrix.UpperQuartile.EXPR.matrix	Tue Jul 12 11:36:37 2016 -0400
+++ b/test-data/count/matrix_rsem_bowtie_UpperQuartile/matrix.UpperQuartile.EXPR.matrix	Mon Aug 01 14:42:55 2016 -0400
@@ -0,0 +1,8 @@
+sample_A	sample_B
+TRINITY_DN2_c0_g1	0	0
+TRINITY_DN1_c0_g1	329523.81	329523.81
+TRINITY_DN0_c0_g1	0	0
+TRINITY_DN2_c1_g1	145165.14	525311.05
+TRINITY_DN3_c0_g1	0	0
+TRINITY_DN2_c2_g1	525311.05	145165.14
+TRINITY_DN2_c3_g1	0	0
diff -r 8bd817614cc8 -r 831abd20e690 test-data/count/qcheck/input.matrix.CPM.log2.principal_components.pdf
Binary file test-data/count/qcheck/input.matrix.CPM.log2.principal_components.pdf has changed
diff -r 8bd817614cc8 -r 831abd20e690 test-data/count/qcheck/input.matrix.CPM.log2.sample_cor_matrix.pdf
Binary file test-data/count/qcheck/input.matrix.CPM.log2.sample_cor_matrix.pdf has changed
diff -r 8bd817614cc8 -r 831abd20e690 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 8bd817614cc8 -r 831abd20e690 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 8bd817614cc8 -r 831abd20e690 test-data/count/qcheck/wt_37.rep_compare.pdf
Binary file test-data/count/qcheck/wt_37.rep_compare.pdf has changed
diff -r 8bd817614cc8 -r 831abd20e690 test-data/count/qcheck/wt_GSNO.rep_compare.pdf
Binary file test-data/count/qcheck/wt_GSNO.rep_compare.pdf has changed
diff -r 8bd817614cc8 -r 831abd20e690 test-data/count/qcheck/wt_ph8.rep_compare.pdf
Binary file test-data/count/qcheck/wt_ph8.rep_compare.pdf has changed
diff -r 8bd817614cc8 -r 831abd20e690 test-data/count/salmon/quant.sf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/salmon/quant.sf	Mon Aug 01 14:42:55 2016 -0400
@@ -0,0 +1,8 @@
+Name	Length	EffectiveLength	TPM	NumReads
+TRINITY_DN1_c0_g1_i1	380	120.403	179183	13
+TRINITY_DN0_c0_g1_i1	229	229	55271.5	7.62686
+TRINITY_DN2_c0_g1_i1	279	31.1522	565494	10.6151
+TRINITY_DN2_c1_g1_i1	541	278.129	113370	19
+TRINITY_DN2_c2_g1_i1	240	240	32900.7	4.75801
+TRINITY_DN2_c3_g1_i1	202	202	0	0
+TRINITY_DN3_c0_g1_i1	216	216	53781.8	7
diff -r 8bd817614cc8 -r 831abd20e690 test-data/count/salmon/quant.sf.genes
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/salmon/quant.sf.genes	Mon Aug 01 14:42:55 2016 -0400
@@ -0,0 +1,8 @@
+Name	Length	EffectiveLength	TPM	NumReads
+TRINITY_DN2_c2_g1	240.00	240.00	32900.70	4.76
+TRINITY_DN0_c0_g1	229.00	229.00	55271.50	7.63
+TRINITY_DN1_c0_g1	380.00	120.40	179183.00	13.00
+TRINITY_DN2_c0_g1	279.00	31.15	565494.00	10.62
+TRINITY_DN2_c3_g1	202.00	202.00	0.00	0.00
+TRINITY_DN3_c0_g1	216.00	216.00	53781.80	7.00
+TRINITY_DN2_c1_g1	541.00	278.13	113370.00	19.00
diff -r 8bd817614cc8 -r 831abd20e690 test-data/filtered/Trinity_filtered_exp.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/filtered/Trinity_filtered_exp.fasta	Mon Aug 01 14:42:55 2016 -0400
