Mercurial > repos > iuc > medaka_variant_pipeline
changeset 2:ce2bf68a260d draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 7fec11af843c91c70413844368c1d5f5f78ce45e"
| author | iuc |
|---|---|
| date | Thu, 18 Jun 2020 05:08:40 -0400 |
| parents | 92cdc29a8620 |
| children | 148f32860445 |
| files | macros.xml medaka_variant.xml test-data/variants.vcf.gz |
| diffstat | 3 files changed, 20 insertions(+), 11 deletions(-) [+] |
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--- a/macros.xml Thu May 28 02:39:16 2020 -0400 +++ b/macros.xml Thu Jun 18 05:08:40 2020 -0400 @@ -1,6 +1,6 @@ <?xml version="1.0"?> <macros> - <token name="@TOOL_VERSION@">1.0.1</token> + <token name="@TOOL_VERSION@">1.0.3</token> <token name="@PROFILE@">18.01</token> <xml name="requirements"> <requirements> @@ -55,13 +55,13 @@ <option value="r941_min_high_g330">r941_min_high_g330</option> <option value="r941_min_high_g340_rle">r941_min_high_g340_rle</option> <option value="r941_min_high_g344">r941_min_high_g344</option> - <option value="r941_min_high_g351" selected="true">r941_min_high_g351</option> + <option value="r941_min_high_g351">r941_min_high_g351</option> <option value="r941_min_high_g360">r941_min_high_g360</option> <option value="r941_prom_fast_g303">r941_prom_fast_g303</option> <option value="r941_prom_high_g303">r941_prom_high_g303</option> <option value="r941_prom_high_g330">r941_prom_high_g330</option> <option value="r941_prom_high_g344">r941_prom_high_g344</option> - <option value="r941_prom_high_g360">r941_prom_high_g360</option> + <option value="r941_prom_high_g360" selected="true">r941_prom_high_g360</option> <option value="r941_prom_snp_g303">r941_prom_snp_g303</option> <option value="r941_prom_snp_g322">r941_prom_snp_g322</option> <option value="r941_prom_variant_g303">r941_prom_variant_g303</option> @@ -77,14 +77,14 @@ <when value="cached"> <param name="ref_file" type="select" label="Using reference genome" help="Select genome from the list"> <options from_data_table="all_fasta"> - <filter type="sort_by" column="2" /> - <validator type="no_options" message="No reference genomes are available" /> + <filter type="sort_by" column="2"/> + <validator type="no_options" message="No reference genomes are available"/> </options> <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> </param> </when> <when value="history"> - <param name="ref_file" type="data" format="fasta,fastq" label="Use the following dataset as the reference sequence" help="You can upload a FASTA or FASTQ sequence to the history and use it as reference" /> + <param name="ref_file" type="data" format="fasta,fastq" label="Use the following dataset as the reference sequence" help="You can upload a FASTA or FASTQ sequence to the history and use it as reference"/> </when> </conditional> </xml> @@ -94,11 +94,11 @@ --> <token name="@WID@"><![CDATA[ -medaka is a tool suite to create a consensus sequence from nanopore sequencing data. +*medaka* is a tool suite to create a consensus sequence from nanopore sequencing data. This task is performed using neural networks applied from a pileup of individual sequencing reads against a draft assembly. It outperforms graph-based methods operating on basecalled data, and can be competitive with state-of-the-art signal-based methods, whilst being much faster. ]]></token> <token name="@REFERENCES@"><![CDATA[ More information are available in the `manual <https://nanoporetech.github.io/medaka/index.html>`_ and `github <https://github.com/nanoporetech/medaka>`_. ]]></token> -</macros> +</macros> \ No newline at end of file
--- a/medaka_variant.xml Thu May 28 02:39:16 2020 -0400 +++ b/medaka_variant.xml Thu Jun 18 05:08:40 2020 -0400 @@ -22,6 +22,7 @@ -s $s -m $m -t \${GALAXY_SLOTS:-4} +-p -b $b -N $N -P $P @@ -53,17 +54,18 @@ <option value="round_1_hap_2_vcf">round_1_hap_2.vcf</option> <option value="round_1_hap_1_probs_hdf">round_1_hap_1_probs.hdf</option> <option value="round_1_hap_2_probs_hdf">round_1_hap_2_probs.hdf</option> + <option value="round_1_phased.vcf">round_1_phased.vcf</option> <option value="round_1_unfiltered_vcf">round_1_unfiltered.vcf</option> <option value="round_1_vcf" selected="true">round_1.vcf</option> <option value="log">Log</option> </param> </inputs> <outputs> - <!-- standard --> + <!-- standard output--> <data name="out_round_1_vcf" format="vcf" label="${tool.name} on ${on_string}: round_1.vcf" from_work_dir="results/round_1.vcf"> <filter>'round_1_vcf' in out</filter> </data> - <!-- optional --> + <!-- optional output: round 0 --> <data name="out_round_0_hap_mixed_probs_hdf" format="h5" label="${tool.name} on ${on_string}: round_0_hap_mixed_probs_hdf" from_work_dir="results/round_0_hap_mixed_probs.hdf"> <filter>'round_0_hap_mixed_probs_hdf' in out</filter> </data> @@ -76,7 +78,7 @@ <data name="out_round_0_hap_mixed_unphased_vcf" format="vcf" label="${tool.name} on ${on_string}: round_0_hap_mixed_unphased_vcf" from_work_dir="results/round_0_hap_mixed_unphased.vcf"> <filter>'round_0_hap_mixed_unphased_vcf' in out</filter> </data> - <!-- round 1 --> + <!-- optional output: round 1 --> <data name="out_round_1_hap_1_vcf" format="vcf" label="${tool.name} on ${on_string}: round_1_hap_1.vcf" from_work_dir="results/round_1_hap_1.vcf"> <filter>'round_1_hap_1_vcf' in out</filter> </data> @@ -89,9 +91,13 @@ <data name="out_round_1_hap_2_probs_hdf" format="h5" label="${tool.name} on ${on_string}: round_1_hap_2_probs.hdf" from_work_dir="results/round_1_hap_2_probs.hdf"> <filter>'round_1_hap_2_probs_hdf' in out</filter> </data> + <data name="out_round_1_phased.vcf" format="vcf" label="${tool.name} on ${on_string}: round_1_phased.vcf" from_work_dir="results/round_1_phased.vcf"> + <filter>'round_1_phased.vcf' in out</filter> + </data> <data name="out_round_1_unfiltered_vcf" format="vcf" label="${tool.name} on ${on_string}: round_1_unfiltered.vcf" from_work_dir="results/round_1_unfiltered.vcf"> <filter>'round_1_unfiltered_vcf' in out</filter> </data> + <!-- optional output: log --> <data name="out_log" format="txt" label="${tool.name} on ${on_string}: Log"> <filter>'log' in out</filter> </data> @@ -141,6 +147,7 @@ **Output** +- round_0_hap_mixed_phased.bam - round_0_hap_mixed_phased.vcf - round_0_hap_mixed_probs.hdf - round_0_hap_mixed_unphased.vcf @@ -148,8 +155,10 @@ - round_1_hap_1.vcf - round_1_hap_2_probs.hdf - round_1_hap_2.vcf +- round_1_phased.vcf - round_1_unfiltered.vcf - round_1.vcf +- log **References**