# HG changeset patch
# User iuc
# Date 1503953713 14400
# Node ID 74217fbfba4da1d4fd9479f9f46e7b99f1f7e66e
# Parent  8b5039bdf1f6dca5a7f0ab2d6a1d06eaf4d3ebf6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bc4ea54f0deec4ddec8e6cf79fd547491e165686

diff -r 8b5039bdf1f6 -r 74217fbfba4d abundance_estimates_to_matrix.xml
--- a/abundance_estimates_to_matrix.xml	Fri Mar 31 11:37:24 2017 -0400
+++ b/abundance_estimates_to_matrix.xml	Mon Aug 28 16:55:13 2017 -0400
@@ -1,4 +1,4 @@
-<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>
@@ -7,6 +7,7 @@
         <requirement type="package" version="3.16.5">bioconductor-edger</requirement>
         <!-- Cannot update to salmon 0.8.2 because in Bioconda it requires icu 58, while r-base 3.3.1 requires icu 54 -->
         <requirement type="package" version="0.8.1">salmon</requirement>
+        <requirement type="package" version="0.43.1">kallisto</requirement>
     </expand>
     <command detect_errors="aggressive"><![CDATA[
         #import re
@@ -30,6 +31,7 @@
             <option value="RSEM">RSEM</option>
             <option value="eXpress">eXpress</option>
             <option value="salmon">Salmon</option>
+            <option value="kallisto">Kallisto</option>
         </param>
 
         <section name="additional_params" title="Additional Options" expanded="False">
@@ -176,6 +178,29 @@
                 </assert_contents>
             </output>
         </test>
+        <test>
+            <param name="samples" ftype="tabular" value="count/kallisto/abundance.tsv.genes,count/kallisto/abundance_B.tsv.genes"/>
+            <param name="est_method" value="kallisto"/>
+            <param name="cross_sample_norm" value="TMM"/>
+            <output name="trans_counts">
+                <assert_contents>
+                    <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
+                    <has_n_columns n="3" />
+                </assert_contents>
+            </output>
+            <output name="TPM_no_norm">
+                <assert_contents>
+                    <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
+                    <has_n_columns n="3" />
+                </assert_contents>
+            </output>
+            <output name="norm">
+                <assert_contents>
+                    <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
+                    <has_n_columns n="3" />
+                </assert_contents>
+            </output>
+        </test>
     </tests>
     <help>
 <![CDATA[
diff -r 8b5039bdf1f6 -r 74217fbfba4d test-data/count/kallisto/abundance.tsv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/kallisto/abundance.tsv	Mon Aug 28 16:55:13 2017 -0400
@@ -0,0 +1,8 @@
+target_id	length	eff_length	est_counts	tpm
+TRINITY_DN1_c0_g1_i1	380	133.091	13	114025
+TRINITY_DN0_c0_g1_i1	229	31.75	7	257370
+TRINITY_DN2_c0_g1_i1	279	55.7143	1	20952.6
+TRINITY_DN2_c1_g1_i1	541	279.667	15	62611.6
+TRINITY_DN2_c2_g1_i1	240	42.75	4	109227
+TRINITY_DN2_c3_g1_i1	202	19	0	0
+TRINITY_DN3_c0_g1_i1	216	18.75	7	435814
diff -r 8b5039bdf1f6 -r 74217fbfba4d test-data/count/kallisto/abundance.tsv.genes
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/kallisto/abundance.tsv.genes	Mon Aug 28 16:55:13 2017 -0400
@@ -0,0 +1,8 @@
+target_id	length	eff_length	est_counts	tpm
+TRINITY_DN3_c0_g1	216.00	18.75	7.00	435814.00
+TRINITY_DN2_c2_g1	240.00	42.75	4.00	109227.00
+TRINITY_DN2_c3_g1	202.00	19.00	0.00	0.00
+TRINITY_DN0_c0_g1	229.00	31.75	7.00	257370.00
+TRINITY_DN2_c0_g1	279.00	55.71	1.00	20952.60
+TRINITY_DN1_c0_g1	380.00	133.09	13.00	114025.00
+TRINITY_DN2_c1_g1	541.00	279.67	15.00	62611.60
diff -r 8b5039bdf1f6 -r 74217fbfba4d test-data/count/kallisto/abundance_B.tsv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/kallisto/abundance_B.tsv	Mon Aug 28 16:55:13 2017 -0400
@@ -0,0 +1,8 @@
+target_id	length	eff_length	est_counts	tpm
+TRINITY_DN1_c0_g1_i1	229	31.75	7	257370
+TRINITY_DN0_c0_g1_i1	380	133.091	13	114025
+TRINITY_DN2_c0_g1_i1	279	55.7143	1	20952.6
+TRINITY_DN2_c2_g1_i1	541	279.667	15	62611.6
+TRINITY_DN2_c1_g1_i1	240	42.75	4	109227
+TRINITY_DN2_c3_g1_i1	202	19	0	0
+TRINITY_DN3_c0_g1_i1	216	18.75	7	435814
diff -r 8b5039bdf1f6 -r 74217fbfba4d test-data/count/kallisto/abundance_B.tsv.genes
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/kallisto/abundance_B.tsv.genes	Mon Aug 28 16:55:13 2017 -0400
@@ -0,0 +1,8 @@
+target_id	length	eff_length	est_counts	tpm
+TRINITY_DN3_c0_g1	216.00	18.75	7.00	435814.00
+TRINITY_DN2_c1_g1	240.00	42.75	4.00	109227.00
+TRINITY_DN2_c3_g1	202.00	19.00	0.00	0.00
+TRINITY_DN0_c0_g1	380.00	133.09	13.00	114025.00
+TRINITY_DN2_c0_g1	279.00	55.71	1.00	20952.60
+TRINITY_DN1_c0_g1	229.00	31.75	7.00	257370.00
+TRINITY_DN2_c2_g1	541.00	279.67	15.00	62611.60