@@ -0,0 +1,34 @@
+>TRINITY_DN1_c0_g1_i1 len=380 path=[358:0-379] [-1, 358, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100
+CCAAGGTAGAAAACATCCCTGCTGACAAGACCTACCTGTGACATACTCACTCTCTTAGGG
+CTTTTAAAGACAAGCCATTAAAATAGATGACCTTTCACAGACTGAAACTTGAATCACTGC
+AAAATGAATCTAGGTTGCTGTCACTTTTTCTTTTGGGTGGCGGGGCTTGATGTAGATTTT
+ATTCTATGTACAGAATTTAATGTTGAATATATTAAAAATAACAAACCTGGCATGGTTTTG
+GGAGGTTAGATTTACTGGAAATGTATTCATACTGTGAACTGTGCTCTGATGGTTAGAATG
+AAAAGCTTATCAAGCATTCCATATAACAGTGGATGTAGAAAATGTTTTCAGGTGGATATG
+TATATGGTACAGATGTAAAG
+>TRINITY_DN0_c0_g1_i1 len=229 path=[207:0-228] [-1, 207, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100
+AAATATCACAACCACCTGAACAGGAACTTGGGATAAACAGGCAATGATGAGAGCCGATGT
+TTTTCTGTTGGTGTTTACATTGCTCTGCTCTGTGAAAGGATCCTGCAGCAGAGGCTTCCT
+ACCTGAAAAATGTTTCTCTCAATTGTAGTGTGTGAGTTACTGGTAAGACGCTTACACCTA
+TAACTCAAGGTCGGAATAGTCCCTCCAGTCCCTTTAGTAACCCAGTGGC
+>TRINITY_DN2_c1_g1_i1 len=541 path=[519:0-540] [-1, 519, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100
+GTCTGAATTCGCATGTAATGCAGCTTTCCCAGACACAAGTATGGAAGCAATCCGACTTAT
+TCGCCATTGTGCAAAATATGTGTCTGATAGACCGCAGGCTTTCAAGGAGTACACAAGTGA
+TGACATGAGCGTGGCACCTGAAGACAGGGTGTGGGTGAGAGGGTGGTTCCCGATCCTCTT
+TGAGTTGTCTTGTATCATCAATAGATGCAAATTAGATGTAAGAACCAGGGGCTTAACAGT
+AATGTTTGAAATAATGAAAACATATGGCCACACTTATGAAAAACATTGGTGGCAGGACTT
+ATTCAGAATTGTTTTCAGAATCTTTGACAACATGAAATTGCCAGAACAGCAGACAGAGAA
+AGCTGAATGGATGACAACAACTTGTAACCATGTCCTTTATGCAATATGTGATGTATTCAC
+CCAGTATTTAGAAGTTCTCAGCGATGTACTTTTGGATGATATTTTTGCCCAGCTTTACTG
+GTGTGTACAACAAGACAATGAGCAGTTAGCACGATCTGGTACAAACTGCTTAGAAAACGT
+G
+>TRINITY_DN2_c3_g1_i1 len=202 path=[180:0-201] [-1, 180, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100
+GGTGAAAAGTTTACTCTTGAAATCTGGGATAAAACGTGTAACTGCACCCTGGATATCTTC
+AAAACCACAATTCCTCACGCGCTTCTGACTTGGCGTCCCACCTCTGGCGAGGCCGAACCC
+CCATCTCCATCAGCTGTGAGTGAAAAGCCGTTGGATGCAATATCACAAAAATCTGTAGAC
+ATACATGATTCTATTCAACCAA
+>TRINITY_DN3_c0_g1_i1 len=216 path=[194:0-215] [-1, 194, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100
+ATTGATTTATTTAATAAGAAACCAAAGAGAGGAATACAATACCTCCAAGAACAAGGGATG
+CTTGGCACCACACCCGAAGATATAGCTCAGTTCTTACATCAAGAAGAAAGATTAGACTCT
+ACTCAGGTGGGTGAGTTCCTGGGAGATAATGATAAATTCAATAAAGAAGTCATGTATGCA
+TATGTAGACCAACATGACTTTTCAGGAAAAGACTTT
diff -r 8bd817614cc8 -r 831abd20e690 test-data/filtered/Trinity_filtered_pct_iso.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/filtered/Trinity_filtered_pct_iso.fasta	Mon Aug 01 14:42:55 2016 -0400
@@ -0,0 +1,45 @@
+>TRINITY_DN1_c0_g1_i1 len=380 path=[358:0-379] [-1, 358, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100
