Mercurial > repos > prog > isa2w4m
changeset 1:1facef3ba64a draft default tip
"planemo upload commit 9683b1655539660ed1e983783a72a5c3016238bd-dirty"
| author | prog |
|---|---|
| date | Wed, 27 Apr 2022 16:38:56 +0000 |
| parents | 1883d5274962 |
| children | |
| files | README.md isa2w4m.xml test-data/MTBLS174-w4m-sample-metadata.tsv test-data/MTBLS174-w4m-sample-variable-matrix.tsv test-data/MTBLS174-w4m-variable-metadata.tsv test-data/MTBLS174.zip test-data/MTBLS719.zip |
| diffstat | 7 files changed, 78 insertions(+), 10 deletions(-) [+] |
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--- a/README.md Wed Jan 08 09:56:00 2020 -0500 +++ b/README.md Wed Apr 27 16:38:56 2022 +0000 @@ -6,6 +6,10 @@ ## Updates +### 1.1.2 + + * Changed double quotes in single quotes inside XML Command tag. + ### 1.1.1 * Correct planemo test.
--- a/isa2w4m.xml Wed Jan 08 09:56:00 2020 -0500 +++ b/isa2w4m.xml Wed Apr 27 16:38:56 2022 +0000 @@ -1,10 +1,11 @@ <!-- vi: se fdm=marker : --> -<tool id="isa2w4m" name="ISA to W4M" version="1.1.1"> +<tool id="isa2w4m" name="ISA to W4M" version="1.1.3"> <description>Convert ISA data type into W4M format</description> <requirements> - <requirement type="package" version="0.10.3">isatools</requirement> + <requirement type="package" version="1.2.5">pandas</requirement> + <requirement type="package" version="0.12.2">isatools</requirement> </requirements> <!-- Command {{{1 --> @@ -13,29 +14,33 @@ ## @@@BEGIN_CHEETAH@@@ $__tool_directory__/isa2w4m.py - -i "$isa.extra_files_path" - -s "$w4m_sample_metadata" - -v "$w4m_variable_metadata" - -m "$w4m_data_matrix" + -i '$isa.extra_files_path' + -s '$w4m_sample_metadata' + -v '$w4m_variable_metadata' + -m '$w4m_data_matrix' ## Choose study to output #if $study: - -n "$study" + -n '$study' #end if ## Choose assay to output #if $assay: - -f "$assay" + -f '$assay' #end if ## Filtering #if $sample_na_filtering: - -S "$sample_na_filtering" + -S '$sample_na_filtering' #end if #if $variable_na_filtering: - -V "$variable_na_filtering" + -V '$variable_na_filtering' #end if + ## Redirect stderr to stdout otherwise Galaxy thinks the tool fails if + ## it sees just one character on stderr. + 2>&1 + ## @@@END_CHEETAH@@@ ]]></command> @@ -65,6 +70,12 @@ <output name="w4m_sample_metadata" file="MTBLS30-w4m-sample-metadata.tsv"/> <output name="w4m_data_matrix" file="MTBLS30-w4m-sample-variable-matrix.tsv"/> </test> + <test> + <param name="isa" value="MTBLS174.zip" ftype="isa-tab"/> + <output name="w4m_variable_metadata" file="MTBLS174-w4m-variable-metadata.tsv"/> + <output name="w4m_sample_metadata" file="MTBLS174-w4m-sample-metadata.tsv"/> + <output name="w4m_data_matrix" file="MTBLS174-w4m-sample-variable-matrix.tsv"/> + </test> </tests> <!-- Help {{{1 -->
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/MTBLS174-w4m-sample-metadata.tsv Wed Apr 27 16:38:56 2022 +0000 @@ -0,0 +1,19 @@ +"sample.name" "Sample.Name" "Protocol.REF_x" "Parameter.Value.Extraction.Method." "Extract.Name" "Protocol.REF.1" "Parameter.Value.NMR.tube.type." "Term.Source.REF_x" "Term.Accession.Number_x" "Parameter.Value.Solvent." "Term.Source.REF.1_x" "Term.Accession.Number.1_x" "Parameter.Value.Sample.pH." "Parameter.Value.Temperature." "Unit_x" "Term.Source.REF.2_x" "Term.Accession.Number.2_x" "Labeled.Extract.Name" "Label" "Term.Source.REF.3_x" "Term.Accession.Number.3_x" "Protocol.REF.2" "Parameter.Value.Instrument." "Term.Source.REF.4_x" "Term.Accession.Number.4_x" "Parameter.Value.NMR.Probe." "Term.Source.REF.5_x" "Term.Accession.Number.5_x" "Parameter.Value.Number.of.transients." "Parameter.Value.Pulse.sequence.name." "Parameter.Value.Magnetic.field.strength." "Unit.1_x" "Term.Source.REF.6_x" "Term.Accession.Number.6_x" "Acquisition.Parameter.Data.File" "Protocol.REF.3" "NMR.Assay.Name" "Free.Induction.Decay.Data.File" "Protocol.REF.4" "Normalization.Name" "Derived.Spectral.Data.File" "Protocol.REF.5" "Data.Transformation.Name" "Metabolite.Assignment.File" "Source.Name" "Characteristics.Organism." "Term.Source.REF_y" "Term.Accession.Number_y" "Characteristics.Organism.part." "Term.Source.REF.1_y" "Term.Accession.Number.1_y" "Protocol.REF_y" "Factor.Value.Metabolic.syndrome." "Term.Source.REF.2_y" "Term.Accession.Number.2_y" "Factor.Value.Gender." "Term.Source.REF.3_y" "Term.Accession.Number.3_y" "Factor.Value.BMI." "Unit_y" "Term.Source.REF.4_y" "Term.Accession.Number.4_y" "Factor.Value.Age." "Unit.1_y" "Term.Source.REF.5_y" "Term.Accession.Number.5_y" "Factor.Value.Steatosis.." "Unit.2" "Term.Source.REF.6_y" "Term.Accession.Number.6_y" +"SH0004" "SH0004" "Extraction" "NA" "NA" "NMR sample" "4.25 mm (Bruker BioSpin)" "NA" "NA" "0.07 M phosphate buffered D2O" "NA" "NA" "7.4" "313.4" "kelvin" "UO" "http://purl.obolibrary.org/obo/UO_0000012" "NA" "hydrogen molecular entity" "CHEBI" "http://purl.obolibrary.org/obo/CHEBI_33608" "NMR spectroscopy" "Bruker 600 MHz spectrometer" "NA" "NA" "5 mm CPTCI" "NA" "NA" "64" "1D CPMG with presaturation (cpmgpr1d)" "14.1" "Tesla" "NCIT" "NA" "NA" "NMR assay" "SH0004" "1.zip" "Data transformation" "SH0004" "NA" "Metabolite identification" "SH0004" "m_hna_fld_metabolite_profiling_NMR_spectroscopy_v2_maf.tsv" "H0004" "Homo sapiens" "NCBITAXON" "http://purl.bioontology.org/ontology/NCBITAXON/9606" "blood serum" "BTO" "http://purl.obolibrary.org/obo/BTO_0000133" "Sample collection" "Human non-alcoholic fatty liver disease" "NA" "NA" "Female Gender" "NCIT" "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C46110" "47" "kilogram per 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/MTBLS174-w4m-variable-metadata.tsv Wed Apr 27 16:38:56 2022 +0000 @@ -0,0 +1,17 @@ +"variable.name" "database_identifier" "chemical_formula" "smiles" "inchi" "metabolite_identification" "chemical_shift" "multiplicity" "taxid" "species" "database" "database_version" "reliability" "uri" "search_engine" "search_engine_score" "smallmolecule_abundance_sub" "smallmolecule_abundance_stdev_sub" "smallmolecule_abundance_std_error_sub" +"X" "CHEBI:16977" "C3H7NO2" "C[C@H](N)C(O)=O" "InChI=1S/C3H7NO2/c1-2(4)3(5)6/h2H,4H2,1H3,(H,5,6)/t2-/m0/s1" "L-alanine" "NA" "NA" "NCBITAXON:http://purl.bioontology.org/ontology/NCBITAXON/9606" "Homo sapiens" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" +"X.1" "CHEBI:15366" "C2H4O2" "CC(O)=O" "InChI=1S/C2H4O2/c1-2(3)4/h1H3,(H,3,4)" "Acetate" "NA" "NA" "NCBITAXON:http://purl.bioontology.org/ontology/NCBITAXON/9606" "Homo sapiens" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" +"X.2" "CHEBI:28300" "C5H10N2O3" "NC(CCC(N)=O)C(O)=O" "InChI=1S/C5H10N2O3/c6-3(5(9)10)1-2-4(7)8/h3H,1-2,6H2,(H2,7,8)(H,9,10)" "Glutamine" "NA" "NA" "NCBITAXON:http://purl.bioontology.org/ontology/NCBITAXON/9606" "Homo