Mercurial > repos > iuc > trinity_abundance_estimates_to_matrix
changeset 1:fba77b1f69b4 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 95f3e6a69bf939326c73a98e3306bccae8414ecd
| author | iuc |
|---|---|
| date | Fri, 18 Nov 2016 06:07:28 -0500 |
| parents | 77fc547df6ff |
| children | 5a97898c6e63 |
| files | abundance_estimates_to_matrix.xml test-data/count/express_bowtie/results.xprs.genes test-data/count/express_bowtie/results_B.xprs.genes test-data/count/express_bowtie/sample_A test-data/count/express_bowtie/sample_B test-data/count/rsem_bowtie/RSEM.genes.results test-data/count/rsem_bowtie/RSEM.genes_B.results test-data/count/rsem_bowtie/sample_A test-data/count/rsem_bowtie/sample_B test-data/count/rsem_bowtie2/RSEM.genes.results test-data/count/rsem_bowtie2/RSEM.genes_B.results test-data/count/rsem_bowtie2/sample_A test-data/count/rsem_bowtie2/sample_B test-data/count/salmon/quant.sf test-data/count/salmon/quant.sf.genes test-data/count/salmon/sample_A test-data/count/salmon/sample_B test-data/samples.tsv tool_dependencies.xml |
| diffstat | 19 files changed, 83 insertions(+), 104 deletions(-) [+] |
line wrap: on
line diff
--- a/abundance_estimates_to_matrix.xml Mon Aug 01 14:42:33 2016 -0400 +++ b/abundance_estimates_to_matrix.xml Fri Nov 18 06:07:28 2016 -0500 @@ -1,16 +1,17 @@ -<tool id="trinity_abundance_estimates_to_matrix" name="Build expression matrix" version="@WRAPPER_VERSION@.0"> +<tool id="trinity_abundance_estimates_to_matrix" name="Build expression matrix" version="@WRAPPER_VERSION@.1"> <description>for a de novo assembly of RNA-Seq data by Trinity</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"> <requirement type="package" version="3.14.0">bioconductor-edger</requirement> - <requirement type="package" version="0.6.0">salmon</requirement> + <requirement type="package" version="0.7.2">salmon</requirement> </expand> <expand macro="stdio"/> <command><![CDATA[ + #import re #for $entry in $samples: - ln -s "${entry.file}" "${entry.sample_name}" && + ln -s '${entry}' '${re.sub('[^\w\-_]', '_', entry.element_identifier)}' && #end for abundance_estimates_to_matrix.pl @@ -19,16 +20,11 @@ --cross_sample_norm ${additional_params.cross_sample_norm} #for $entry in $samples: - "${entry.sample_name}" + '${re.sub('[^\w\-_]', '_', entry.element_identifier)}' #end for ]]></command> <inputs> - <repeat name="samples" title="Abundance estimates for samples"> - <param name="file" label="Add file" type="data" format="tabular"/> - <param name="sample_name" label="Sample name" type="text"> - <validator type="regex" message="Value must be a not empty string composed by alphanumeric characters and underscores">^\w+$</validator> - </param> - </repeat> + <param name="samples" label="Abundance estimates" type="data" multiple="true" format="tabular" help="output(s) from 'Align reads and estimate abundance' tool" /> <param type="select" name="est_method" argument="--est_method" label="Abundance estimation method"> <option value="RSEM">RSEM</option> @@ -56,10 +52,7 @@ </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="samples" ftype="tabular" value="count/rsem_bowtie/sample_A,count/rsem_bowtie/sample_B"/> <param name="est_method" value="RSEM"/> <param name="cross_sample_norm" value="TMM"/> <output name="trans_counts"> @@ -82,10 +75,7 @@ </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="samples" ftype="tabular" value="count/rsem_bowtie2/sample_A,count/rsem_bowtie2/sample_B"/> <param name="est_method" value="RSEM"/> <param name="cross_sample_norm" value="TMM"/> <output name="trans_counts"> @@ -108,10 +98,7 @@ </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="samples" ftype="tabular" value="count/express_bowtie/sample_A,count/express_bowtie/sample_B"/> <param name="est_method" value="eXpress"/> <param name="cross_sample_norm" value="TMM"/> <output name="trans_counts"> @@ -134,10 +121,7 @@ </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="samples" ftype="tabular" value="count/rsem_bowtie/sample_A,count/rsem_bowtie/sample_B"/> <param name="est_method" value="RSEM"/> <param name="cross_sample_norm" value="UpperQuartile"/> <output name="trans_counts"> @@ -159,10 +143,7 @@ </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="samples" ftype="tabular" value="count/rsem_bowtie/sample_A,count/rsem_bowtie/sample_B"/> <param name="est_method" value="RSEM"/> <param name="cross_sample_norm" value="none"/> <output name="trans_counts"> @@ -179,10 +160,7 @@ </output> </test> <test> - <param name="samples_0|file" value="count/salmon/quant.sf"/> - <param name="samples_0|sample_name" value="sample_A"/> - <param name="samples_1|file" value="count/salmon/quant.sf.genes"/> - <param name="samples_1|sample_name" value="sample_B"/> + <param name="samples" ftype="tabular" value="count/salmon/sample_A,count/salmon/sample_B"/> <param name="est_method" value="salmon"/> <param name="cross_sample_norm" value="none"/> <output name="trans_counts">
--- a/test-data/count/express_bowtie/results.xprs.genes Mon Aug 01 14:42:33 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,8 +0,0 @@ -bundle_id target_id length eff_length tot_counts uniq_counts est_counts eff_counts ambig_distr_alpha ambig_distr_beta fpkm fpkm_conf_low fpkm_conf_high solvable tpm -NA TRINITY_DN3_c0_g1 216.00 1.00 NA NA NA 0.00 NA NA 0.00 NA NA NA 0 -NA TRINITY_DN2_c2_g1 240.00 240.00 NA NA NA 1.00 NA NA 378787.90 NA NA NA 60178.11 -NA TRINITY_DN2_c3_g1 202.00 1.00 NA NA NA 0.00 NA NA 0.00 NA NA NA 0 -NA TRINITY_DN0_c0_g1 229.00 1.00 NA NA NA 0.00 NA NA 0.00 NA NA NA 0 -NA TRINITY_DN2_c0_g1 279.00 1.00 NA NA NA 0.00 NA NA 0.00 NA NA NA 0 -NA TRINITY_DN1_c0_g1 380.00 109.25 NA NA NA 17.39 NA NA 4160711.00 NA NA NA 661013.1 -NA TRINITY_DN2_c1_g1 541.00 259.01 NA NA NA 10.44 NA NA 1754947.00 NA NA NA 278808.8
--- a/test-data/count/express_bowtie/results_B.xprs.genes Mon Aug 01 14:42:33 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,8 +0,0 @@ -bundle_id target_id length eff_length tot_counts uniq_counts est_counts eff_counts ambig_distr_alpha ambig_distr_beta fpkm fpkm_conf_low fpkm_conf_high solvable tpm -NA TRINITY_DN3_c0_g1 216.00 1.00 NA NA NA 0.00 NA NA 0.00 NA NA NA 0 -NA TRINITY_DN2_c1_g1 240.00 240.00 NA NA NA 1.00 NA NA 378787.90 NA NA NA 60178.11 -NA TRINITY_DN2_c3_g1 202.00 1.00 NA NA NA 0.00 NA NA 0.00 NA NA NA 0 -NA TRINITY_DN0_c0_g1 380.00 109.25 NA NA NA 17.39 NA NA 4160711.00 NA NA NA 661013.1 -NA TRINITY_DN1_c0_g1 229.00 1.00 NA NA NA 0.00 NA NA 0.00 NA NA NA 0 -NA TRINITY_DN2_c0_g1 279.00 1.00 NA NA NA 0.00 NA NA 0.00 NA NA NA 0 -NA TRINITY_DN2_c2_g1 541.00 259.01 NA NA NA 10.44 NA NA 1754947.00 NA NA NA 278808.8
