diff abundance_estimates_to_matrix.xml @ 6:74217fbfba4d draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bc4ea54f0deec4ddec8e6cf79fd547491e165686

--- 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>
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