sapiens" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" +"X.3" "CHEBI:30751" "CH2O2" "[H]C(O)=O" "InChI=1S/CH2O2/c2-1-3/h1H,(H,2,3)" "Formate" "NA" "NA" "NCBITAXON:http://purl.bioontology.org/ontology/NCBITAXON/9606" "Homo sapiens" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" +"X.4" "CHEBI:17234" "C6H12O6" "NA" "NA" "Glucose" "NA" "NA" "NCBITAXON:http://purl.bioontology.org/ontology/NCBITAXON/9606" "Homo sapiens" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" +"X.5" "CHEBI:78320" "C3H6O3" "CC(O)C(O)=O" "InChI=1S/C3H6O3/c1-2(4)3(5)6/h2,4H,1H3,(H,5,6)" "Lactate" "NA" "NA" "NCBITAXON:http://purl.bioontology.org/ontology/NCBITAXON/9606" "Homo sapiens" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" +"X.6" "CHEBI:28044" "C9H11NO2" "NC(Cc1ccccc1)C(O)=O" "InChI=1S/C9H11NO2/c10-8(9(11)12)6-7-4-2-1-3-5-7/h1-5,8H,6,10H2,(H,11,12)" "Phenylalanine" "NA" "NA" "NCBITAXON:http://purl.bioontology.org/ontology/NCBITAXON/9606" "Homo sapiens" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" +"X.7" "CHEBI:18186" "C9H11NO3" "NC(Cc1ccc(O)cc1)C(O)=O" "InChI=1S/C9H11NO3/c10-8(9(12)13)5-6-1-3-7(11)4-2-6/h1-4,8,11H,5,10H2,(H,12,13)" "Tyrosine" "NA" "NA" "NCBITAXON:http://purl.bioontology.org/ontology/NCBITAXON/9606" "Homo sapiens" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" +"X.8" "CHEBI:25017" "C6H13NO2" "CC(C)CC(N)C(O)=O" "InChI=1S/C6H13NO2/c1-4(2)3-5(7)6(8)9/h4-5H,3,7H2,1-2H3,(H,8,9)" "Leucine" "NA" "NA" "NCBITAXON:http://purl.bioontology.org/ontology/NCBITAXON/9606" "Homo sapiens" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" +"X.9" "CHEBI:27266" "C5H11NO2" "CC(C)C(N)C(O)=O" "InChI=1S/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)" "Valine" "NA" "NA" "NCBITAXON:http://purl.bioontology.org/ontology/NCBITAXON/9606" "Homo sapiens" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" +"X.10" "CHEBI:15971" "C6H9N3O2" "N[C@@H](Cc1c[nH]cn1)C(O)=O" "InChI=1S/C6H9N3O2/c7-5(6(10)11)1-4-2-8-3-9-4/h2-3,5H,1,7H2,(H,8,9)(H,10,11)/t5-/m0/s1" "L-histidine" "NA" "NA" "NCBITAXON:http://purl.bioontology.org/ontology/NCBITAXON/9606" "Homo sapiens" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" +"X.11" "CHEBI:16919" "C4H9N3O2" "CN(CC(O)=O)C(N)=N" "InChI=1S/C4H9N3O2/c1-7(4(5)6)2-3(8)9/h2H2,1H3,(H3,5,6)(H,8,9)" "Creatine" "NA" "NA" "NCBITAXON:http://purl.bioontology.org/ontology/NCBITAXON/9606" "Homo sapiens" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" +"X.12" "CHEBI:16737" "C4H7N3O" "CN1CC(=O)NC1=N" "InChI=1S/C4H7N3O/c1-7-2-3(8)6-4(7)5/h2H2,1H3,(H2,5,6,8)" "Creatinine" "NA" "NA" "NCBITAXON:http://purl.bioontology.org/ontology/NCBITAXON/9606" "Homo sapiens" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" +"X.13" "CHEBI:28831" "C3H8O" "CCCO" "InChI=1S/C3H8O/c1-2-3-4/h4H,2-3H2,1H3" "Propanol" "NA" "NA" "NCBITAXON:http://purl.bioontology.org/ontology/NCBITAXON/9606" "Homo sapiens" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" +"X.14" "CHEBI:16236" "C2H6O" "CCO" "InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3" "Ethanol" "NA" "NA" "NCBITAXON:http://purl.bioontology.org/ontology/NCBITAXON/9606" "Homo sapiens" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" +"X.15" "CHEBI:20067" "C4H8O3" "CC(O)CC(O)=O" "InChI=1S/C4H8O3/c1-3(5)2-4(6)7/h3,5H,2H2,1H3,(H,6,7)" "3-hydroxybutyrate" "NA" "NA" "NCBITAXON:http://purl.bioontology.org/ontology/NCBITAXON/9606" "Homo sapiens" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA" "NA"