| Previous changeset 2:09ebaa5192ab (2017-10-27) Next changeset 4:c0d08ba0c6ee (2018-01-26) |
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Commit message:
planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4f09991d49a1701c54d5b97601a622e111c7290c |
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modified:
bio_hansel.xml |
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| diff -r 09ebaa5192ab -r 29faaa849e41 bio_hansel.xml --- a/bio_hansel.xml Fri Oct 27 12:40:00 2017 -0400 +++ b/bio_hansel.xml Fri Dec 22 10:31:41 2017 -0500 |
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| b'@@ -1,7 +1,7 @@\n-<tool id="bio_hansel" name="Salmonella Subtyping" version="0.1.3">\n- <description>Genome assemblies and/or whole-genome sequencing readset</description>\n+<tool id="bio_hansel" name="Bio Hansel" version="1.0.0">\n+ <description>SNV Subtyping with genome assemblies or reads</description>\n <requirements>\n- <requirement type="package" version="0.1.0">bio_hansel</requirement>\n+ <requirement type="package" version="1.1.0">bio_hansel</requirement>\n <requirement type="package" version="17.2.0">attrs</requirement>\n </requirements>\n <command detect_errors="exit_code"><![CDATA[\n@@ -52,16 +52,32 @@\n #end if\n \n \n- #if $kmer_min\n- --min-kmer-freq $kmer_min\n+ #if $kmer_vals.kmer_min\n+ --min-kmer-freq $kmer_vals.kmer_min\n+ #end if\n+\n+ #if $kmer_vals.kmer_max\n+ --max-kmer-freq $kmer_vals.kmer_max\n #end if\n \n- #if $kmer_max\n- --max-kmer-freq $kmer_max\n+ #if $qc_vals.low_cov_depth_freq\n+ --low-cov-depth-freq $qc_vals.low_cov_depth_freq\n+ #end if\n+\n+ #if $qc_vals.max_missing_tiles\n+ --max-missing-tiles $qc_vals.max_missing_tiles\n+ #end if\n+\n+ #if $qc_vals.min_ambiguous_tiles\n+ --min-ambiguous-tiles $qc_vals.min_ambiguous_tiles\n+ #end if\n+\n+ #if $qc_vals.max_intermediate_tiles\n+ --max-intermediate-tiles $qc_vals.max_intermediate_tiles\n #end if\n \n ## Adding more parameters to the command.\n- -vvv -t "\\${GALAXY_SLOTS:-1}" -o results.tab -O match_results.tab \n+ -vvv -t "\\${GALAXY_SLOTS:-1}" -o results.tab -O match_results.tab -S tech_results.tab\n \n \n ## Entering the file inputs\n@@ -109,12 +125,23 @@\n <param name="scheme_input" type="data" format="fasta" label="Scheme Input"/>\n </when>\n </conditional>\n- <param name="kmer_min" argument="--min-kmer-freq" optional="True" type="integer" min="0" label="Min k-mer freq/coverage" value="10" help="default = 10"/>\n- <param name="kmer_max" argument="--max-kmer-freq" optional="True" type="integer" min="1" label="Max k-mer freq/coverage" value="200" help="default = 200"/>\n+ <!-- K-mer frequencies. -->\n+ <section name="kmer_vals" title="K-mer Frequency Thresholds" expanded="False">\n+ <param name="kmer_min" argument="--min-kmer-freq" optional="True" type="integer" min="0" label="Min k-mer freq/coverage" value="8" help="default = 8"/>\n+ <param name="kmer_max" argument="--max-kmer-freq" optional="True" type="integer" min="1" label="Max k-mer freq/coverage" value="1000" help="default = 1000"/>\n+ </section>\n+ <!-- Quality Checking Parameters -->\n+ <section name="qc_vals" title="Quality Checking Thresholds" expanded="False">\n+ <param name="low_cov_depth_freq" argument="--low-cov-depth-freq" optional="True" type="integer" min="0" label="QC: Frequency below this coverage are considered low coverage" value="20" help="default = 20"/>\n+ <param name="min_ambiguous_tiles" argument="--min-ambiguous-tiles" optional="True" type="integer" min="0" label="QC: Min number of tiles missing for Ambiguous Result" value="3" help="default = 3"/>\n+ <param name="max_missing_tiles" argument="--max-missing-tiles" optional="True" type="float" min="0" max="1" label="QC: Decimal Proportion of max allowed missing tiles" value="0.05" help="default = 0.05, valid values {0.0 - 1.0}"/>\n+ <param name="max_intermediate_tiles" argument="--max-intermediate-tiles" optional="True" type="float" min="0" max="1" label="QC: Decimal Proportion of max allowed missing tiles for an intermediate subtype" value="0.05" help="default = 0.05, valid values {0.0 - 1.0}"/> \n+ </section>\n </inputs>\n <outputs>\n <data format="tabular" name="results.tab" from_work_dir="results.tab" label="results.tab"/>\n <data format="tabu'..b'e\\s+n_tiles_matching_positive_total\\s+n_tiles_matching_subtype\\s+n_tiles_matching_subtype_total\\s+file_path"/>\n- <!