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/express_bowtie/sample_A Fri Nov 18 06:07:28 2016 -0500 @@ -0,0 +1,8 @@ +bundle_id target_id length eff_length tot_counts uniq_counts est_counts eff_counts ambig_distr_alpha ambig_distr_beta fpkm fpkm_conf_low fpkm_conf_high solvable tpm +NA TRINITY_DN3_c0_g1 216.00 1.00 NA NA NA 0.00 NA NA 0.00 NA NA NA 0 +NA TRINITY_DN2_c2_g1 240.00 240.00 NA NA NA 1.00 NA NA 378787.90 NA NA NA 60178.11 +NA TRINITY_DN2_c3_g1 202.00 1.00 NA NA NA 0.00 NA NA 0.00 NA NA NA 0 +NA TRINITY_DN0_c0_g1 229.00 1.00 NA NA NA 0.00 NA NA 0.00 NA NA NA 0 +NA TRINITY_DN2_c0_g1 279.00 1.00 NA NA NA 0.00 NA NA 0.00 NA NA NA 0 +NA TRINITY_DN1_c0_g1 380.00 109.25 NA NA NA 17.39 NA NA 4160711.00 NA NA NA 661013.1 +NA TRINITY_DN2_c1_g1 541.00 259.01 NA NA NA 10.44 NA NA 1754947.00 NA NA NA 278808.8
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/express_bowtie/sample_B Fri Nov 18 06:07:28 2016 -0500 @@ -0,0 +1,8 @@ +bundle_id target_id length eff_length tot_counts uniq_counts est_counts eff_counts ambig_distr_alpha ambig_distr_beta fpkm fpkm_conf_low fpkm_conf_high solvable tpm +NA TRINITY_DN3_c0_g1 216.00 1.00 NA NA NA 0.00 NA NA 0.00 NA NA NA 0 +NA TRINITY_DN2_c1_g1 240.00 240.00 NA NA NA 1.00 NA NA 378787.90 NA NA NA 60178.11 +NA TRINITY_DN2_c3_g1 202.00 1.00 NA NA NA 0.00 NA NA 0.00 NA NA NA 0 +NA TRINITY_DN0_c0_g1 380.00 109.25 NA NA NA 17.39 NA NA 4160711.00 NA NA NA 661013.1 +NA TRINITY_DN1_c0_g1 229.00 1.00 NA NA NA 0.00 NA NA 0.00 NA NA NA 0 +NA TRINITY_DN2_c0_g1 279.00 1.00 NA NA NA 0.00 NA NA 0.00 NA NA NA 0 +NA TRINITY_DN2_c2_g1 541.00 259.01 NA NA NA 10.44 NA NA 1754947.00 NA NA NA 278808.8
--- a/test-data/count/rsem_bowtie/RSEM.genes.results Mon Aug 01 14:42:33 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,8 +0,0 @@ -gene_id transcript_id(s) length effective_length expected_count TPM FPKM -TRINITY_DN0_c0_g1 TRINITY_DN0_c0_g1_i1 229.00 11.55 0.00 0.00 0.00 -TRINITY_DN1_c0_g1 TRINITY_DN1_c0_g1_i1 380.00 123.91 5.00 329523.81 3668378.58 -TRINITY_DN2_c0_g1 TRINITY_DN2_c0_g1_i1 279.00 35.45 0.00 0.00 0.00 -TRINITY_DN2_c1_g1 TRINITY_DN2_c1_g1_i1 541.00 281.27 5.00 145165.14 1616031.03 -TRINITY_DN2_c2_g1 TRINITY_DN2_c2_g1_i1 240.00 15.55 1.00 525311.05 5847953.22 -TRINITY_DN2_c3_g1 TRINITY_DN2_c3_g1_i1 202.00 3.45 0.00 0.00 0.00 -TRINITY_DN3_c0_g1 TRINITY_DN3_c0_g1_i1 216.00 6.82 0.00 0.00 0.00
--- a/test-data/count/rsem_bowtie/RSEM.genes_B.results Mon Aug 01 14:42:33 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,8 +0,0 @@ -gene_id transcript_id(s) length effective_length expected_count TPM FPKM -TRINITY_DN0_c0_g1 TRINITY_DN0_c0_g1_i1 229.00 11.55 0.00 0.00 0.00 -TRINITY_DN1_c0_g1 TRINITY_DN1_c0_g1_i1 380.00 123.91 5.00 329523.81 3668378.58 -TRINITY_DN2_c0_g1 TRINITY_DN2_c0_g1_i1 279.00 35.45 0.00 0.00 0.00 -TRINITY_DN2_c2_g1 TRINITY_DN2_c2_g1_i1 541.00 281.27 5.00 145165.14 1616031.03 -TRINITY_DN2_c1_g1 TRINITY_DN2_c1_g1_i1 240.00 15.55 1.00 525311.05 5847953.22 -TRINITY_DN2_c3_g1 TRINITY_DN2_c3_g1_i1 202.00 3.45 0.00 0.00 0.00 -TRINITY_DN3_c0_g1 TRINITY_DN3_c0_g1_i1 216.00 6.82 0.00 0.00 0.00