+CCAAGGTAGAAAACATCCCTGCTGACAAGACCTACCTGTGACATACTCACTCTCTTAGGG
+CTTTTAAAGACAAGCCATTAAAATAGATGACCTTTCACAGACTGAAACTTGAATCACTGC
+AAAATGAATCTAGGTTGCTGTCACTTTTTCTTTTGGGTGGCGGGGCTTGATGTAGATTTT
+ATTCTATGTACAGAATTTAATGTTGAATATATTAAAAATAACAAACCTGGCATGGTTTTG
+GGAGGTTAGATTTACTGGAAATGTATTCATACTGTGAACTGTGCTCTGATGGTTAGAATG
+AAAAGCTTATCAAGCATTCCATATAACAGTGGATGTAGAAAATGTTTTCAGGTGGATATG
+TATATGGTACAGATGTAAAG
+>TRINITY_DN0_c0_g1_i1 len=229 path=[207:0-228] [-1, 207, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100
+AAATATCACAACCACCTGAACAGGAACTTGGGATAAACAGGCAATGATGAGAGCCGATGT
+TTTTCTGTTGGTGTTTACATTGCTCTGCTCTGTGAAAGGATCCTGCAGCAGAGGCTTCCT
+ACCTGAAAAATGTTTCTCTCAATTGTAGTGTGTGAGTTACTGGTAAGACGCTTACACCTA
+TAACTCAAGGTCGGAATAGTCCCTCCAGTCCCTTTAGTAACCCAGTGGC
+>TRINITY_DN2_c0_g1_i1 len=279 path=[257:0-278] [-1, 257, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100
+TCCAGACCATCGACAACATTGTCTTCTTCCCAGCCACAAGCAAGAAGGAGGATGCAGAGA
+ACTTAGCTGCAGCCCAGAGAGATGCAGTAGACTTCGATGTTCGAGTTGATACTCAAGACC
+AAGGAATGTACCGCTTTTTAACATCACAACAACTGTTCAAGCTACTGGACTGCTTATTAG
+AGTCGCATAGATTTGCAAAAGCATTTAATTCCAACAATGAACAGAGGACTGCTCTGTGGA
+AAGCAGGCTTCAAAGGCAAGTCCAAGCCCAATCTTCTAA
+>TRINITY_DN2_c1_g1_i1 len=541 path=[519:0-540] [-1, 519, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100
+GTCTGAATTCGCATGTAATGCAGCTTTCCCAGACACAAGTATGGAAGCAATCCGACTTAT
+TCGCCATTGTGCAAAATATGTGTCTGATAGACCGCAGGCTTTCAAGGAGTACACAAGTGA
+TGACATGAGCGTGGCACCTGAAGACAGGGTGTGGGTGAGAGGGTGGTTCCCGATCCTCTT
+TGAGTTGTCTTGTATCATCAATAGATGCAAATTAGATGTAAGAACCAGGGGCTTAACAGT
+AATGTTTGAAATAATGAAAACATATGGCCACACTTATGAAAAACATTGGTGGCAGGACTT
+ATTCAGAATTGTTTTCAGAATCTTTGACAACATGAAATTGCCAGAACAGCAGACAGAGAA
+AGCTGAATGGATGACAACAACTTGTAACCATGTCCTTTATGCAATATGTGATGTATTCAC
+CCAGTATTTAGAAGTTCTCAGCGATGTACTTTTGGATGATATTTTTGCCCAGCTTTACTG
+GTGTGTACAACAAGACAATGAGCAGTTAGCACGATCTGGTACAAACTGCTTAGAAAACGT
+G
+>TRINITY_DN2_c2_g1_i1 len=240 path=[218:0-239] [-1, 218, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100
+ACAAGCAGCCTGGCGTGTGGGCTGCGCATTCTCTTCCGGATGTACATGGACGAGAGCAGA
+GTCAGTGCCTGGGAAGAAGTCCAGCAGAGGCTTTTAAACGTCTGCAGGGAAGCGCTGAGC
+TACTTCCTCACTCTAACATCCGAAAGTCACCGGGAAGCCTGGACTAACTTACTGTTACTG
+TTCCTCACTAAAGTTCTGAAGATCAGTGACAGCAGGTTTAAAGCTCACGCATCATTCTAC
+>TRINITY_DN2_c3_g1_i1 len=202 path=[180:0-201] [-1, 180, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100
+GGTGAAAAGTTTACTCTTGAAATCTGGGATAAAACGTGTAACTGCACCCTGGATATCTTC
+AAAACCACAATTCCTCACGCGCTTCTGACTTGGCGTCCCACCTCTGGCGAGGCCGAACCC
+CCATCTCCATCAGCTGTGAGTGAAAAGCCGTTGGATGCAATATCACAAAAATCTGTAGAC
+ATACATGATTCTATTCAACCAA
+>TRINITY_DN3_c0_g1_i1 len=216 path=[194:0-215] [-1, 194, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100
+ATTGATTTATTTAATAAGAAACCAAAGAGAGGAATACAATACCTCCAAGAACAAGGGATG
