| Previous changeset 4:c0d08ba0c6ee (2018-01-26) Next changeset 6:5a42e475436e (2018-02-22) |
|
Commit message:
planemo upload for repository https://github.com/phac-nml/bio_hansel commit f9ecb9b31d5cace7e1a1ded13dd2e5eb8ef7759e-dirty |
|
modified:
bio_hansel.xml |
|
added:
test-data/match_results.tab test-data/results.tab test-data/tech_results.tab |
| b |
| diff -r c0d08ba0c6ee -r 6396d043667b bio_hansel.xml --- a/bio_hansel.xml Fri Jan 26 11:27:16 2018 -0500 +++ b/bio_hansel.xml Wed Feb 21 12:13:32 2018 -0500 |
| [ |
| @@ -1,29 +1,29 @@ -<tool id="bio_hansel" name="Bio Hansel" version="1.0.1"> +<tool id="bio_hansel" name="Bio Hansel" version="1.2.0"> <description>SNV Subtyping with genome assemblies or reads</description> <requirements> - <requirement type="package" version="1.1.3">bio_hansel</requirement> + <requirement type="package" version="1.2.0">bio_hansel</requirement> <requirement type="package" version="17.2.0">attrs</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ ## Preparing file input. #if $data_type.type == "paired": - ln -s '$data_type.fastq_input1' '$data_type.fastq_input1.name' && - ln -s '$data_type.fastq_input2' '$data_type.fastq_input2.name' && + ln -s '$data_type.fastq_input1' '$data_type.fastq_input1.name'.fastq && + ln -s '$data_type.fastq_input2' '$data_type.fastq_input2.name'.fastq && #elif $data_type.type == "collection": - ln -s '$data_type.fastq_input1.forward' '$data_type.fastq_input1.name'_1 && - ln -s '$data_type.fastq_input1.reverse' '$data_type.fastq_input1.name'_2 && + ln -s '$data_type.fastq_input1.forward' '$data_type.fastq_input1.name'_1.fastq && + ln -s '$data_type.fastq_input1.reverse' '$data_type.fastq_input1.name'_2.fastq && #elif $data_type.type == "single": #if $data_type.fastq_input1.is_of_type('fastqsanger') or $data_type.fastq_input1.is_of_type('fastq'): - ln -s '$data_type.fastq_input1' '$data_type.fastq_input1.name' && + ln -s '$data_type.fastq_input1' '$data_type.fastq_input1.name'.fastq && #end if #if $data_type.fastq_input1.is_of_type('fasta'): - ln -s '$data_type.fastq_input1' '$data_type.fastq_input1.name' && + ln -s '$data_type.fastq_input1' '$data_type.fastq_input1.name'.fasta && #end if #end if @@ -51,6 +51,10 @@ '$type_of_scheme.scheme_input.name' #end if + ## Use Json output + #if $dev_args.use_json == "yes": + --json + #end if #if $kmer_vals.kmer_min --min-kmer-freq $kmer_vals.kmer_min @@ -83,13 +87,20 @@ ## Entering the file inputs #if $data_type.type == "single": - '$data_type.fastq_input1.name' + + #if $data_type.fastq_input1.is_of_type('fastqsanger') or $data_type.fastq_input1.is_of_type('fastq'): + '$data_type.fastq_input1.name'.fastq + #end if + + #if $data_type.fastq_input1.is_of_type('fasta'): + '$data_type.fastq_input1.name'.fasta + #end if #elif $data_type.type =="collection": - -p '$data_type.fastq_input1.name'_1 '$data_type.fastq_input1.name'_2 + -p '$data_type.fastq_input1.name'_1.fastq '$data_type.fastq_input1.name'_2.fastq #elif $data_type.type =="paired": - -p '$data_type.fastq_input1.name' '$data_type.fastq_input2.name' + -p '$data_type.fastq_input1.name'.fastq '$data_type.fastq_input2.name'.fastq #end if @@ -137,11 +148,26 @@ <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}"/> <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}"/> </section> + <section name="dev_args" title="Developer Options" expanded="False"> + <param name="use_json" type="select" label="Enable JSON output" help="Use this option of you need json representations of analysis' details"> + <option value="no">no</option> + <option value="yes">yes</option> + </param> + </section> </inputs> <outputs> <data format="tabular" name="results.tab" from_work_dir="results.tab" label="results.tab"/> <data format="tabular" name="match_results.tab" from_work_dir="match_results.tab" label="match_results.tab"/> <data format="tabular" name="tech_results.tab" from_work_dir="tech_results.tab" label="tech_results.tab"/> + <data format="json" name="results.json" from_work_dir="results.tab.json" label="results.json"> + <filter>dev_args['use_json'] == "yes"</filter> + </data> + <data format="json" name="match_results.json" from_work_dir="match_results.tab.json" label="match_results.json"> + <filter>dev_args['use_json'] == "yes"</filter> + </data> + <data format="json" name="tech_results.json" from_work_dir="tech_results.tab.json" label="tech_results.json"> + <filter>dev_args['use_json'] == "yes"</filter> + </data> </outputs> <tests> <test> @@ -150,7 +176,7 @@ <param name="fastq_input1" value="SRR1002850_SMALL.fasta"/> <output name="results.tab"> <assert_contents> - <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"/> + <has_text_matching expression="sample\s+scheme\s+scheme_version\s+subtype\s+all_subtypes\s+tiles_matching_subtype\s+are_subtypes_consistent\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"/> </assert_contents> </output> <output name="match_results.tab"> @@ -171,7 +197,7 @@ <param name="fastq_input2" value="SRR5646583_SMALL_2.fastq"/> <output name="results.tab"> <assert_contents> - <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"/> + <has_text_matching expression="sample\s+scheme\s+scheme_version\s+subtype\s+all_subtypes\s+tiles_matching_subtype\s+are_subtypes_consistent\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"/> </assert_contents> </output> <output name="match_results.tab"> @@ -181,7 +207,7 @@ </output> <output name="tech_results.tab"> <assert_contents> - <has_text_matching expression="sample\s+subtype\s+qc_status\s+qc_message"/> + <has_text_matching expression="sample\s+subtype\s+avg_tile_coverage\s+qc_status\s+qc_message"/> </assert_contents> </output> </test> |
| b |
| diff -r c0d08ba0c6ee -r 6396d043667b test-data/match_results.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/match_results.tab Wed Feb 21 12:13:32 2018 -0500 |
| b |
