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changeset 1:3f1ee30e39e9 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 4f31c74918fc999e01c3e8bc1156ecd79efbc39b
author iuc
date Tue, 29 Apr 2025 06:04:35 +0000
parents 5e7401777990
children
files fastq_dl.xml macros.xml test-data/Metadata_files/SRR9678965.tsv
diffstat 3 files changed, 4 insertions(+), 4 deletions(-) [+]
line wrap: on
line diff
--- a/fastq_dl.xml	Sat Nov 16 18:43:55 2024 +0000
+++ b/fastq_dl.xml	Tue Apr 29 06:04:35 2025 +0000
@@ -47,11 +47,11 @@
         </collection>
         <collection name="single_end_collection" type="list" label="Single-end data">
             <filter>only_download_metadata == False</filter>
-            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.fastq\.gz" directory="single-end" ext="fastq.gz" />
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.fastq\.gz" directory="single-end" ext="fastqsanger.gz" />
         </collection>
         <collection name="paired_end_collection" type="list:paired" label="Paired-end data">
             <filter>only_download_metadata == False</filter>
-            <discover_datasets pattern="(?P&lt;identifier_0&gt;[^_]+)_(?P&lt;identifier_1&gt;[^_]+)\.fastq.gz" directory="paired-end" ext="fastq.gz" />
+            <discover_datasets pattern="(?P&lt;identifier_0&gt;[^_]+)_(?P&lt;identifier_1&gt;[^_]+)\.fastq.gz" directory="paired-end" ext="fastqsanger.gz" />
         </collection>
     </outputs>
     <tests>
--- a/macros.xml	Sat Nov 16 18:43:55 2024 +0000
+++ b/macros.xml	Tue Apr 29 06:04:35 2025 +0000
@@ -1,5 +1,5 @@
 <macros>
-    <token name="@TOOL_VERSION@">3.0.0</token>
+    <token name="@TOOL_VERSION@">3.0.1</token>
     <token name="@VERSION_SUFFIX@">0</token>
     <xml name="requirements">
         <requirements>
--- a/test-data/Metadata_files/SRR9678965.tsv	Sat Nov 16 18:43:55 2024 +0000
+++ b/test-data/Metadata_files/SRR9678965.tsv	Tue Apr 29 06:04:35 2025 +0000
@@ -1,2 +1,2 @@
 run_accession	experiment_title	sample_accession	project_name	submission_accession	library_min_fragment_size	bam_md5	assembly_software	library_prep_longitude	library_selection	pcr_isolation_protocol	chip_protocol	sequencing_primer_provider	serotype	environment_feature	last_updated	submitted_galaxy	extraction_protocol	germline	secondary_project	culture_collection	submission_tool	sra_bytes	read_strand	rna_purity_280_ratio	hi_c_protocol	collected_by	submitted_ftp	restriction_enzyme_target_sequence	isolate	fastq_bytes	instrument_platform	variety	sequencing_date_format	temperature	sra_aspera	ecotype	submitted_aspera	sampling_campaign	bam_ftp	tissue_lib	environmental_sample	control_experiment	sex	submitted_md5	checklist	fastq_galaxy	library_gen_protocol	specimen_voucher	library_prep_latitude	submitted_bytes	taxonomic_identity_marker	run_date	country	ncbi_reporting_standard	sample_description	sra_galaxy	sample_prep_interval	fastq_md5	secondary_study_accession	experimental_protocol	read_count	study_title	bio_material	rna_prep_5_protocol	host_body_site	local_environmental_context	assembly_quality	collection_date_end	sample_capture_status	sample_title	host_genotype	host_phenotype	environmental_medium	cultivar	instrument_model	faang_library_selection	target_gene	bam_bytes	library_max_fragment_size	experiment_target	sequencing_date	description	nominal_sdev	chip_ab_provider	environment_material	host_tax_id	sample_material	sample_storage_processing	sra_md5	cell_type	fastq_ftp	disease	sample_prep_interval_units	broker_name	sub_strain	base_count	library_strategy	restriction_site	serovar	investigation_type	location	library_source	sra_ftp	age	library_layout	experimental_factor	sequencing_primer_catalog	environment_biome	rna_purity_230_ratio	dnase_protocol	dev_stage	library_prep_date_format	bam_aspera	binning_software	datahub	rna_integrity_num	library_prep_date	location_start	marine_region	aligned	file_location	sample_collection	chip_target	nominal_length	broad_scale_environmental_context	sequencing_location	status	