# HG changeset patch
# User chrisw
# Date 1573540054 18000
# Node ID 368ec7e775cedda53526097f856154cd2b2ab4bb
# Parent  d2770bc432e119234265b75afaf5f06a4ecf26d9
Uploaded

diff -r d2770bc432e1 -r 368ec7e775ce monorail.xml
--- a/monorail.xml	Wed Feb 13 18:39:50 2019 -0500
+++ b/monorail.xml	Tue Nov 12 01:27:34 2019 -0500
@@ -2,8 +2,8 @@
     <!-- much of this was based on https://github.com/galaxyproject/tools-iuc/blob/master/tools/rgrnastar/rg_rnaStar.xml -->
     <requirements>
         <requirement type="package" version="1.9">samtools</requirement>
-        <requirement type="package" version="2.6.1b">star</requirement>
-        <requirement type="package" version="0.2.6">bamcount</requirement>
+        <requirement type="package" version="2.7.3a">star</requirement>
+        <requirement type="package" version="0.4.0">bamcount</requirement>
         <requirement type="package" version="5.4.0">snakemake-minimal</requirement>
         <requirement type="package" version="1.3.3">zstd</requirement>
         <requirement type="package" version="1.3">seqtk</requirement>
@@ -34,8 +34,8 @@
                             compressed=1
                         #end if
                     #end if
-                    ref="$refGenomeSource.GTFconditional.genomeDir.fields.path"
-                    exon_bed="$exons"
+                    ref="$refGenomeSource.genomeDir.fields.path"
+                    exon_bed="$refGenomeSource.genomeDir.fields.exons_path"
                     output="."
                     temp="./tmp"
     ]]></command>
@@ -71,41 +71,12 @@
 
  <!-- Genome source. -->
         <conditional name="refGenomeSource">
-            <param name="geneSource" type="select" label="Custom or built-in reference genome" help="Built-ins were indexed using default options">
-                <option value="indexed" selected="True">Use a built-in index</option>
-                <option value="history">Use reference genome from history and create temporary index</option>
-            </param>
-            <when value="indexed">
-                <conditional name="GTFconditional">
-                    <param name="GTFselect" type="select" label="Reference genome with or without an annotation" help="Must the index have been created WITH a GTF file (if not you can specify one afterward).">
-                        <option value="without-gtf">use genome reference without builtin gene-model</option>
-                        <option value="with-gtf">use genome reference with builtin gene-model</option>
-                    </param>
-                    <when value="with-gtf">
-                        <param name="genomeDir" argument="--genomeDir" type="select" label="Select reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
-                            <options from_data_table="rnastar_index2">
-                                <filter type="static_value" column="4" value="1"/>
-                                <filter type="sort_by" column="2" />
+                        <param name="genomeDir" argument="--genomeDir" type="select" label="Select reference genome index set" help="If your genome of interest is not listed, contact the Galaxy team">
+                            <options from_data_table="monorail_index">
                                 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
                             </options>
                         </param>
-                    </when>
-                    <when value="without-gtf">
-                        <param name="genomeDir" argument="--genomeDir" type="select" label="Select reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
-                            <options from_data_table="rnastar_index2">
-                                <filter type="static_value" column="4" value="0"/>
-                                <filter type="sort_by" column="2" />
-                                <validator type="no_options" message="No indexes are available for the selected input dataset"/>
-                            </options>
-                        </param>
-                    </when>
-                </conditional>
-            </when>
-            <when value="history">
-                <param argument="--genomeFastaFiles" type="data" format="fasta" label="Select a reference genome" />
-            </when>
         </conditional>
-        <param name="exons" type="data" format="bed" label="Exon annotation BED file" help="Upload/use a BED formatted list of exon intervals for quantifying"/>
         </inputs>
     <outputs>
         <data format="txt" name="auc" label="${tool.name} on ${on_string}: AUC" from_work_dir="bamcount_auc.tsv"/>