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/rsem_bowtie/sample_A Fri Nov 18 06:07:28 2016 -0500 @@ -0,0 +1,8 @@ +gene_id transcript_id(s) length effective_length expected_count TPM FPKM +TRINITY_DN0_c0_g1 TRINITY_DN0_c0_g1_i1 229.00 11.55 0.00 0.00 0.00 +TRINITY_DN1_c0_g1 TRINITY_DN1_c0_g1_i1 380.00 123.91 5.00 329523.81 3668378.58 +TRINITY_DN2_c0_g1 TRINITY_DN2_c0_g1_i1 279.00 35.45 0.00 0.00 0.00 +TRINITY_DN2_c1_g1 TRINITY_DN2_c1_g1_i1 541.00 281.27 5.00 145165.14 1616031.03 +TRINITY_DN2_c2_g1 TRINITY_DN2_c2_g1_i1 240.00 15.55 1.00 525311.05 5847953.22 +TRINITY_DN2_c3_g1 TRINITY_DN2_c3_g1_i1 202.00 3.45 0.00 0.00 0.00 +TRINITY_DN3_c0_g1 TRINITY_DN3_c0_g1_i1 216.00 6.82 0.00 0.00 0.00
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/rsem_bowtie/sample_B Fri Nov 18 06:07:28 2016 -0500 @@ -0,0 +1,8 @@ +gene_id transcript_id(s) length effective_length expected_count TPM FPKM +TRINITY_DN0_c0_g1 TRINITY_DN0_c0_g1_i1 229.00 11.55 0.00 0.00 0.00 +TRINITY_DN1_c0_g1 TRINITY_DN1_c0_g1_i1 380.00 123.91 5.00 329523.81 3668378.58 +TRINITY_DN2_c0_g1 TRINITY_DN2_c0_g1_i1 279.00 35.45 0.00 0.00 0.00 +TRINITY_DN2_c2_g1 TRINITY_DN2_c2_g1_i1 541.00 281.27 5.00 145165.14 1616031.03 +TRINITY_DN2_c1_g1 TRINITY_DN2_c1_g1_i1 240.00 15.55 1.00 525311.05 5847953.22 +TRINITY_DN2_c3_g1 TRINITY_DN2_c3_g1_i1 202.00 3.45 0.00 0.00 0.00 +TRINITY_DN3_c0_g1 TRINITY_DN3_c0_g1_i1 216.00 6.82 0.00 0.00 0.00
--- a/test-data/count/rsem_bowtie2/RSEM.genes.results Mon Aug 01 14:42:33 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,8 +0,0 @@ -gene_id transcript_id(s) length effective_length expected_count TPM FPKM -TRINITY_DN0_c0_g1 TRINITY_DN0_c0_g1_i1 229.00 10.58 0.00 0.00 0.00 -TRINITY_DN1_c0_g1 TRINITY_DN1_c0_g1_i1 380.00 122.00 5.00 309046.31 3415300.55 -TRINITY_DN2_c0_g1 TRINITY_DN2_c0_g1_i1 279.00 32.50 0.00 0.00 0.00 -TRINITY_DN2_c1_g1 TRINITY_DN2_c1_g1_i1 541.00 279.67 6.00 161779.66 1787842.67 -TRINITY_DN2_c2_g1 TRINITY_DN2_c2_g1_i1 240.00 14.25 1.00 529174.03 5847953.22 -TRINITY_DN2_c3_g1 TRINITY_DN2_c3_g1_i1 202.00 3.17 0.00 0.00 0.00 -TRINITY_DN3_c0_g1 TRINITY_DN3_c0_g1_i1 216.00 6.25 0.00 0.00 0.00
--- a/test-data/count/rsem_bowtie2/RSEM.genes_B.results Mon Aug 01 14:42:33 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,8 +0,0 @@ -gene_id transcript_id(s) length effective_length expected_count TPM FPKM -TRINITY_DN0_c0_g1 TRINITY_DN0_c0_g1_i1 380.00 122.00 5.00 309046.31 3415300.55 -TRINITY_DN1_c0_g1 TRINITY_DN1_c0_g1_i1 229.00 10.58 0.00 0.00 0.00 -TRINITY_DN2_c0_g1 TRINITY_DN2_c0_g1_i1 279.00 32.50 0.00 0.00 0.00 -TRINITY_DN2_c2_g1 TRINITY_DN2_c2_g1_i1 541.00 279.67 6.00 161779.66 1787842.67 -TRINITY_DN2_c1_g1 TRINITY_DN2_c1_g1_i1 240.00 14.25 1.00 529174.03 5847953.22 -TRINITY_DN2_c3_g1 TRINITY_DN2_c3_g1_i1 202.00 3.17 0.00 0.00 0.00 -TRINITY_DN3_c0_g1 TRINITY_DN3_c0_g1_i1 216.00 6.25 0.00 0.00 0.00
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/rsem_bowtie2/sample_A Fri Nov 18 06:07:28 2016 -0500 @@ -0,0 +1,8 @@ +gene_id transcript_id(s) length effective_length expected_count TPM FPKM +TRINITY_DN0_c0_g1 TRINITY_DN0_c0_g1_i1 229.00 10.58 0.00 0.00 0.00 +TRINITY_DN1_c0_g1 TRINITY_DN1_c0_g1_i1 380.00 122.00 5.00 309046.31 3415300.55 +TRINITY_DN2_c0_g1 TRINITY_DN2_c0_g1_i1 279.00 32.50 0.00 0.00 0.00 +TRINITY_DN2_c1_g1 TRINITY_DN2_c1_g1_i1 541.00 279.67 6.00 161779.66 1787842.67 +TRINITY_DN2_c2_g1 TRINITY_DN2_c2_g1_i1 240.00 14.25 1.00 529174.03 5847953.22 +TRINITY_DN2_c3_g1 TRINITY_DN2_c3_g1_i1 202.00 3.17 0.00 0.00 0.00 +TRINITY_DN3_c0_g1 TRINITY_DN3_c0_g1_i1 216.00 6.25 0.00 0.00 0.00
