Mercurial > repos > iuc > enasearch_retrieve_taxons

changeset 2:92e869104274 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/enasearch commit a0adc28145cce02ecaed3a90156ed54c4385d1a0"
author iuc
date Tue, 21 Jan 2020 19:05:45 -0500
parents 8881ac3eebd7
children
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, 11 insertions(+), 6 deletions(-) [+]
line wrap: on
line diff
--- a/enasearch_retrieve_taxons.xml	Thu Nov 09 13:09:05 2017 -0500
+++ b/enasearch_retrieve_taxons.xml	Tue Jan 21 19:05:45 2020 -0500
@@ -40,7 +40,12 @@
             <conditional name="display_opt">
                 <param name="display" value="fasta"/>
             </conditional>
-            <output name="output" ftype="fasta" md5="e2fe353d00ffdec2f8b884903add458b"/>
+            <output name="output" ftype="fasta">
+                <assert_contents>
+                    <has_text text="Arion rufus partial 5.8S rRNA gene"/>
+                    <has_text text="cytochrome c oxidase subunit I gene"/>
+                </assert_contents>
+            </output>
         </test>
         <test>
             <param name="ids" value="Human,Cat,Mouse,Zebrafish"/>
@@ -51,7 +56,7 @@
                 <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;Mus&quot;" />
                     <has_text text="taxon scientificName=&quot;Danio rerio&quot;" />
                 </assert_contents>
             </output>
@@ -61,6 +66,8 @@
 **What it does**
 
 This tool retrieve ENA taxon data
+
+See also [command line documentation](http://bebatut.fr/enasearch/cli_usage.html#enasearch-retrieve-taxons)
     ]]></help>
     <expand macro="citations"/>
 </tool>
--- a/macros.xml	Thu Nov 09 13:09:05 2017 -0500
+++ b/macros.xml	Tue Jan 21 19:05:45 2020 -0500
@@ -2,7 +2,7 @@
 <macros>
     <token name="@WRAPPER_VERSION@">0.1.1</token>
     <xml name="version">
-        <version_command>@WRAPPER_VERSION@</version_command>
+        <version_command>echo @WRAPPER_VERSION@</version_command>
     </xml>
     <xml name="requirements">
         <requirements>
--- a/test-data/retrieve_analysis_report_output1.tabular	Thu Nov 09 13:09:05 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
-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	
--- a/test-data/retrieve_run_report_output1.tabular	Thu Nov 09 13:09:05 2017 -0500
+++ b/test-data/retrieve_run_report_output1.tabular	Tue Jan 21 19:05:45 2020 -0500
@@ -1,2 +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	
+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	2015-06-19	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