| b'@@ -0,0 +1,203 @@\n+tilename\tseq\tis_revcomp\tcontig_id\tmatch_index\trefposition\tsubtype\tis_pos_tile\tsample\tfile_path\tscheme\tscheme_version\tqc_status\tqc_message\n+2154958-2.2.2.2.1.4\tGGCGCGCCACGGTTACTCCCCGGTGGTCAGCCG\tTrue\tNODE_1_length_726282_cov_40.4705_ID_1\t13732\t2154958\t2.2.2.2.1.4\tTrue\tSRR1002850_SMALL.fasta\t/tmp/tmpUDraZv/job_working_directory/000/4/working/SRR1002850_SMALL.fasta.fasta\theidelberg\t0.5.0\tPASS\t\n+negative2131791-2.2.3.1.3\tGCTGGGCGAAATGATGCAGTTCACCACTTGCTC\tTrue\tNODE_1_length_726282_cov_40.4705_ID_1\t36900\t2131791\t2.2.3.1.3\tFalse\tSRR1002850_SMALL.fasta\t/tmp/tmpUDraZv/job_working_directory/000/4/working/SRR1002850_SMALL.fasta.fasta\theidelberg\t0.5.0\tPASS\t\n+2069216-2.2.2\tATACTTAGGCTGTCAGTAACCCGTGAGGTAGTG\tTrue\tNODE_1_length_726282_cov_40.4705_ID_1\t99475\t2069216\t2.2.2\tTrue\tSRR1002850_SMALL.fasta\t/tmp/tmpUDraZv/job_working_directory/000/4/working/SRR1002850_SMALL.fasta.fasta\theidelberg\t0.5.0\tPASS\t\n+negative2048364-2.1\tGGTCGCGACAGGCCGAGCCAGAACAGGAAAAGC\tTrue\tNODE_1_length_726282_cov_40.4705_ID_1\t120327\t2048364\t2.1\tFalse\tSRR1002850_SMALL.fasta\t/tmp/tmpUDraZv/job_working_directory/000/4/working/SRR1002850_SMALL.fasta.fasta\theidelberg\t0.5.0\tPASS\t\n+negative2045923-2.1.3\tCGACATATTCCCGCACCGTGCCATGGCTCATCT\tTrue\tNODE_1_length_726282_cov_40.4705_ID_1\t122768\t2045923\t2.1.3\tFalse\tSRR1002850_SMALL.fasta\t/tmp/tmpUDraZv/job_working_directory/000/4/working/SRR1002850_SMALL.fasta.fasta\theidelberg\t0.5.0\tPASS\t\n+negative1983064-2.2.1.1.1.1\tTCCAGCATATCGCCCAGGCGACTGAACGCAGGC\tTrue\tNODE_1_length_726282_cov_40.4705_ID_1\t185627\t1983064\t2.2.1.1.1.1\tFalse\tSRR1002850_SMALL.fasta\t/tmp/tmpUDraZv/job_working_directory/000/4/working/SRR1002850_SMALL.fasta.fasta\theidelberg\t0.5.0\tPASS\t\n+negative1976727-2.1\tTACTTTATCTTTGTACTTATTCCACAATACGGA\tTrue\tNODE_1_length_726282_cov_40.4705_ID_1\t191964\t1976727\t2.1\tFalse\tSRR1002850_SMALL.fasta\t/tmp/tmpUDraZv/job_working_directory/000/4/working/SRR1002850_SMALL.fasta.fasta\theidelberg\t0.5.0\tPASS\t\n+negative1950957-2.2.2.2.2.2\tTTTCCTTGCCCTAATCGCGCCCTACGGCTGGTC\tTrue\tNODE_1_length_726282_cov_40.4705_ID_1\t217734\t1950957\t2.2.2.2.2.2\tFalse\tSRR1002850_SMALL.fasta\t/tmp/tmpUDraZv/job_working_directory/000/4/working/SRR1002850_SMALL.fasta.fasta\theidelberg\t0.5.0\tPASS\t\n+negative1910623-2.2.3.3\tGCTCCGATTTTTGCCTGATAATTATCCAATTAC\tTrue\tNODE_1_length_726282_cov_40.4705_ID_1\t258068\t1910623\t2.2.3.3\tFalse\tSRR1002850_SMALL.fasta\t/tmp/tmpUDraZv/job_working_directory/000/4/working/SRR1002850_SMALL.fasta.fasta\theidelberg\t0.5.0\tPASS\t\n+negative1856421-2.1.1.1\tGTTTGCGCAGCAGGCAGCCCCTGGCGAGCGGCT\tTrue\tNODE_1_length_726282_cov_40.4705_ID_1\t312270\t1856421\t2.1.1.1\tFalse\tSRR1002850_SMALL.fasta\t/tmp/tmpUDraZv/job_working_directory/000/4/working/SRR1002850_SMALL.fasta.fasta\theidelberg\t0.5.0\tPASS\t\n+negative1840959-2.2.2.2.7\tCACCATTGAGCCGGTAATAATGCCGACAAAGGC\tTrue\tNODE_1_length_726282_cov_40.4705_ID_1\t327846\t1840959\t2.2.2.2.7\tFalse\tSRR1002850_SMALL.fasta\t/tmp/tmpUDraZv/job_working_directory/000/4/working/SRR1002850_SMALL.fasta.fasta\theidelberg\t0.5.0\tPASS\t\n+negative1831783-2.2.2.1.2\tTTTTCCGGGCTTATCGGCAACGCTATTCTGGCC\tTrue\tNODE_1_length_726282_cov_40.4705_ID_1\t337022\t1831783\t2.2.2.1.2\tFalse\tSRR1002850_SMALL.fasta\t/tmp/tmpUDraZv/job_working_directory/000/4/