Repository 'trinity_abundance_estimates_to_matrix'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/trinity_abundance_estimates_to_matrix

Changeset 1:fba77b1f69b4 (2016-11-18)
Previous changeset 0:77fc547df6ff (2016-08-01) Next changeset 2:5a97898c6e63 (2016-11-21)
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 95f3e6a69bf939326c73a98e3306bccae8414ecd
modified:
abundance_estimates_to_matrix.xml
tool_dependencies.xml
added:
test-data/count/express_bowtie/sample_A
test-data/count/express_bowtie/sample_B
test-data/count/rsem_bowtie/sample_A
test-data/count/rsem_bowtie/sample_B
test-data/count/rsem_bowtie2/sample_A
test-data/count/rsem_bowtie2/sample_B
test-data/count/salmon/sample_A
test-data/count/salmon/sample_B
test-data/samples.tsv
removed:
test-data/count/express_bowtie/results.xprs.genes
test-data/count/express_bowtie/results_B.xprs.genes
test-data/count/rsem_bowtie/RSEM.genes.results
test-data/count/rsem_bowtie/RSEM.genes_B.results
test-data/count/rsem_bowtie2/RSEM.genes.results
test-data/count/rsem_bowtie2/RSEM.genes_B.results
test-data/count/salmon/quant.sf
test-data/count/salmon/quant.sf.genes
b
diff -r 77fc547df6ff -r fba77b1f69b4 abundance_estimates_to_matrix.xml
--- 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">
b
diff -r 77fc547df6ff -r fba77b1f69b4 test-data/count/express_bowtie/results.xprs.genes
--- 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
b
@@ -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
b
diff -r 77fc547df6ff -r fba77b1f69b4 test-data/count/express_bowtie/results_B.xprs.genes
--- 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
b
@@ -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
b
diff -r 77fc547df6ff -r fba77b1f69b4 test-data/count/express_bowtie/sample_A
--- /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
b
@@ -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
b
diff -r 77fc547df6ff -r fba77b1f69b4 test-data/count/express_bowtie/sample_B
--- /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
b
@@ -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
b
diff -r 77fc547df6ff -r fba77b1f69b4 test-data/count/rsem_bowtie/RSEM.genes.results
--- 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
b
@@ -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
b
diff -r 77fc547df6ff -r fba77b1f69b4 test-data/count/rsem_bowtie/RSEM.genes_B.results
--- 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
b
@@ -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
b
diff -r 77fc547df6ff -r fba77b1f69b4 test-data/count/rsem_bowtie/sample_A
--- /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
b
@@ -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
b
diff -r 77fc547df6ff -r fba77b1f69b4 test-data/count/rsem_bowtie/sample_B
--- /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
b
@@ -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
b
diff -r 77fc547df6ff -r fba77b1f69b4 test-data/count/rsem_bowtie2/RSEM.genes.results
--- 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
b
@@ -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
b
diff -r 77fc547df6ff -r fba77b1f69b4 test-data/count/rsem_bowtie2/RSEM.genes_B.results
--- 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
b
@@ -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
b
diff -r 77fc547df6ff -r fba77b1f69b4 test-data/count/rsem_bowtie2/sample_A
--- /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
b
@@ -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
b
diff -r 77fc547df6ff -r fba77b1f69b4 test-data/count/rsem_bowtie2/sample_B
--- /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
b
@@ -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
b
diff -r 77fc547df6ff -r fba77b1f69b4 test-data/count/salmon/quant.sf
--- 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
b
@@ -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
b
diff -r 77fc547df6ff -r fba77b1f69b4 test-data/count/salmon/quant.sf.genes
--- 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
b
@@ -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
b
diff -r 77fc547df6ff -r fba77b1f69b4 test-data/count/salmon/sample_A
--- /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
b
@@ -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
b
diff -r 77fc547df6ff -r fba77b1f69b4 test-data/count/salmon/sample_B
--- /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
b
@@ -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
b
diff -r 77fc547df6ff -r fba77b1f69b4 test-data/samples.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/samples.tsv Fri Nov 18 06:07:28 2016 -0500
b
@@ -0,0 +1,4 @@
+ConditionA CondA_replicate1
+ConditionA CondA_replicate2
+ConditionB CondB_replicate1
+ConditionB CondB_replicate2
b
diff -r 77fc547df6ff -r fba77b1f69b4 tool_dependencies.xml
--- a/tool_dependencies.xml Mon Aug 01 14:42:33 2016 -0400
+++ b/tool_dependencies.xml Fri Nov 18 06:07:28 2016 -0500
b
@@ -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" />