-- Verifying that the output of running the test file is expected. This is done via REGEX because the name and path of the file outputted to results.tab changes each test. -->\n- <has_text_matching expression="(heidelberg)\\s+(2.2.2.2.1.4)\\s+(2;)\\s+(2.2;)\\s+(2.2.2;)\\s+(2.2.2.2;)\\s+(2.2.2.2.1;)\\s+(2.2.2.2.1.4)\\s+(1037658-2.2.2.2.1.4;)\\s+(2154958-2.2.2.2.1.4;)\\s+(3785187-2.2.2.2.1.4)\\s+(True)\\s+(202)\\s+(202)\\s+(17)\\s+(17)\\s+(3)\\s+(3)"/>\n+ <has_text_matching expression="sample\\s+scheme\\s+scheme_version\\s+subtype\\s+all_subtypes\\s+tiles_matching_subtype\\s+are_subtypes_consistent\\s+inconsistent_subtypes\\s+n_tiles_matching_all\\s+n_tiles_matching_all_expected\\s+n_tiles_matching_positive\\s+n_tiles_matching_positive_expected\\s+n_tiles_matching_subtype\\s+n_tiles_matching_subtype_expected\\s+file_path\\s+qc_status\\s+qc_message"/>\n </assert_contents>\n </output>\n <output name="match_results.tab">\n <assert_contents>\n- <!-- This is the last line in the file, this assertion is to make sure that we have the correct number of items. -->\n- <has_text_matching expression="negative4738855-1.1"/>\n+ <has_text_matching expression="tilename\\s+seq\\s+is_revcomp\\s+contig_id\\s+match_index\\s+refposition\\s+subtype\\s+is_pos_tile\\s+sample\\s+file_path\\s+scheme\\s+scheme_version\\s+qc_status\\s+qc_message"/>\n+ </assert_contents>\n+ </output>\n+ <output name="tech_results.tab">\n+ <assert_contents>\n+ <has_text_matching expression="sample\\s+subtype\\s+qc_status\\s+qc_message"/>\n </assert_contents>\n </output>\n </test>\n@@ -143,10 +171,17 @@\n <param name="fastq_input2" value="SRR5646583_SMALL_2.fastq"/>\n <output name="results.tab">\n <assert_contents>\n- <!-- Verifying that the columns are as expected. -->\n- <has_text_matching expression="sample\\s+scheme\\s+subtype\\s+all_subtypes\\s+tiles_matching_subtype\\s+are_subtypes_consistent\\s+inconsistent_subtypes\\s+n_tiles_matching_all\\s+n_tiles_matching_all_total\\s+n_tiles_matching_positive\\s+n_tiles_matching_positive_total\\s+n_tiles_matching_subtype\\s+n_tiles_matching_subtype_total\\s+file_path"/>\n- <!-- Verifying that the output of running the test file is expected. This is done via REGEX because the name and path of the file outputted to results.tab changes each test. -->\n- <has_text_matching expression="(heidelberg)\\s+(2.2.1.1.1.1)\\s+(2;)\\s+(2.2;)\\s+(2.2.1;)\\s+(2.2.1.1;)\\s+(2.2.1.1.1;)\\s+(2.2.1.1.1.1)\\s+(1983064-2.2.1.1.1.1;)\\s+(4211912-2.2.1.1.1.1)\\s+(True)\\s+(202)\\s+(202)\\s+(20)\\s+(20)\\s+(2)\\s+(2)"/>\n+ <has_text_matching expression="sample\\s+scheme\\s+scheme_version\\s+subtype\\s+all_subtypes\\s+tiles_matching_subtype\\s+are_subtypes_consistent\\s+inconsistent_subtypes\\s+n_tiles_matching_all\\s+n_tiles_matching_all_expected\\s+n_tiles_matching_positive\\s+n_tiles_matching_positive_expected\\s+n_tiles_matching_subtype\\s+n_tiles_matching_subtype_expected\\s+file_path\\s+qc_status\\s+qc_message"/>\n+ </assert_contents>\n+ </output>\n+ <output name="match_results.tab">\n+ <assert_contents>\n+ <has_text_matching expression="tilename\\s+seq\\s+freq\\s+refposition\\s+subtype\\s+is_pos_tile\\s+is_kmer_freq_okay\\s+sample\\s+scheme\\s+scheme_version\\s+qc_status\\s+qc_message"/>\n+ </assert_contents>\n+ </output>\n+ <output name="tech_results.tab">\n+ <assert_contents>\n+ <has_text_matching expression="sample\\s+subtype\\s+qc_status\\s+qc_message"/>\n </assert_contents>\n </output>\n </test>\n' |