Mercurial > repos > iuc > trinity
changeset 10:831abd20e690 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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--- 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	.*" /> - <has_n_columns n="3" /> - </assert_contents> - </output> - <output name="TPM_no_norm"> - <assert_contents> - <has_line_matching expression="TRINITY_DN3_c0_g1	.*" /> - <has_n_columns n="3" /> - </assert_contents> - </output> - <output name="norm"> - <assert_contents> - <has_line_matching expression="TRINITY_DN3_c0_g1	.*" /> - <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	.*" /> - <has_n_columns n="3" /> - </assert_contents> - </output> - <output name="TPM_no_norm"> - <assert_contents> - <has_line_matching expression="TRINITY_DN3_c0_g1	.*" /> - <has_n_columns n="3" /> - </assert_contents> - </output> - <output name="norm"> - <assert_contents> - <has_line_matching expression="TRINITY_DN3_c0_g1	.*" /> - <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	.*" /> - <has_n_columns n="3" /> - </assert_contents> - </output> - <output name="TPM_no_norm"> - <assert_contents> - <has_line_matching expression="TRINITY_DN3_c0_g1	.*" /> - <has_n_columns n="3" /> - </assert_contents> - </output> - <output name="norm"> - <assert_contents> - <has_line_matching expression="TRINITY_DN3_c0_g1	.*" /> - <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	.*" /> - <has_n_columns n="3" /> - </assert_contents> - </output> - <output name="TPM_no_norm"> - <assert_contents> - <has_line_matching expression="TRINITY_DN3_c0_g1	.*" /> - <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	.*" /> - <has_n_columns n="3" /> - </assert_contents> - </output> - <output name="TPM_no_norm"> - <assert_contents> - <has_line_matching expression="TRINITY_DN3_c0_g1	.*" /> - <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> -
--- 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	.*" /> - <has_n_columns n="8" /> - </assert_contents> - </output> - <output name="genes_counts_rsem"> - <assert_contents> - <has_line_matching expression="TRINITY_DN0_c0_g1	.*" /> - <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	.*" /> - <has_n_columns n="8" /> - </assert_contents> - </output> - <output name="genes_counts_rsem"> - <assert_contents> - <has_line_matching expression="TRINITY_DN0_c0_g1	.*" /> - <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=".*	TRINITY_DN2_c3_g1_i1	.*" /> - <has_n_columns n="15" /> - </assert_contents> - </output> - <output name="genes_counts_express"> - <assert_contents> - <has_line_matching expression="NA	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> -
--- /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>
--- 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 ${on_string}"> - <discover_datasets pattern="(?P<name>.+)\.DE_results$" ext="tabular" directory="results" /> - </collection> - <collection name="PDF_results" type="list" label="Differential expression plots on ${on_string}"> - <discover_datasets pattern="(?P<name>.+)\.pdf$" 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> -
--- 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> -
--- /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
Binary file test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.MA_n_Volcano.pdf has changed
--- /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
Binary file test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.edgeR.DE_results.MA_n_Volcano.pdf has changed
--- /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
Binary file test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.voom.DE_results.MA_n_Volcano.pdf has changed
--- /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
Binary file test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano.pdf has changed
--- /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
Binary file test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.edgeR.DE_results.MA_n_Volcano.pdf has changed
--- /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
Binary file test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.voom.DE_results.MA_n_Volcano.pdf has changed
--- /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
Binary file test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano.pdf has changed
--- /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
Binary file test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.edgeR.DE_results.MA_n_Volcano.pdf has changed
--- /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
Binary file test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.voom.DE_results.MA_n_Volcano.pdf has changed
--- 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
Binary file test-data/count/exp_diff/matrix.counts.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.MA_n_Volcano.pdf has changed
--- 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
Binary file test-data/count/exp_diff/matrix.counts.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano.pdf has changed
--- 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
Binary file test-data/count/exp_diff/matrix.counts.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano.pdf has changed
--- 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
Binary file test-data/count/qcheck/matrix.counts.matrix.minCol10.minRow10.CPM.log2.principal_components.pdf has changed
Binary file test-data/count/qcheck/matrix.counts.matrix.minCol10.minRow10.CPM.log2.sample_cor_matrix.pdf has changed
--- /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
--- /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
--- /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
--- /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
--- /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
--- /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
--- 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" />
--- 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> -