working/SRR1002850_SMALL.fasta.fasta\theidelberg\t0.5.0\tPASS\t\n+negative1825773-2.2.2.2.2\tCATCCCGGTTCATAGCGGCTCCGCTACGCTAAA\tTrue\tNODE_1_length_726282_cov_40.4705_ID_1\t343032\t1825773\t2.2.2.2.2\tFalse\tSRR1002850_SMALL.fasta\t/tmp/tmpUDraZv/job_working_directory/000/4/working/SRR1002850_SMALL.fasta.fasta\theidelberg\t0.5.0\tPASS\t\n+negative1760974-2.2.3.1.3\tTCGCGATGCGCAGGTCGGAGAAATCGCGCTAAA\tTrue\tNODE_1_length_726282_cov_40.4705_ID_1\t407831\t1760974\t2.2.3.1.3\tFalse\tSRR1002850_SMALL.fasta\t/tmp/tmpUDraZv/job_working_directory/000/4/working/SRR1002850_SMALL.fasta.fasta\theidelberg\t0.5.0\tPASS\t\n+negative1697407-2.2.2.2.1.5\tACACTGCCCAGAATAAGCGACACACAGCGCGCC\tTrue\tNODE_1_length_726282_cov_40.4705_ID_1\t471398\t1697407\t2.2.2.2.1.5\tFalse\tSRR1002850_SMALL.fasta\t/tmp/tmpUDraZv/job_working_directory/000/4/working/SRR1002850_SMALL.fasta.fasta\thei'..b'L.fasta\t/tmp/tmpUDraZv/job_working_directory/000/4/working/SRR1002850_SMALL.fasta.fasta\theidelberg\t0.5.0\tPASS\t\n+negative3204925-2.2.3.1.5\tCTCGCTGGCAAGCAGTGCGGGTACTATCGGCGG\tFalse\tNODE_3_length_427905_cov_48.1477_ID_5\t175791\t3204925\t2.2.3.1.5\tFalse\tSRR1002850_SMALL.fasta\t/tmp/tmpUDraZv/job_working_directory/000/4/working/SRR1002850_SMALL.fasta.fasta\theidelberg\t0.5.0\tPASS\t\n+3212817-2.2.2.2\tCAAAACTACGAATACGACGCAGCGGGCGACCGT\tFalse\tNODE_3_length_427905_cov_48.1477_ID_5\t183683\t3212817\t2.2.2.2\tTrue\tSRR1002850_SMALL.fasta\t/tmp/tmpUDraZv/job_working_directory/000/4/working/SRR1002850_SMALL.fasta.fasta\theidelberg\t0.5.0\tPASS\t\n+negative3230678-2.2.2.1.1.1\tAGCGGTGCGCCAAACCACCCGGAATGATGAGTG\tFalse\tNODE_3_length_427905_cov_48.1477_ID_5\t201544\t3230678\t2.2.2.1.1.1\tFalse\tSRR1002850_SMALL.fasta\t/tmp/tmpUDraZv/job_working_directory/000/4/working/SRR1002850_SMALL.fasta.fasta\theidelberg\t0.5.0\tPASS\t\n+negative3233869-2.1.1.1.1\tCAGCGCTGGTATGTGGCTGCACCATCGTCATTA\tFalse\tNODE_3_length_427905_cov_48.1477_ID_5\t204735\t3233869\t2.1.1.1.1\tFalse\tSRR1002850_SMALL.fasta\t/tmp/tmpUDraZv/job_working_directory/000/4/working/SRR1002850_SMALL.fasta.fasta\theidelberg\t0.5.0\tPASS\t\n+negative3254229-2.2.3.1.3\tCGCCACCACGCGGTTAGCGTCACGCTGACATTC\tFalse\tNODE_3_length_427905_cov_48.1477_ID_5\t225095\t3254229\t2.2.3.1.3\tFalse\tSRR1002850_SMALL.fasta\t/tmp/tmpUDraZv/job_working_directory/000/4/working/SRR1002850_SMALL.fasta.fasta\theidelberg\t0.5.0\tPASS\t\n+negative3257074-2.2.1\tCGGCAACCAGACCGACTACGCCGCCAAGCAGAC\tFalse\tNODE_3_length_427905_cov_48.1477_ID_5\t227940\t3257074\t2.2.1\tFalse\tSRR1002850_SMALL.fasta\t/tmp/tmpUDraZv/job_working_directory/000/4/working/SRR1002850_SMALL.fasta.fasta\theidelberg\t0.5.0\tPASS\t\n+negative3264474-2.2.2.1.1.1\tAATGGCGCCGATCGTCGCCAGATAACCGTTGCC\tFalse\tNODE_3_length_427905_cov_48.1477_ID_5\t235340\t3264474\t2.2.2.1.1.1\tFalse\tSRR1002850_SMALL.fasta\t/tmp/tmpUDraZv/job_working_directory/000/4/working/SRR1002850_SMALL.fasta.fasta\theidelberg\t0.5.0\tPASS\t\n+negative3267927-2.2.2.2.2.1\tAAAGAGAAATATGATGCCAGGCTGATACATGAC\tFalse\tNODE_3_length_427905_cov_48.1477_ID_5\t238793\t3267927\t2.2.2.2.2.1\tFalse\tSRR1