# HG changeset patch
# User iuc
# Date 1617743319 0
# Node ID 01247aaf0a10e5a88230656274c2861b5bf7de00
# Parent  5ae5c312d718bd4ec5fa54af51d120cc5ca3b06d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 94e4019f3e5e81d3a09cd92ce1e93587600847d8"

diff -r 5ae5c312d718 -r 01247aaf0a10 kallisto_pseudo.xml
--- a/kallisto_pseudo.xml	Thu Sep 26 09:11:24 2019 -0400
+++ b/kallisto_pseudo.xml	Tue Apr 06 21:08:39 2021 +0000
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="kallisto_pseudo" name="Kallisto pseudo" version="@VERSION@.1">
+<tool id="kallisto_pseudo" name="Kallisto pseudo" version="@VERSION@.2">
     <description>- run pseudoalignment on RNA-Seq transcripts</description>
     <macros>
         <import>macros.xml</import>
@@ -66,7 +66,7 @@
                 <option value="paired">Paired</option>
             </param>
             <when value="single">
-                <param name="reads" type="data" format="fastq" multiple="True" label="Reads in FASTQ format" />
+                <param name="reads" type="data" format="fastq,fastq.gz" multiple="True" label="Reads in FASTQ format" />
                 <param name="fragment_length" argument="--fragment-length" type="integer" value="200" label="Average fragment length" />
                 <param argument="--sd" type="integer" value="20" label="Estimated standard deviation of fragment length" />
             </when>
@@ -84,16 +84,16 @@
                             </param>
                             <when value="yes">
                                 <param name="forward" type="data" format="tabular" multiple="True" label="UMI file" />
-                                <param name="reverse" type="data" format="fastq" multiple="True" label="FASTQ reads" />
+                                <param name="reverse" type="data" format="fastq,fastq.gz" multiple="True" label="FASTQ reads" />
                             </when>
                             <when value="no">
-                                <param name="forward" type="data" format="fastq" multiple="True" label="Forward reads" />
-                                <param name="reverse" type="data" format="fastq" multiple="True" label="Reverse reads" />
+                                <param name="forward" type="data" format="fastq,fastq.gz" multiple="True" label="Forward reads" />
+                                <param name="reverse" type="data" format="fastq,fastq.gz" multiple="True" label="Reverse reads" />
                             </when>
                         </conditional>
                     </when>
                     <when value="collection">
-                        <param name="reads" type="data_collection" format="fastq" collection_type="paired" label="Collection of reads" />
+                        <param name="reads" type="data_collection" format="fastq,fastq.gz" collection_type="paired" label="Collection of reads" />
                     </when>
                 </conditional>
             </when>
@@ -112,7 +112,7 @@
             <param name="collection_selector" value="datasets" />
             <param name="umi" value="yes" />
             <param name="forward" ftype="tabular" value="mm10_chrM.umi" />
-            <param name="reverse" ftype="fastq" value="mm10_chrM-1.r.fq" />
+            <param name="reverse" ftype="fastq.gz" value="mm10_chrM-1.r.fq.gz" />
             <output name="sample">
                 <discovered_dataset designation="Matrix.tabular" file="kallisto_pseudo_out1.tab" ftype="tabular" />
                 <discovered_dataset designation="Matrix.ec" file="kallisto_pseudo_out1.ec" ftype="tabular" />
@@ -127,8 +127,8 @@
             <param name="umi" value="no" />
             <param name="reads">
                 <collection type="paired">
-                    <element name="forward" value="mm10_chrM-1.f.fq" />
-                    <element name="reverse" value="mm10_chrM-1.r.fq" />
+                    <element name="forward" value="mm10_chrM-1.f.fq.gz" ftype="fastq.gz"/>
+                    <element name="reverse" value="mm10_chrM-1.r.fq.gz" ftype="fastq.gz"/>
                 </collection>
             </param>
             <output name="sample">
@@ -141,7 +141,7 @@
             <param name="reference" ftype="fasta" value="mm10_chrM.fa" />
             <param name="single_paired_selector" value="single" />
             <param name="collection_selector" value="collection" />
-            <param name="reads" ftype="fastq" value="mm10_chrM-1.f.fq" />
+            <param name="reads" ftype="fastq.gz" value="mm10_chrM-1.f.fq.gz" />
             <output name="sample">
                 <discovered_dataset designation="Pseudoalignments.tabular" file="kallisto_pseudo_out3.tab" ftype="tabular" />
                 <discovered_dataset designation="Pseudoalignments.ec" file="kallisto_pseudo_out3.ec" ftype="tabular" />
diff -r 5ae5c312d718 -r 01247aaf0a10 test-data/mm10_chrM-1.f.fq.gz
Binary file test-data/mm10_chrM-1.f.fq.gz has changed
diff -r 5ae5c312d718 -r 01247aaf0a10 test-data/mm10_chrM-1.r.fq.gz
Binary file test-data/mm10_chrM-1.r.fq.gz has changed