Mercurial > repos > iuc > hamronize_summarize
changeset 5:88045b4d5597 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
| author | iuc |
|---|---|
| date | Tue, 05 Mar 2024 19:47:21 +0000 |
| parents | f8bcc852f6b3 |
| children | |
| files | hamronize_summarize.xml macros.xml test-data/mykrobe/mykrobe.json |
| diffstat | 3 files changed, 354 insertions(+), 60 deletions(-) [+] |
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--- a/hamronize_summarize.xml Fri Feb 09 21:27:25 2024 +0000 +++ b/hamronize_summarize.xml Tue Mar 05 19:47:21 2024 +0000 @@ -1,5 +1,5 @@ -<tool id="hamronize_summarize" name="hamronize: summarize" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@"> - <description> harmorization reports</description> +<tool id="hamronize_summarize" name="hamronize summarize:" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> + <description>Concatenate and summarize AMR detection reports</description> <macros> <import>macros.xml</import> </macros> @@ -7,45 +7,35 @@ <expand macro="requirements" /> <expand macro="version_command" /> <command detect_errors="exit_code"><![CDATA[ - #for $counter, $report in enumerate($reports): - #if $report.is_of_type('tsv', 'tabular'): - #set $ext = 'tsv' - #elif $report.is_of_type('json'): - #set $ext = 'json' - #end if - ln -s '$report' ./report_${counter}.${ext} && - #end for +#for $counter, $report in enumerate($reports): + #if $report.is_of_type('tsv', 'tabular'): + #set $ext = 'tsv' + #elif $report.is_of_type('json'): + #set $ext = 'json' + #end if + ln -s '$report' 'report_${counter}.${ext}' && +#end for - hamronize summarize - --summary_type $summary_type - #if $summary_type == "tsv" - --output output.tsv - #elif $summary_type == "json" - --output output.json - #else - --output output.html - #end if - ./report_* - ]]> </command> - +hamronize + summarize + --summary_type '$summary_type' + --output '$output' + report_* +]]></command> <inputs> <param name="reports" type="data" multiple="true" format="tabular,json" label="Report files"/> - <param name="summary_type" type="select" label="Output format" multiple="false"> - <option value="tsv">tsv</option> - <option value="json">json</option> - <option value="interactive">interactive</option> + <param argument="--summary_type" type="select" label="Output format" multiple="false"> + <option value="tsv">Tabular</option> + <option value="json">JSON</option> + <option value="interactive">Interactive HTML</option> </param> </inputs> - <outputs> - <data format="tabular" name="output_tsv" label="${tool.name} on ${on_string}: Table" from_work_dir="output.tsv"> - <filter>summary_type == "tsv"</filter> - </data> - <data format="json" name="output_json" label="${tool.name} on ${on_string}: JSON" from_work_dir="output.json"> - <filter>summary_type == "json"</filter> - </data> - <data format="html" name="output_html" label="${tool.name} on ${on_string}: Interactive" from_work_dir="output.html"> - <filter>summary_type == "interactive"</filter> + <data name="output" format="tabular" label="${tool.name} on ${on_string}: Concatenated and summarized reports" from_work_dir="output.tsv"> + <change_format> + <when input="summary_type" value="json" format="json"/> + <when input="summary_type" value="interactive" format="html"/> + </change_format> </data> </outputs> <tests> @@ -53,30 +43,49 @@ <test expect_num_outputs="1"> <param name="reports" value="hamronized_abricate.tsv,hamronized_abricate.json,hamronized_ariba.tsv,hamronized_ariba.json,hamronized_rgi.tsv,hamronized_rgi.json" /> <param name="summary_type" value="tsv" /> - <output name="output_tsv" ftype="tabular" file="summary.tsv" /> + <output name="output" ftype="tabular"> + <assert_contents> + <has_n_lines n="155"/> + <has_n_columns n="37"/> + <has_text text="GCF_010120755.1_ASM1012075v1_genomic" /> + <has_text text="ariba_report" /> + <has_text text="rgi_report" /> + </assert_contents> + </output> </test> <!-- json output --> <test expect_num_outputs="1"> <param name="reports" value="hamronized_abricate.tsv,hamronized_abricate.json,hamronized_ariba.tsv,hamronized_ariba.json,hamronized_rgi.tsv,hamronized_rgi.json" /> <param name="summary_type" value="json" /> - <output name="output_json" ftype="json"> + <output name="output" ftype="json"> <assert_contents> <has_text text="GCF_010120755.1_ASM1012075v1_genomic" /> - <has_text text="H_NS.3000676.BA000007.3.1737690_1738104.5476" /> - <has_text text="NODE_9_length_203843_cov_42.4911_20" /> + <has_text text="ariba_report" /> + <has_text text="rgi_report" /> + </assert_contents> + </output> + </test> + <!-- html output --> + <test expect_num_outputs="1"> + <param name="reports" value="hamronized_abricate.tsv,hamronized_abricate.json,hamronized_ariba.tsv,hamronized_ariba.json,hamronized_rgi.tsv,hamronized_rgi.json" /> + <param name="summary_type" value="interactive" /> + <output name="output" ftype="html"> + <assert_contents> + <has_text text="GCF_010120755.1_ASM1012075v1_genomic" /> + <has_text text="ariba_report" /> + <has_text text="rgi_report" /> </assert_contents> </output> </test> </tests> - <help> - <![CDATA[ - **What it does** - This tool will take a list of report and create single sorted report in the specified format - just containing the unique entries across input reports. It can handle mixed json and tsv hamronized report formats - **Inputs** - A list of hamronize reports - - ]]> - </help> + <help><![CDATA[ +**What it does** + +This tool will take a list of report and create single sorted report in the specified format +just containing the unique entries across input reports. It can handle mixed json and tsv hamronized report formats + +**Inputs** +A list of hamronize reports + ]]></help> <expand macro="citations"/> </tool>
--- a/macros.xml Fri Feb 09 21:27:25 2024 +0000 +++ b/macros.xml Tue Mar 05 19:47:21 2024 +0000 @@ -1,6 +1,6 @@ <macros> - <token name="@TOOL_VERSION@">1.0.3</token> - <token name="@PROFILE@">20.05</token> + <token name="@TOOL_VERSION@">1.1.4</token> + <token name="@PROFILE@">23.1</token> <xml name="bio_tools"> <xrefs> <xref type="bio.tools">hamronization</xref> @@ -11,20 +11,36 @@ <requirement type="package" version="@TOOL_VERSION@">hamronization</requirement> </requirements> </xml> - <xml name="input_file_name"> - <param name="input_file_name" type="text" label="Input file name" help="Sample name which was scanned with the tool"></param> + <xml name="version_command"> + <version_command>hamronize --version</version_command> + </xml> + <xml name="report" token_format="tabular" token_label="Report" > + <param argument="report" type="data" format="@FORMAT@" label="@LABEL@"/> </xml> - <xml name="reference_database_id"> - <param name="reference_database_id" type="text" label="Reference database ID" help="String containing the reference_database_id of this tool"></param> + <xml name="input_file_name"> + <param argument="--input_file_name" type="text" label="Sample name" help="If not provided, the input dataset will be taken"/> + </xml> + <xml name="analysis_software_version" token_software=""> + <param argument="--analysis_software_version" type="text" label="@SOFTWARE@ version"/> </xml> <xml name="reference_database_version"> - <param name="reference_database_version" type="text" label="Reference database version"></param> + <param name="reference_database_version" type="text" label="Reference database version"/> </xml> - <xml name="analysis_software_version"> - <param name="analysis_software_version" type="text" label="Analysis software version"></param> + <xml name="origin" token_software=""> + <conditional name="origin"> + <param name="origin" type="select" label="Input generated within Galaxy on this server without leaving it?"> + <option value="true" selected="true">Yes</option> + <option value="false">No</option> + </param> + <when value="true"/> + <when value="false"> + <expand macro="analysis_software_version" software="@SOFTWARE@" /> + </when> + </conditional> + <expand macro="reference_database_version"/> </xml> - <xml name="version_command"> - <version_command>hamronize --version</version_command> + <xml name="reference_database_name" token_software=""> + <param name="reference_database_name" type="text" label="Reference database name for @SOFTWARE@"/> </xml> <xml name="citations"> <citations>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mykrobe/mykrobe.json Tue Mar 05 19:47:21 2024 +0000 @@ -0,0 +1,269 @@ +{ + "SRR6916544": { + "susceptibility": { + "Rifampicin": { + "predict": "r", + "called_by": { + "rpoB_S450L-TCG761154TTG": { + "variant": null, + "genotype": [ + 0, + 1 + ], + "genotype_likelihoods": [ + -3594.140082249598, + -136.57739012799902, + -2127.6812715680494 + ], + "info": { + "coverage": { + "reference": { + "percent_coverage": 100.0, + "median_depth": 40, + "min_non_zero_depth": 32, + "kmer_count": 796, + "klen": 21 + }, + "alternate": { + "percent_coverage": 