Mercurial > repos > iuc > kallisto_quant

diff kallisto_quant.xml @ 3:da068c8ea6d8 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit da0d5249fc7bd787ace5dac67bf273891756f324
author iuc
date Tue, 05 Sep 2017 03:24:11 -0400
parents 7f698e0094e5
children 22c498dc4bc6
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--- a/kallisto_quant.xml	Tue Aug 22 04:14:22 2017 -0400
+++ b/kallisto_quant.xml	Tue Sep 05 03:24:11 2017 -0400
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="kallisto_quant" name="Kallisto quant" version="@VERSION@.1">
+<tool id="kallisto_quant" name="Kallisto quant" version="@VERSION@.2">
     <description>- quantify abundances of RNA-Seq transcripts</description>
     <macros>
         <import>macros.xml</import>
@@ -98,9 +98,12 @@
     <outputs>
         <data format="h5" name="abundance_h5" from_work_dir="abundance.h5" label="${tool.name} on ${on_string}: Abundances (HDF5)" />
         <data format="tabular" name="abundance_tab" from_work_dir="abundance.tsv" label="${tool.name} on ${on_string}: Abundances (tabular)" />
-        <data format="bam" name="pseudobam_output" label="${tool.name} on ${on_string}: Pseudoalignments">
+        <data format="bam" name="pseudobam_output" from_work_dir="abundance.txt" label="${tool.name} on ${on_string}: Pseudoalignments">
             <filter>pseudobam</filter>
         </data>
+        <data format="tabular" name="fusion_output" from_work_dir="fusion.txt" label="${tool.name} on ${on_string}: Pizzly input (tabular)">
+            <filter>fusion</filter>
+        </data>
     </outputs>
     <tests>
         <test>
@@ -154,6 +157,17 @@
             <output name="abundance_tab" file="kallisto_quant_out5.tab" ftype="tabular" />
             <output name="pseudobam_output" file="kallisto_quant_out5.bam" ftype="bam" />
         </test>
+        <test>
+            <param name="reference_genome_source" value="history" />
+            <param name="reference" ftype="fasta" value="hg38_transcripts.fa" />
+            <param name="single_paired_selector" value="paired" />
+            <param name="collection_selector" value="datasets" />
+            <param name="fusion" value="true" />
+            <param name="forward" ftype="fastq" dbkey="hg38" value="hg38_F.fq.gz" />
+            <param name="reverse" ftype="fastq" dbkey="hg38" value="hg38_R.fq.gz" />
+            <output name="fusion_output" file="fusion.txt" ftype="tabular" />
+        </test>
+
     </tests>
     <help>
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