Mercurial > repos > iuc > enasearch_retrieve_taxons

changeset 1:8881ac3eebd7 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/enasearch commit 11ee7ac206d41894c0b6a11f2439aaea490824f0
author iuc
date Thu, 09 Nov 2017 13:09:05 -0500
parents 34d21959dc25
children 92e869104274
files enasearch_retrieve_taxons.xml macros.xml test-data/retrieve_analysis_report_output1.tabular test-data/retrieve_run_report_output1.tabular
diffstat 4 files changed, 13 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/enasearch_retrieve_taxons.xml	Tue Aug 29 04:14:07 2017 -0400
+++ b/enasearch_retrieve_taxons.xml	Thu Nov 09 13:09:05 2017 -0500
@@ -47,7 +47,14 @@
             <conditional name="display_opt">
                 <param name="display" value="xml"/>
             </conditional>
-            <output name="output" ftype="xml" md5="0833f5ac248a3e7f382e4d53762fc71d"/>
+            <output name="output" ftype="xml">
+                <assert_contents>
+                    <has_text text="taxon scientificName=&quot;Felis catus&quot;" />
+                    <has_text text="taxon scientificName=&quot;Homo sapiens&quot;" />
+                    <has_text text="taxon scientificName=&quot;Mus musculus&quot;" />
+                    <has_text text="taxon scientificName=&quot;Danio rerio&quot;" />
+                </assert_contents>
+            </output>
         </test>
     </tests>
     <help><![CDATA[
--- a/macros.xml	Tue Aug 29 04:14:07 2017 -0400
+++ b/macros.xml	Thu Nov 09 13:09:05 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	Thu Nov 09 13:09:05 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	Thu Nov 09 13:09:05 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