+CTTGGCACCACACCCGAAGATATAGCTCAGTTCTTACATCAAGAAGAAAGATTAGACTCT
+ACTCAGGTGGGTGAGTTCCTGGGAGATAATGATAAATTCAATAAAGAAGTCATGTATGCA
+TATGTAGACCAACATGACTTTTCAGGAAAAGACTTT
diff -r 8bd817614cc8 -r 831abd20e690 test-data/filtered/counts.matrix
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/filtered/counts.matrix	Mon Aug 01 14:42:55 2016 -0400
@@ -0,0 +1,8 @@
+	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
+TRINITY_DN1_c0_g1_i1	90.00	67.00	85.00	36.00	35.00	34.00	222.00	196.00	201.00
+TRINITY_DN0_c0_g1_i1	186.00	137.00	217.00	147.00	186.00	197.00	1088.00	1094.00	1086.00
+TRINITY_DN2_c0_g1_i1	9.00	23.00	16.00	2.00	0.00	1.00	3.00	1.00	1.00
+TRINITY_DN2_c1_g1_i1	59.00	65.00	47.00	6.00	6.00	7.00	3.00	1.00	2.00
+TRINITY_DN2_c2_g1_i1	11.00	4.00	4.00	8.00	5.00	7.00	3.00	4.00	8.00
+TRINITY_DN2_c3_g1_i1	368.00	422.00	425.00	172.00	216.00	210.00	234.00	254.00	212.00
+TRINITY_DN3_c0_g1_i1	36.00	17.00	27.00	4.00	7.00	3.00	4.00	4.00	11.00
diff -r 8bd817614cc8 -r 831abd20e690 test-data/raw/map.tsv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/raw/map.tsv	Mon Aug 01 14:42:55 2016 -0400
@@ -0,0 +1,7 @@
+TRINITY_DN1_c0_g1	TRINITY_DN1_c0_g1_i1
+TRINITY_DN0_c0_g1	TRINITY_DN0_c0_g1_i1
+TRINITY_DN2_c0_g1	TRINITY_DN2_c0_g1_i1
+TRINITY_DN2_c1_g1	TRINITY_DN2_c1_g1_i1
+TRINITY_DN2_c2_g1	TRINITY_DN2_c2_g1_i1
+TRINITY_DN2_c3_g1	TRINITY_DN2_c3_g1_i1
+TRINITY_DN3_c0_g1	TRINITY_DN3_c0_g1_i1
diff -r 8bd817614cc8 -r 831abd20e690 tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Jul 12 11:36:37 2016 -0400
+++ b/tool_dependencies.xml	Mon Aug 01 14:42:55 2016 -0400
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="trinity" version="2.1.1">
-        <repository changeset_revision="1585b0b46b84" name="package_trinity_2_1_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    <package name="trinity" version="2.2.0">
+        <repository changeset_revision="729219ec7049" name="package_trinity_2_2_0" 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" />
diff -r 8bd817614cc8 -r 831abd20e690 trinity.xml
--- a/trinity.xml	Tue Jul 12 11:36:37 2016 -0400
+++ b/trinity.xml	Mon Aug 01 14:42:55 2016 -0400
@@ -1,11 +1,14 @@
-<tool id="trinity" name="Trinity" version="2.1.1.1">
+<tool id="trinity" name="Trinity" version="@WRAPPER_VERSION@.0">
     <description>de novo assembly of RNA-Seq data</description>
-    <requirements>
-        <requirement type="package" version="2.1.1">trinity</requirement>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements">
         <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>
-    </requirements>
+    </expand>
+    <expand macro="stdio"/>
     <command><![CDATA[
        Trinity
 
