| Previous changeset 18:7068f48d0ef9 (2020-06-08) Next changeset 20:964579f93c54 (2020-07-01) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 1e2492fa4557ddc6ffefc16b249ed9ef0207d5e1" |
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modified:
fasterq_dump.xml fastq_dump.xml sam_dump.xml sra_macros.xml |
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added:
test-data/SRR11953971_1.fastq.gz test-data/SRR11953971_2.fastq.gz test-data/sra_manifest.tabular |
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| diff -r 7068f48d0ef9 -r 248f85ff0733 fasterq_dump.xml --- a/fasterq_dump.xml Mon Jun 08 05:49:21 2020 -0400 +++ b/fasterq_dump.xml Tue Jun 23 17:18:45 2020 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="fasterq_dump" name="Faster Download and Extract Reads in FASTQ" version="@VERSION@+galaxy0" profile="18.01"> +<tool id="fasterq_dump" name="Faster Download and Extract Reads in FASTQ" version="@VERSION@+galaxy1" profile="18.01"> <description>format from NCBI SRA</description> <macros> <import>sra_macros.xml</import> @@ -169,6 +169,28 @@ <element name="SRR002702" file="SRR002702_2.fastq.gz" ftype="fastqsanger.gz" decompress="True"/> </output_collection> </test> + <test> + <param name="input_select" value="file_list"/> + <param name="file_list" value="sra_manifest.tabular" ftype="sra_manifest.tabular"/> + <output_collection name="list_paired" type="list:paired"> + <element name="SRR11857975"> + <element name="forward" file="SRR11857975_1.fastq.gz" decompress="True"> + </element> + <element name="reverse" file="SRR11857975_2.fastq.gz" decompress="True"> + </element> + </element> + </output_collection> + </test> + <test> + <param name="input_select" value="file_list"/> + <param name="file_list" value="sra_manifest.tabular" ftype="sra_manifest.tabular"/> + <output_collection name="list_paired" type="list:paired"> + <element name="SRR11953971"> + <element name="forward" file="SRR11953971_1.fastq.gz" decompress="True"/> + <element name="reverse" file="SRR11953971_2.fastq.gz" decompress="True"/> + </element> + </output_collection> + </test> </tests> <help><![CDATA[ **What it does?** |
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| diff -r 7068f48d0ef9 -r 248f85ff0733 fastq_dump.xml --- a/fastq_dump.xml Mon Jun 08 05:49:21 2020 -0400 +++ b/fastq_dump.xml Tue Jun 23 17:18:45 2020 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="fastq_dump" name="Download and Extract Reads in FASTA/Q" version="@VERSION@+galaxy0" profile="18.01"> +<tool id="fastq_dump" name="Download and Extract Reads in FASTA/Q" version="@VERSION@+galaxy1" profile="18.01"> <description>format from NCBI SRA</description> <macros> <import>sra_macros.xml</import> |
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| diff -r 7068f48d0ef9 -r 248f85ff0733 sam_dump.xml --- a/sam_dump.xml Mon Jun 08 05:49:21 2020 -0400 +++ b/sam_dump.xml Tue Jun 23 17:18:45 2020 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="sam_dump" name="Download and Extract Reads in BAM" version="@VERSION@+galaxy0" profile="18.01"> +<tool id="sam_dump" name="Download and Extract Reads in BAM" version="@VERSION@+galaxy1" profile="18.01"> <description>format from NCBI SRA</description> <macros> <import>sra_macros.xml</import> |
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| diff -r 7068f48d0ef9 -r 248f85ff0733 sra_macros.xml --- a/sra_macros.xml Mon Jun 08 05:49:21 2020 -0400 +++ b/sra_macros.xml Tue Jun 23 17:18:45 2020 -0400 |
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| @@ -19,7 +19,13 @@ ]]></token> <token name="@SET_ACCESSIONS@"><![CDATA[ #if $input.input_select=="file_list": - for acc in `@ACCESSIONS_FROM_FILE@ '$input.file_list'` ; + #if $input.file_list.is_of_type('sra_manifest.tabular'): + #set $column = $input.file_list.unsanitized.metadata.column_names.index('Run') + 1 + cut -f $column '$input.file_list'| tail -n +2 > "manifest" && + #else + ln -s '$input.file_list' > manifest && + #end if + for acc in `@ACCESSIONS_FROM_FILE@ manifest` ; do ( #elif $input.input_select=="accession_number": acc='${input.accession}' && [ ""\$acc" =~ ^[E|S|D]RR[0-9]{1,}$" ] && ( |
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| diff -r 7068f48d0ef9 -r 248f85ff0733 test-data/SRR11953971_1.fastq.gz |
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| Binary file test-data/SRR11953971_1.fastq.gz has changed |
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| diff -r 7068f48d0ef9 -r 248f85ff0733 test-data/SRR11953971_2.fastq.gz |
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| Binary file test-data/SRR11953971_2.fastq.gz has changed |
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| diff -r 7068f48d0ef9 -r 248f85ff0733 test-data/sra_manifest.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sra_manifest.tabular Tue Jun 23 17:18:45 2020 -0400 |
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| @@ -0,0 +1,2 @@ +Run Assay Type BioProject BioSample Center Name Consent DATASTORE filetype DATASTORE provider DATASTORE region Experiment Instrument LibraryLayout LibrarySelection LibrarySource Organism Platform Sample Name SRA Study Bytes ReleaseDate Library Name Collection_Date isolate AvgSpotLen Bases BioSampleModel Host geo_loc_name_country geo_loc_name_country_continent geo_loc_name host_disease collected_by isolation_source lat_lon host_sex passage_history strain host_age host_subject_id ENA-FIRST-PUBLIC (run) ENA-FIRST-PUBLIC ENA-LAST-UPDATE (run) ENA-LAST-UPDATE geographic_location_(country_and/or_sea) host_health_state collecting_institution collector_name geographic_location_(region_and_locality) host_common_name host_scientific_name gisaid_id isolation_source_host-associated sample_capture_status isolate (run) ARTIC_barcode_identifiers host_tissue_sampled library_id AssemblyName GEO_Accession (exp) source_name tissue barcode_identifiers Cell_type host_description sample_type age_event Age Biomaterial_provider cell_number cell_processing_protocol cell_quality disease disease_stage ETHNICITY health_state sex single_cell synthetic tissue_processing cell_subsets patient_group disease_state subject_status tissue/cell_type sample_origin organ host_disease_stage stock_production_date culture_collection COUNTRY Extraction-method host_disease_outcome identification_method Laboratory_Host link_addit_analys ref_biomaterial datatype (run) +SRR11953971 RNA-Seq PRJNA622837 SAMN14938999 BROAD INSTITUTE OF HARVARD AND MIT public bam,sra gs,ncbi,s3 gs.US,ncbi.public,s3.us-east-1 SRX8498148 Illumina NovaSeq 6000 PAIRED cDNA VIRAL RNA Severe acute respiratory syndrome coronavirus 2 ILLUMINA MA_MGH_00524 SRP266465 207470 2020-06-08T00:00:00Z SAMN14938999_ERCC-00040_RandomHexamer_NexteraXT 2020-03-17 not applicable 202 415514 Pathogen.cl Homo sapiens USA North America USA: Massachusetts COVID-19 Massachusetts General Hospital nasopharyngeal swab missing not applicable not applicable MA_MGH_00524 |