completeness_score	lon	fastq_aspera	tax_lineage	host_sex	library_pcr_isolation_protocol	sample_alias	mating_type	collection_date_start	sub_species	contamination_score	run_alias	restriction_enzyme	depth	submitted_read_type	library_construction_protocol	host_growth_conditions	collection_date	experiment_alias	host_gravidity	center_name	identified_by	cell_line	sampling_site	host	library_name	tag	first_created	lat	strain	experiment_accession	scientific_name	host_status	tax_id	study_accession	submitted_format	submitted_host_sex	bisulfite_protocol	altitude	rt_prep_protocol	host_scientific_name	bam_galaxy	accession	secondary_sample_accession	sample_storage	cage_protocol	sampling_platform	taxonomic_classification	location_end	protocol_label	elevation	salinity	sequencing_method	sequencing_primer_lot	first_public	transposase_protocol	study_alias	library_prep_location	rna_prep_3_protocol	ph	sequencing_longitude	tissue_type	isolation_source
-SRR9678965	454 GS FLX sequencing: Amplicon seqencing of Homo sapiens: adult skin surface	SAMN12272107		SRA920837					PCR						2019-09-12							3528954								2465043	LS454				fasp.sra.ebi.ac.uk:/vol1/srr/SRR967/005/SRR9678965											ftp.sra.ebi.ac.uk/vol1/fastq/SRR967/005/SRR9678965/SRR9678965.fastq.gz							Germany: Duesseldorf	Metagenome or environmental	Metagenome or environmental sample from human skin metagenome	ftp.sra.ebi.ac.uk/vol1/srr/SRR967/005/SRR9678965		6c04efc21529bb1b4bbd2758435dd491	SRP214545		11487	16S rRNA gene profiling of atopic dermatitis and psoriasis patients compared to healthy volunteers						2016-12-31		Metagenome or environmental sample from human skin metagenome					454 GS FLX							454 GS FLX sequencing: Amplicon seqencing of Homo sapiens: adult skin surface				9606			9ba2d40c7ef09e349804bcae64879eae		ftp.sra.ebi.ac.uk/vol1/fastq/SRR967/005/SRR9678965/SRR9678965.fastq.gz					5809265	AMPLICON				51.15 N 6.48 E	METAGENOMIC	ftp.sra.ebi.ac.uk/vol1/srr/SRR967/005/SRR9678965		SINGLE										dcc_metagenome			51.15 N 6.48 E									public		6.48	fasp.sra.ebi.ac.uk:/vol1/fastq/SRR967/005/SRR9678965/SRR9678965.fastq.gz	1;2787823;12908;408169;410656;539655			MAARS Cohort		2016-01-01			plate1_3.007.01.sff.fastq						2016	plate1_3.007.01		SUB5942029				Homo sapiens	plate1_3.007.01	env_geo:terrestrial	2019-09-12	51.15		SRX6439351	human skin metagenome		539655	PRJNA554499						Homo sapiens		SRR9678965	SRS5093728					51.15 N 6.48 E						2019-09-12		PRJNA554499						skin surface
+SRR9678965	454 GS FLX sequencing: Amplicon seqencing of Homo sapiens: adult skin surface	SAMN12272107		SRA920837					PCR						2019-09-12							3528954								2465043	LS454				fasp.sra.ebi.ac.uk:/vol1/srr/SRR967/005/SRR9678965											ftp.sra.ebi.ac.uk/vol1/fastq/SRR967/005/SRR9678965/SRR9678965.fastq.gz							Germany: Duesseldorf	Metagenome or environmental	Metagenome or environmental sample from human skin metagenome	ftp.sra.ebi.ac.uk/vol1/srr/SRR967/005/SRR9678965		6c04efc21529bb1b4bbd2758435dd491	SRP214545		11487	16S rRNA gene profiling of atopic dermatitis and psoriasis patients compared to healthy volunteers						2016-12-31		Metagenome or environmental sample from human skin metagenome					454 GS FLX							454 GS FLX sequencing: Amplicon seqencing of Homo sapiens: adult skin surface				9606			9ba2d40c7ef09e349804bcae64879eae		ftp.sra.ebi.ac.uk/vol1/fastq/SRR967/005/SRR9678965/SRR9678965.fastq.gz					5809265	AMPLICON				51.15 N 6.48 E	METAGENOMIC	ftp.sra.ebi.ac.uk/vol1/srr/SRR967/005/SRR9678965		SINGLE										dcc_metagenome			51.15 N 6.48 E									public		6.48	fasp.sra.ebi.ac.uk:/vol1/fastq/SRR967/005/SRR9678965/SRR9678965.fastq.gz	1;2787823;12908;408169;410656;539655			MAARS Cohort		2016-01-01			plate1_3.007.01.sff.fastq						2016	plate1_3.007.01		SUB5942029				Homo sapiens	plate1_3.007.01	env_geo;env_geo:terrestrial	2019-09-12	51.15		SRX6439351	human skin metagenome		539655	PRJNA554499						Homo sapiens		SRR9678965	SRS5093728					51.15 N 6.48 E						2019-09-12		PRJNA554499						skin surface