Mercurial > repos > chrisw > monorail_test
changeset 17:368ec7e775ce draft
Uploaded
| author | chrisw |
|---|---|
| date | Tue, 12 Nov 2019 01:27:34 -0500 |
| parents | d2770bc432e1 |
| children | 7fdb59956920 |
| files | monorail.xml |
| diffstat | 1 files changed, 6 insertions(+), 35 deletions(-) [+] |
line wrap: on
line diff
--- 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"/>