100.0, + "median_depth": 60, + "min_non_zero_depth": 58, + "kmer_count": 1150, + "klen": 20 + } + }, + "expected_depths": [ + 124 + ], + "contamination_depths": [], + "filter": [], + "conf": 3458 + }, + "_cls": "Call.VariantCall" + } + } + } + }, + "phylogenetics": { + "phylo_group": { + "Mycobacterium_tuberculosis_complex": { + "percent_coverage": 99.681, + "median_depth": 124 + } + }, + "sub_complex": { + "Unknown": { + "percent_coverage": -1, + "median_depth": -1 + } + }, + "species": { + "Mycobacterium_tuberculosis": { + "percent_coverage": 98.804, + "median_depth": 121 + } + }, + "lineage": { + "lineage": [ + "lineage2.2.10", + "lineage3" + ], + "calls_summary": { + "lineage2.2.10": { + "good_nodes": 3, + "tree_depth": 3, + "genotypes": { + "lineage2": 0.5, + "lineage2.2": 0.5, + "lineage2.2.10": 0.5 + } + }, + "lineage3": { + "good_nodes": 1, + "tree_depth": 1, + "genotypes": { + "lineage3": 0.5 + } + } + }, + "calls": { + "lineage2.2.10": { + "lineage2": { + "G497491A": { + "variant": "ref-G497491A?var_name=G497491A&num_alts=1&ref=NC_000962.3&enum=0&gene=NA&mut=G497491A", + "genotype": [ + 0, + 1 + ], + "genotype_likelihoods": [ + -4852.294042193726, + -68.00214340670391, + -4045.7527933854217 + ], + "info": { + "coverage": { + "reference": { + "percent_coverage": 100.0, + "median_depth": 76, + "min_non_zero_depth": 70, + "kmer_count": 1498, + "klen": 21 + }, + "alternate": { + "percent_coverage": 100.0, + "median_depth": 85, + "min_non_zero_depth": 82, + "kmer_count": 1695, + "klen": 21 + } + }, + "expected_depths": [ + 124 + ], + "contamination_depths": [], + "filter": [], + "conf": 4784 + }, + "_cls": "Call.VariantCall" + } + }, + "lineage2.2": { + "G2505085A": { + "variant": "ref-G2505085A?var_name=G2505085A&num_alts=2&ref=NC_000962.3&enum=0&gene=NA&mut=G2505085A", + "genotype": [ + 0, + 1 + ], + "genotype_likelihoods": [ + -3967.5854789566783, + -20.859193826341652, + -3054.5971617777313 + ], + "info": { + "coverage": { + "reference": { + "percent_coverage": 100.0, + "median_depth": 58, + "min_non_zero_depth": 56, + "kmer_count": 1160, + "klen": 21 + }, + "alternate": { + "percent_coverage": 100.0, + "median_depth": 69, + "min_non_zero_depth": 64, + "kmer_count": 1383, + "klen": 21 + } + }, + "expected_depths": [ + 124 + ], + "contamination_depths": [], + "filter": [], + "conf": 3947 + }, + "_cls": "Call.VariantCall" + } + }, + "lineage2.2.10": { + "G1364706A": { + "variant": "ref-G1364706A?var_name=G1364706A&num_alts=2&ref=NC_000962.3&enum=0&gene=NA&mut=G1364706A", + "genotype": [ + 0, + 1 + ], + "genotype_likelihoods": [ + -2360.5217287767423, + -145.4041778818164, + -3052.427673185898 + ], + "info": { + "coverage": { + "reference": { + "percent_coverage": 100.0, + "median_depth": 51, + "min_non_zero_depth": 47, + "kmer_count": 1017, + "klen": 21 + }, + "alternate": { + "percent_coverage": 100.0, + "median_depth": 42, + "min_non_zero_depth": 42, + "kmer_count": 848, + "klen": 21 + } + }, + "expected_depths": [ + 124 + ], + "contamination_depths": [], + "filter": [], + "conf": 2215 + }, + "_cls": "Call.VariantCall" + } + } + }, + "lineage3": { + "lineage3": { + "C3273107A": { + "variant": "ref-C3273107A?var_name=C3273107A&num_alts=1&ref=NC_000962.3&enum=0&gene=NA&mut=C3273107A", + "genotype": [ + 0, + 1 + ], + "genotype_likelihoods": [ + -3093.863597972382, + -19.52878016336399, + -3761.204834296007 + ], + "info": { + "coverage": { + "reference": { + "percent_coverage": 100.0, + "median_depth": 66, + "min_non_zero_depth": 64, + "kmer_count": 1323, + "klen": 21 + }, + "alternate": { + "percent_coverage": 100.0, + "median_depth": 58, + "min_non_zero_depth": 54, + "kmer_count": 1160, + "klen": 21 + } + }, + "expected_depths": [ + 124 + ], + "contamination_depths": [], + "filter": [], + "conf": 3074 + }, + "_cls": "Call.VariantCall" + } + } + } + } + } + }, + "kmer": 21, + "probe_sets": [ + "/home/pvh/miniconda3/envs/mykrobe/lib/python3.9/site-packages/mykrobe/data/tb/tb-species-170421.fasta.gz", + "/home/pvh/miniconda3/envs/mykrobe/lib/python3.9/site-packages/mykrobe/data/tb/tb-hunt-probe-set-jan-03-2019.fasta.gz", + "/home/pvh/miniconda3/envs/mykrobe/lib/python3.9/site-packages/mykrobe/data/tb/tb.lineage.20200930.probes.fa.gz" + ], + "files": [ + "../SRR6916544_1.fastq.gz", + "../SRR6916544_2.fastq.gz" + ], + "version": { + "mykrobe-predictor": "v0.10.0", + "mykrobe-atlas": "v0.10.0" + }, + "genotype_model": "kmer_count" + } +} \ No newline at end of file