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/rsem_bowtie2/sample_B Fri Nov 18 06:07:28 2016 -0500 @@ -0,0 +1,8 @@ +gene_id transcript_id(s) length effective_length expected_count TPM FPKM +TRINITY_DN0_c0_g1 TRINITY_DN0_c0_g1_i1 380.00 122.00 5.00 309046.31 3415300.55 +TRINITY_DN1_c0_g1 TRINITY_DN1_c0_g1_i1 229.00 10.58 0.00 0.00 0.00 +TRINITY_DN2_c0_g1 TRINITY_DN2_c0_g1_i1 279.00 32.50 0.00 0.00 0.00 +TRINITY_DN2_c2_g1 TRINITY_DN2_c2_g1_i1 541.00 279.67 6.00 161779.66 1787842.67 +TRINITY_DN2_c1_g1 TRINITY_DN2_c1_g1_i1 240.00 14.25 1.00 529174.03 5847953.22 +TRINITY_DN2_c3_g1 TRINITY_DN2_c3_g1_i1 202.00 3.17 0.00 0.00 0.00 +TRINITY_DN3_c0_g1 TRINITY_DN3_c0_g1_i1 216.00 6.25 0.00 0.00 0.00
--- a/test-data/count/salmon/quant.sf Mon Aug 01 14:42:33 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,8 +0,0 @@ -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
--- a/test-data/count/salmon/quant.sf.genes Mon Aug 01 14:42:33 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,8 +0,0 @@ -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/count/salmon/sample_A Fri Nov 18 06:07:28 2016 -0500 @@ -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/sample_B Fri Nov 18 06:07:28 2016 -0500 @@ -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/samples.tsv Fri Nov 18 06:07:28 2016 -0500 @@ -0,0 +1,4 @@ +ConditionA CondA_replicate1 +ConditionA CondA_replicate2 +ConditionB CondB_replicate1 +ConditionB CondB_replicate2
--- a/tool_dependencies.xml Mon Aug 01 14:42:33 2016 -0400 +++ b/tool_dependencies.xml Fri Nov 18 06:07:28 2016 -0500 @@ -1,7 +1,7 @@ <?xml version="1.0"?> <tool_dependency> <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" /> + <repository changeset_revision="76d63b5c571a" 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" /> @@ -9,11 +9,8 @@ <package name="bowtie2" version="2.2.6"> <repository changeset_revision="0d9cd7487cc9" name="package_bowtie_2_2_6" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> - <package name="samtools" version="1.2"> - <repository changeset_revision="f6ae3ba3f3c1" name="package_samtools_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> <package name="bioconductor-edger" version="3.14.0"> - <repository changeset_revision="8ed6cfd2b21f" name="package_bioconductor_edger_3_14_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="5f4abad5b2c1" name="package_bioconductor_edger_3_14_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <package name="rsem" version="1.2.28"> <repository changeset_revision="4567331d510a" name="package_rsem_1_2_28" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> @@ -22,7 +19,7 @@ <repository changeset_revision="93017e8743e5" name="package_express_1_5_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <package name="bioconductor-limma" version="3.28.10"> - <repository changeset_revision="fc78b4bbe0ab" name="package_bioconductor_limma_3_28_10" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="b313488c66bd" name="package_bioconductor_limma_3_28_10" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <package name="deseq2" version="1.10.0"> <repository changeset_revision="e4a11a7d33d6" name="package_deseq2_1_10_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />