# HG changeset patch
# User iuc
# Date 1503953652 14400
# Node ID 04bd98a9c751320198937117b76b1d1b6ae7fca3
# Parent  be3607a306af125b5150793c7a2729562bebdf79
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bc4ea54f0deec4ddec8e6cf79fd547491e165686

diff -r be3607a306af -r 04bd98a9c751 align_and_estimate_abundance.xml
--- a/align_and_estimate_abundance.xml	Fri Mar 31 11:37:01 2017 -0400
+++ b/align_and_estimate_abundance.xml	Mon Aug 28 16:54:12 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="trinity_align_and_estimate_abundance" name="Align reads and estimate abundance" version="@WRAPPER_VERSION@.0">
+<tool id="trinity_align_and_estimate_abundance" name="Align reads and estimate abundance" version="@WRAPPER_VERSION@.2">
     <description>on a de novo assembly of RNA-Seq data</description>
     <macros>
         <import>macros.xml</import>
@@ -8,6 +8,7 @@
         <requirement type="package" version="1.5.1">express</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[
         ln -f -s '$transcripts' input.fa &&
@@ -125,6 +126,7 @@
                 <option value="RSEM">RSEM</option>
                 <option value="eXpress">eXpress</option>
                 <option value="salmon">Salmon</option>
+                <option value="kallisto">Kallisto</option>
             </param>
             <when value="RSEM">
                 <param type="select" name="aln_method" argument="--aln_method" label="Alignment method">
@@ -144,6 +146,8 @@
                     <option value="fmd">FMD</option>
                 </param>
             </when>
+            <when value="kallisto">
+            </when>
         </conditional>
 
         <section name="additional_params" title="Additional Options" expanded="False">
@@ -182,6 +186,13 @@
         <data format="tabular" name="genes_counts_salmon" label="${tool.name} on ${on_string}: genes counts" from_work_dir="output/quant.sf.genes">
             <filter>method['est_method'] == "salmon"</filter>
         </data>
+
+        <data format="tabular" name="isoforms_counts_kallisto" label="${tool.name} on ${on_string}: isoforms counts" from_work_dir="output/abundance.tsv">
+            <filter>method['est_method'] == "kallisto"</filter>
+        </data>
+        <data format="tabular" name="genes_counts_kallisto" label="${tool.name} on ${on_string}: genes counts" from_work_dir="output/abundance.tsv.genes">
+            <filter>method['est_method'] == "kallisto"</filter>
+        </data>
     </outputs>
     <tests>
         <test>
@@ -250,8 +261,7 @@
                 </assert_contents>
             </output>
         </test>
-        <!-- test disabled because broken in travis, probably due to conda/symlink problem-->
-        <!--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"/>
@@ -272,7 +282,28 @@
                     <has_n_columns n="5" />
                 </assert_contents>
             </output>
-        </test-->
+        </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="kallisto"/>
+            <param name="has_gene_map" value="yes"/>
+            <output name="isoforms_counts_kallisto">
+                <assert_contents>
+                    <has_line_matching expression="TRINITY_DN1_c0_g1_i1&#009;.*" />
+                    <has_n_columns n="5" />
+                </assert_contents>
+            </output>
+            <output name="genes_counts_kallisto">
+                <assert_contents>
+                    <has_line_matching expression="TRINITY_DN1_c0_g1&#009;.*" />
+                    <has_n_columns n="5" />
+                </assert_contents>
+            </output>
+        </test>
     </tests>
     <help>
 <![CDATA[
diff -r be3607a306af -r 04bd98a9c751 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 16:54:12 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 be3607a306af -r 04bd98a9c751 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 16:54:12 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 be3607a306af -r 04bd98a9c751 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 16:54:12 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 be3607a306af -r 04bd98a9c751 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 16:54:12 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