Repository 'enasearch_retrieve_taxons'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/enasearch_retrieve_taxons

Changeset 2:92e869104274 (2020-01-21)
Previous changeset 1:8881ac3eebd7 (2017-11-09)
Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/enasearch commit a0adc28145cce02ecaed3a90156ed54c4385d1a0"
modified:
enasearch_retrieve_taxons.xml
macros.xml
test-data/retrieve_run_report_output1.tabular
removed:
test-data/retrieve_analysis_report_output1.tabular
b
diff -r 8881ac3eebd7 -r 92e869104274 enasearch_retrieve_taxons.xml
--- 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>
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diff -r 8881ac3eebd7 -r 92e869104274 macros.xml
--- a/macros.xml Thu Nov 09 13:09:05 2017 -0500
+++ b/macros.xml Tue Jan 21 19:05:45 2020 -0500
b
@@ -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>
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diff -r 8881ac3eebd7 -r 92e869104274 test-data/retrieve_analysis_report_output1.tabular
--- 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
b
@@ -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
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diff -r 8881ac3eebd7 -r 92e869104274 test-data/retrieve_run_report_output1.tabular
--- 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
b
@@ -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