Mercurial > repos > dfornika > mentalist
changeset 26:01d50d174dbb draft
planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit 71cef9adab4b246fee6d7f99e30562e850ffebfd
| author | dfornika |
|---|---|
| date | Wed, 18 Oct 2017 17:51:12 -0400 |
| parents | b9dfa8aa503d |
| children | 916ca1e73ec9 |
| files | data_managers/data_manager_mentalist_download_cgmlst/data_manager/mentalist_download_cgmlst.py data_managers/data_manager_mentalist_download_pubmlst/data_manager/mentalist_download_pubmlst.py tools/mentalist_call/mentalist_call.xml |
| diffstat | 3 files changed, 41 insertions(+), 15 deletions(-) [+] |
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--- a/data_managers/data_manager_mentalist_download_cgmlst/data_manager/mentalist_download_cgmlst.py Thu Oct 12 19:13:11 2017 -0400 +++ b/data_managers/data_manager_mentalist_download_cgmlst/data_manager/mentalist_download_cgmlst.py Wed Oct 18 17:51:12 2017 -0400 @@ -3,6 +3,7 @@ from __future__ import print_function import argparse +import datetime import errno import os import string @@ -18,10 +19,11 @@ def mentalist_download_cgmlst( data_manager_dict, kmer_size, scheme, params, target_directory, data_table_names=DEFAULT_DATA_TABLE_NAMES ): translation_table = string.maketrans(string.punctuation, ("_" * 32)) base_path = scheme.lower().replace(" ", "_").translate(translation_table) + "_cgmlst" - scheme_files_path = base_path + "_scheme" - database_path = base_path + "_k" + str(kmer_size) - database_name = base_path + "_k" + str(kmer_size) + ".jld" - display_name = scheme + " k=" + str(kmer_size) + " (PubMLST)" + today = datetime.date.today().isoformat() + scheme_files_path = base_path + "_scheme_" + today + database_path = base_path + "_k" + str(kmer_size) + "_" + today + database_name = base_path + "_k" + str(kmer_size) + "_" + today + ".jld" + display_name = scheme + " k=" + str(kmer_size) + " (cgMLST) " + today args = [ 'mentalist', 'download_cgmlst', '-s', scheme, '-k', str(kmer_size), '--db', database_name, '-o', scheme_files_path] proc = subprocess.Popen( args=args, shell=False, cwd=target_directory ) return_code = proc.wait()
--- a/data_managers/data_manager_mentalist_download_pubmlst/data_manager/mentalist_download_pubmlst.py Thu Oct 12 19:13:11 2017 -0400 +++ b/data_managers/data_manager_mentalist_download_pubmlst/data_manager/mentalist_download_pubmlst.py Wed Oct 18 17:51:12 2017 -0400 @@ -18,10 +18,11 @@ def mentalist_download_pubmlst( data_manager_dict, kmer_size, scheme, params, target_directory, data_table_names=DEFAULT_DATA_TABLE_NAMES ): translation_table = string.maketrans(string.punctuation, ("_" * 32)) base_path = scheme.lower().replace(" ", "_").translate(translation_table) + "_pubmlst" - scheme_files_path = base_path + "_scheme" - database_path = base_path + "_k" + str(kmer_size) - database_name = base_path + "_k" + str(kmer_size) + ".jld" - display_name = scheme + " k=" + str(kmer_size) + " (PubMLST)" + today = datetime.date.today().isoformat() + scheme_files_path = base_path + "_scheme_" + today + database_path = base_path + "_k" + str(kmer_size) + "_" + today + database_name = base_path + "_k" + str(kmer_size) + "_" + today + ".jld" + display_name = scheme + " k=" + str(kmer_size) + " (PubMLST)" + today args = [ 'mentalist', 'download_pubmlst', '-s', scheme, '-k', str(kmer_size), '--db', database_name, '-o', scheme_files_path] proc = subprocess.Popen( args=args, shell=False, cwd=target_directory ) return_code = proc.wait()
--- a/tools/mentalist_call/mentalist_call.xml Thu Oct 12 19:13:11 2017 -0400 +++ b/tools/mentalist_call/mentalist_call.xml Wed Oct 18 17:51:12 2017 -0400 @@ -6,16 +6,24 @@ mentalist call -o '$output_file' - -s '$sample_name' --db '$kmer_db.fields.path' #if $discard_threshold -t '$discard_threshold' #end if - $input_fastqs.forward $input_fastqs.reverse + #if '$fastq_input_selector' == "single" + -s '$fastq_input1.name' + '$fastq_input1' + #end if + #if '$fastq_input_selector' == "paired" + -s '$fastq_input1.name' + '$fastq_input1' '$fastq_input2' + #end if + #if '$fastq_input_selector' == "paired_collection" + -s '$fastq_input.name' + '$fastq_input.forward' '$fastq_input.reverse' + #end if ]]></command> <inputs> - <param name="sample_name" type="text" - label="Sample Name" help="Sample Name" /> <param name="kmer_db" type="select"> <options from_data_table="mentalist_databases"> <validator type="no_options" message="No MentaLiST databases are available" /> @@ -27,11 +35,26 @@ <param name="skip_length" type="integer" label="Skip Length" help="Skip length between consecutive k-mers." value="1" min="1" max="32" /> - <param name="input_fastqs" type="data_collection" collection_type="paired" format="fastq" - label="Input FastQ" help="FastQ input files" /> + <conditional name="fastq_input"> + <param name="fastq_input_selector" type="select" label="Single or Paired-end reads" help="Select between paired and single end data"> + <option value="paired">Paired</option> + <option value="single">Single</option> + <option value="paired_collection">Paired Collection</option> + </param> + <when value="paired"> + <param name="fastq_input1" type="data" format="fastq" label="Select first set of reads" help="Specify dataset with forward reads"/> + <param name="fastq_input2" type="data" format="fastq" label="Select second set of reads" help="Specify dataset with reverse reads"/> + </when> + <when value="single"> + <param name="fastq_input1" type="data" format="fastq" label="Select fastq dataset" help="Specify dataset with single reads"/> + </when> + <when value="paired_collection"> + <param name="fastq_input" format="fastq" type="data_collection" collection_type="paired" label="Select a paired collection" label="Select dataset pair" help="Specify paired dataset collection containing paired reads"/> + </when> + </conditional> </inputs> <outputs> - <data name="output_file" format="tsv"/> + <data name="output_file" format="tabular"/> </outputs> <help><![CDATA[ ]]></help>