# HG changeset patch
# User jackcurragh
# Date 1660995535 0
# Node ID 5f3a3790cc79226e71581b4fb793a3cea7f4d806
# Parent  15e6eb67d7100dd6a47b1fae092e1d461cb60d12
Uploaded

diff -r 15e6eb67d710 -r 5f3a3790cc79 bowtie_transcriptome_wrapper/bowtie_transcriptomic_wrapper.xml
--- a/bowtie_transcriptome_wrapper/bowtie_transcriptomic_wrapper.xml	Fri May 27 10:12:05 2022 +0000
+++ b/bowtie_transcriptome_wrapper/bowtie_transcriptomic_wrapper.xml	Sat Aug 20 11:38:55 2022 +0000
@@ -1,4 +1,4 @@
-<tool id="bowtie_transcriptomic_wrapper" name="Bowtie Transcriptome Alignment" version="1.4.0">
+<tool id="bowtie_transcriptomic_wrapper" name="Bowtie Transcriptome Alignment" version="1.5.0">
   <description>Align to Transcriptome using Bowtie</description>
   <requirements>
     <requirement type="package" version="1.2.0">bowtie</requirement>
@@ -222,7 +222,7 @@
         <option value="paired">Paired-end</option>
       </param>
       <when value="single">
-        <param name="sInput1" type="data" format="fastqsanger,fastqillumina,fastqsolexa" label="FASTQ file" help="Must have ASCII encoded quality scores"/>
+        <param name="sInput1" type="data" format="fastq,fastqsanger,fastqillumina,fastqsolexa" label="FASTQ file" help="Must have ASCII encoded quality scores"/>
         <conditional name="sParams">
           <param name="sSettingsType" type="select" label="Bowtie settings to use" help="For most mapping needs use Commonly used settings. If you want full control use Full parameter list">
             <option value="preSet">Commonly used</option>
@@ -314,8 +314,8 @@
         </conditional> <!-- sParams -->
       </when> <!-- single -->
       <when value="paired">
-        <param name="pInput1" type="data" format="fastqsanger,fastqillumina,fastqsolexa" label="Forward FASTQ file" help="Must have ASCII encoded quality scores"/>
-        <param name="pInput2" type="data" format="fastqsanger,fastqillumina,fastqsolexa" label="Reverse FASTQ file" help="File format must match the Forward FASTQ file">
+        <param name="pInput1" type="data" format="fastq,fastqsanger,fastqillumina,fastqsolexa" label="Forward FASTQ file" help="Must have ASCII encoded quality scores"/>
+        <param name="pInput2" type="data" format="fastq,fastqsanger,fastqillumina,fastqsolexa" label="Reverse FASTQ file" help="File format must match the Forward FASTQ file">
             <options options_filter_attribute="ext" from_parameter="tool.app.datatypes_registry.datatypes_by_extension" transform_lines="obj.keys()">
                <column name="name" index="0"/>
                <column name="value" index="0"/>
diff -r 15e6eb67d710 -r 5f3a3790cc79 bowtie_transcriptome_wrapper/tool-data/bowtie_transcriptome_indexes.loc.sample
--- a/bowtie_transcriptome_wrapper/tool-data/bowtie_transcriptome_indexes.loc.sample	Fri May 27 10:12:05 2022 +0000
+++ b/bowtie_transcriptome_wrapper/tool-data/bowtie_transcriptome_indexes.loc.sample	Sat Aug 20 11:38:55 2022 +0000
@@ -1,6 +1,8 @@
 homo_sapiens_gencode39	hg_gen39	Homo sapiens (gencode 39) Transcriptome	/mnt/data/indices/bowtie/transcriptome/homo_sapiens_gencode39/homo_sapiens_gencode39_transcriptome
 homo_sapiens_gencode28	hg_gen28	Homo sapiens (gencode 28) Transcriptome	/mnt/data/indices/bowtie/transcriptome/homo_sapiens_gencode28/homo_sapiens_gencode28_transcriptome
+homo_sapiens_gencode25	hg_gen25	Homo sapiens (gencode 25) Transcriptome	/mnt/data/indices/bowtie/transcriptome/homo_sapiens_gencode25/homo_sapiens_gencode25_transcriptome
 mus_musculus_m28	m28	Mus musculus (m28) Transcriptome	/mnt/data/indices/bowtie/transcriptome/mus_musculus_m28/mus_musculus_m28_transcriptome
+mus_musculus_m25	m25	Mus musculus (m25) Transcriptome	/mnt/data/indices/bowtie/transcriptome/mus_musculus_m25/mus_musculus_m25_transcriptome
 mus_musculus_m10	m10	Mus musculus (m10) Transcriptome	/mnt/data/indices/bowtie/transcriptome/mus_musculus_m10/mus_musculus_m10_transcriptome
 drosophila_melanogaster_dm3	dm3	Drosophila melanogaster (dm3) Transcriptome	/mnt/data/indices/bowtie/transcriptome/drosophila_melanogater_dm3/drosophila_melanogater_dm3_transcriptome
 drosophila_melanogaster_dm6	dm6	Drosophila melanogaster (dm6) Transcriptome	/mnt/data/indices/bowtie/transcriptome/drosophila_melanogater_dm6/drosophila_melanogater_dm6_transcriptome