002850_SMALL.fasta\t/tmp/tmpUDraZv/job_working_directory/000/4/working/SRR1002850_SMALL.fasta.fasta\theidelberg\t0.5.0\tPASS\t\n+negative3278067-1.1\tTGTGAGTAAGTTGCGCGATATTCTGCTGGATTC\tFalse\tNODE_3_length_427905_cov_48.1477_ID_5\t248933\t3278067\t1.1\tFalse\tSRR1002850_SMALL.fasta\t/tmp/tmpUDraZv/job_working_directory/000/4/working/SRR1002850_SMALL.fasta.fasta\theidelberg\t0.5.0\tPASS\t\n+negative3299717-2.2.3.1.4\tATGCCGGACAGCAGGCGAAACTCGAACCGGATA\tFalse\tNODE_3_length_427905_cov_48.1477_ID_5\t270583\t3299717\t2.2.3.1.4\tFalse\tSRR1002850_SMALL.fasta\t/tmp/tmpUDraZv/job_working_directory/000/4/working/SRR1002850_SMALL.fasta.fasta\theidelberg\t0.5.0\tPASS\t\n+negative3305400-2.1.1.1\tCATCGTGAAGCAGAACAGACGCGCATTCTTGCT\tFalse\tNODE_3_length_427905_cov_48.1477_ID_5\t276266\t3305400\t2.1.1.1\tFalse\tSRR1002850_SMALL.fasta\t/tmp/tmpUDraZv/job_working_directory/000/4/working/SRR1002850_SMALL.fasta.fasta\theidelberg\t0.5.0\tPASS\t\n+3324813-2.2.2.2\tCAGATGAAGCGGGCGCAGGATAACTTCAAGGCC\tFalse\tNODE_3_length_427905_cov_48.1477_ID_5\t295679\t3324813\t2.2.2.2\tTrue\tSRR1002850_SMALL.fasta\t/tmp/tmpUDraZv/job_working_directory/000/4/working/SRR1002850_SMALL.fasta.fasta\theidelberg\t0.5.0\tPASS\t\n+negative3373069-2.2.2.2.1.1\tCTCTCCAGAAGATGAAGCCCGTGATGCGGCGCA\tFalse\tNODE_3_length_427905_cov_48.1477_ID_5\t344042\t3373069\t2.2.2.2.1.1\tFalse\tSRR1002850_SMALL.fasta\t/tmp/tmpUDraZv/job_working_directory/000/4/working/SRR1002850_SMALL.fasta.fasta\theidelberg\t0.5.0\tPASS\t\n+negative3408895-2.1.1\tACAGTAAAAACAGGATCTGCTGCGAGGCCAGAC\tFalse\tNODE_3_length_427905_cov_48.1477_ID_5\t379868\t3408895\t2.1.1\tFalse\tSRR1002850_SMALL.fasta\t/tmp/tmpUDraZv/job_working_directory/000/4/working/SRR1002850_SMALL.fasta.fasta\theidelberg\t0.5.0\tPASS\t\n+negative3436797-2.2.2.1.2\tATGCGGTATTCCTTGGCGTCGGCACCTATCAGT\tFalse\tNODE_3_length_427905_cov_48.1477_ID_5\t407770\t3436797\t2.2.2.1.2\tFalse\tSRR1002850_SMALL.fasta\t/tmp/tmpUDraZv/job_working_directory/000/4/working/SRR1002850_SMALL.fasta.fasta\theidelberg\t0.5.0\tPASS\t\n' |
| b |
| diff -r c0d08ba0c6ee -r 6396d043667b test-data/results.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/results.tab Wed Feb 21 12:13:32 2018 -0500 |
| b |
| @@ -0,0 +1,2 @@ +sample scheme scheme_version subtype all_subtypes tiles_matching_subtype are_subtypes_consistent n_tiles_matching_all n_tiles_matching_all_expected n_tiles_matching_positive n_tiles_matching_positive_expected n_tiles_matching_subtype n_tiles_matching_subtype_expected file_path qc_status qc_message +SRR1002850_SMALL.fasta heidelberg 0.5.0 2.2.2.2.1.4 2; 2.2; 2.2.2; 2.2.2.2; 2.2.2.2.1; 2.2.2.2.1.4 2154958-2.2.2.2.1.4; 1037658-2.2.2.2.1.4; 3785187-2.2.2.2.1.4 True 202 202 17 17 3 3 /tmp/tmpUDraZv/job_working_directory/000/4/working/SRR1002850_SMALL.fasta.fasta PASS |
| b |
| diff -r c0d08ba0c6ee -r 6396d043667b test-data/tech_results.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tech_results.tab Wed Feb 21 12:13:32 2018 -0500 |
| b |
| @@ -0,0 +1,2 @@ +sample subtype qc_status qc_message +SRR1002850_SMALL.fasta 2.2.2.2.1.4 PASS |