@@ -64,6 +67,10 @@
 
         #end if
 
+        #if $additional_params.min_kmer_cov:
+            --min_kmer_cov $additional_params.min_kmer_cov
+        #end if
+
         ## CPU and butterfly options.
         --CPU \${GALAXY_SLOTS:-4} \${TRINITY_MEM_OPTIONS:---max_memory 1G} --bfly_opts "-V 10 --stderr"
 
@@ -77,29 +84,29 @@
                 <option value="single">Single</option>
             </param>
             <when value="paired">
-                <param format="fasta,fastqsanger" name="left_input" multiple="true" type="data" label="Left/Forward strand reads" help=""/>
-                <param format="fasta,fastqsanger" name="right_input" multiple="true" type="data" label="Right/Reverse strand reads" help=""/>
+                <param format="fasta,fastqsanger" argument="--left" name="left_input" multiple="true" type="data" label="Left/Forward strand reads" help=""/>
+                <param format="fasta,fastqsanger" argument="--right" name="right_input" multiple="true" 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">
+                        <param name="library_type" argument="--SS_lib_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="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"/>
+                <param name="jaccard_clip" argument="--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,fastqsanger" name="input" multiple="true" type="data" label="Single-end reads" help=""/>
+                <param format="fasta,fastqsanger" name="input" argument="--single" multiple="true" 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">
+                        <param name="library_type" argument="--SS_lib_type" type="select" label="Strand-specific Library Type">
                             <option value="F">F</option>
                             <option value="R">R</option>
                         </param>
@@ -108,10 +115,10 @@
             </when>
         </conditional>
 
-        <param name="norm" type="boolean" truevalue="--normalize_reads" falsevalue="" checked="true" label="Run in silico normalization of reads" help="Defaults to max. read coverage of 50."/>
+        <param name="norm" type="boolean" argument="--normalize_reads" truevalue="--normalize_reads" falsevalue="" checked="true" label="Run in silico normalization of reads" help="Defaults to max. read coverage of 50."/>
 
         <section name="additional_params" title="Additional Options" expanded="False">
-            <param name="min_contig_length" type="integer" optional="true" value="200" min="1" label="Minimum Contig Length" help="All contigs shorter than this will be discarded"/>
+            <param name="min_contig_length" argument="--min_contig_length" type="integer" optional="true" value="200" min="1" label="Minimum Contig Length" help="All contigs shorter than this will be discarded"/>
 
             <conditional name="guided">
                 <param name="is_guided" type="select" label="Use the genome guided mode?" help="If you already mapped the reads to the genome, Trinity can use this information">
@@ -121,14 +128,15 @@
                 <when value="no">
                 </when>
                 <when value="yes">
-                    <param format="bam" name="genome_guided_bam" type="data" label="Coordinate-sorted BAM file" />
-                    <param name="genome_guided_min_coverage" type="integer" optional="true" value="1" min="1" label="Minimum read coverage for identifying an expressed region of the genome"/>
-                    <param name="genome_guided_min_reads_per_partition" type="integer" optional="true" value="10" min="1" label="Minimum number of reads per partition"/>
+                    <param format="bam" name="genome_guided_bam" argument="--genome_guided_bam" type="data" label="Coordinate-sorted BAM file" />
+                    <param name="genome_guided_min_coverage" argument="--genome_guided_min_coverage" type="integer" optional="true" value="1" min="1" label="Minimum read coverage for identifying an expressed region of the genome"/>
+                    <param name="genome_guided_min_reads_per_partition" argument="--genome_guided_min_reads_per_partition" type="integer" optional="true" value="10" min="1" label="Minimum number of reads per partition"/>
                 </when>
             </conditional>
 
+            <param format="fasta" name="long_reads" argument="--long_reads" type="data" optional="true" label="Error-corrected or circular consensus (CCS) pac bio reads" help="Experimental feature! Long reads must be in the same orientation as short reads if they are strand specific"/>
 
-            <param format="fasta" name="long_reads" type="data" optional="true" label="Error-corrected or circular consensus (CCS) pac bio reads" help="Experimental feature! Long reads must be in the same orientation as short reads if they are strand specific"/>
+            <param name="min_kmer_cov" argument="--min_kmer_cov" type="integer" optional="true" value="1" min="1" label="Minimum count for K-mers to be assembled"/>
         </section>
     </inputs>
     <outputs>
@@ -161,8 +169,5 @@
         .. _Trinity: http://trinityrnaseq.github.io
     </help>
 
-     <citations>
-        <citation type="doi">10.1038/nbt.1883</citation>
-    </citations>
+    <expand macro="citation" />
 </tool>
-