Mercurial > repos > iuc > enasearch_retrieve_run_report

changeset 1:da7585984d1c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/enasearch commit f506c7312d6d9bf4aa5b1719d58b33dbcd49309f
author iuc
date Wed, 08 Nov 2017 13:19:02 -0500
parents 1a4944dd4eaf
children 7a05e5bd8093
files enasearch_retrieve_run_report.xml macros.xml test-data/retrieve_analysis_report_output1.tabular test-data/retrieve_run_report_output1.tabular
diffstat 4 files changed, 6 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/enasearch_retrieve_run_report.xml	Tue Aug 29 04:11:32 2017 -0400
+++ b/enasearch_retrieve_run_report.xml	Wed Nov 08 13:19:02 2017 -0500
@@ -25,7 +25,7 @@
     <tests>
         <test>
             <param name="accession" value="SRX017289"/>
-            <output name="output" md5="0f0c6df8d03b9b26b2906921524d7ad1"/>
+            <output name="output" file="retrieve_run_report_output1.tabular"/>
         </test>
         <test>
             <param name="accession" value="SRX017289"/>
--- a/macros.xml	Tue Aug 29 04:11:32 2017 -0400
+++ b/macros.xml	Wed Nov 08 13:19:02 2017 -0500
@@ -66,7 +66,7 @@
             <when input="display_opt.display" value="fasta" format="fasta" />
             <when input="display_opt.display" value="fastq" format="fastq" />
             <when input="display_opt.display" value="html" format="html" />
-            <when input="display_opt.display" value="text" format="text" />
+            <when input="display_opt.display" value="text" format="txt" />
             <when input="display_opt.display" value="xml" format="xml" />
         </change_format>
     </xml>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/retrieve_analysis_report_output1.tabular	Wed Nov 08 13:19:02 2017 -0500
@@ -0,0 +1,2 @@
+analysis_accession	study_accession	secondary_study_accession	sample_accession	secondary_sample_accession	analysis_title	analysis_type	center_name	first_public	last_updated	study_title	tax_id	scientific_name	analysis_alias	study_alias	submitted_bytes	submitted_md5	submitted_ftp	submitted_aspera	submitted_galaxy	sample_alias	broker_name
+ERZ009929	PRJEB1970	ERP002648	SAMEA2072680	ERS246980	Using a perclinal chimera to determine layer-specific gene expression: S. lycopersicum leaf analysis	REFERENCE_ALIGNMENT	ICL-CFB	2013-10-30	2016-06-17	Using a perclinal chimera to determine layer-specific gene            expression	4081	Solanum lycopersicum	1: lycopersicum leaf analysis	periclinal chimera study	799096;589364146	256c09cc87e998c73a6b31ab34b562a4;3c1e93f150aa843d6b7f06165c182a51	ftp.sra.ebi.ac.uk/vol1/ERZ009/ERZ009929/1.bam.bai;ftp.sra.ebi.ac.uk/vol1/ERZ009/ERZ009929/1.bam	fasp.sra.ebi.ac.uk:/vol1/ERZ009/ERZ009929/1.bam.bai;fasp.sra.ebi.ac.uk:/vol1/ERZ009/ERZ009929/1.bam	ftp.sra.ebi.ac.uk/vol1/ERZ009/ERZ009929/1.bam.bai;ftp.sra.ebi.ac.uk/vol1/ERZ009/ERZ009929/1.bam	1: lycopersicum leaf	
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/retrieve_run_report_output1.tabular	Wed Nov 08 13:19:02 2017 -0500
@@ -0,0 +1,2 @@
+study_accession	secondary_study_accession	sample_accession	secondary_sample_accession	experiment_accession	run_accession	submission_accession	tax_id	scientific_name	instrument_platform	instrument_model	library_name	nominal_length	library_layout	library_strategy	library_source	library_selection	read_count	base_count	center_name	first_public	last_updated	experiment_title	study_title	study_alias	experiment_alias	run_alias	fastq_bytes	fastq_md5	fastq_ftp	fastq_aspera	fastq_galaxy	submitted_bytes	submitted_md5	submitted_ftp	submitted_aspera	submitted_galaxy	submitted_format	sra_bytes	sra_md5	sra_ftp	sra_aspera	sra_galaxy	cram_index_ftp	cram_index_aspera	cram_index_galaxy	sample_alias	broker_name
+PRJNA123835	SRP002056	SAMN00009557	SRS011830	SRX017289	SRR037073	SRA012156	6239	Caenorhabditis elegans	ILLUMINA	Illumina Genome Analyzer II	small RNAs_wild type (fog-2)_adult males_part1		SINGLE	RNA-Seq	TRANSCRIPTOMIC	size fractionation	1068858	38478888	GEO	2010-04-09	2010-04-09	Illumina Genome Analyzer II sequencing; GSM465245: small RNAs_wild type (fog-2)_adult males_part1	High throughput sequencing of endogenous small RNAs from AGO pathway mutants	GSE18729	small RNAs_wild type (fog-2)_adult males_part1	GSM465245_1	25154397	89359f77f5870d2b563ebd77baeeeaf6	ftp.sra.ebi.ac.uk/vol1/fastq/SRR037/SRR037073/SRR037073.fastq.gz	fasp.sra.ebi.ac.uk:/vol1/fastq/SRR037/SRR037073/SRR037073.fastq.gz	ftp.sra.ebi.ac.uk/vol1/fastq/SRR037/SRR037073/SRR037073.fastq.gz							18013387	58a1c3a66ce6414a240e4ea83449db49	ftp.sra.ebi.ac.uk/vol1/srr/SRR037/SRR037073	fasp.sra.ebi.ac.uk:/vol1/srr/SRR037/SRR037073	ftp.sra.ebi.ac.uk/vol1/srr/SRR037/SRR037073				GSM465245