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

Changeset 19:248f85ff0733 (2020-06-23)
Previous changeset 18:7068f48d0ef9 (2020-06-08) Next changeset 20:964579f93c54 (2020-07-01)
Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 1e2492fa4557ddc6ffefc16b249ed9ef0207d5e1"
modified:
fasterq_dump.xml
fastq_dump.xml
sam_dump.xml
sra_macros.xml
added:
test-data/SRR11953971_1.fastq.gz
test-data/SRR11953971_2.fastq.gz
test-data/sra_manifest.tabular
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diff -r 7068f48d0ef9 -r 248f85ff0733 fasterq_dump.xml
--- a/fasterq_dump.xml Mon Jun 08 05:49:21 2020 -0400
+++ b/fasterq_dump.xml Tue Jun 23 17:18:45 2020 -0400
[
@@ -1,4 +1,4 @@
-<tool id="fasterq_dump" name="Faster Download and Extract Reads in FASTQ" version="@VERSION@+galaxy0" profile="18.01">
+<tool id="fasterq_dump" name="Faster Download and Extract Reads in FASTQ" version="@VERSION@+galaxy1" profile="18.01">
     <description>format from NCBI SRA</description>
     <macros>
         <import>sra_macros.xml</import>
@@ -169,6 +169,28 @@
                 <element name="SRR002702" file="SRR002702_2.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
             </output_collection>
         </test>
+        <test>
+            <param name="input_select" value="file_list"/>
+            <param name="file_list" value="sra_manifest.tabular" ftype="sra_manifest.tabular"/>
+            <output_collection name="list_paired" type="list:paired">
+                <element name="SRR11857975">
+                    <element name="forward" file="SRR11857975_1.fastq.gz" decompress="True">
+                    </element>
+                    <element name="reverse" file="SRR11857975_2.fastq.gz" decompress="True">
+                    </element>
+                </element>
+            </output_collection>
+        </test>
+        <test>
+            <param name="input_select" value="file_list"/>
+            <param name="file_list" value="sra_manifest.tabular" ftype="sra_manifest.tabular"/>
+            <output_collection name="list_paired" type="list:paired">
+                <element name="SRR11953971">
+                    <element name="forward" file="SRR11953971_1.fastq.gz" decompress="True"/>
+                    <element name="reverse" file="SRR11953971_2.fastq.gz" decompress="True"/>
+                </element>
+            </output_collection>
+        </test>
     </tests>
     <help><![CDATA[
 **What it does?**
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diff -r 7068f48d0ef9 -r 248f85ff0733 fastq_dump.xml
--- a/fastq_dump.xml Mon Jun 08 05:49:21 2020 -0400
+++ b/fastq_dump.xml Tue Jun 23 17:18:45 2020 -0400
b
@@ -1,4 +1,4 @@
-<tool id="fastq_dump" name="Download and Extract Reads in FASTA/Q" version="@VERSION@+galaxy0" profile="18.01">
+<tool id="fastq_dump" name="Download and Extract Reads in FASTA/Q" version="@VERSION@+galaxy1" profile="18.01">
     <description>format from NCBI SRA</description>
     <macros>
         <import>sra_macros.xml</import>
b
diff -r 7068f48d0ef9 -r 248f85ff0733 sam_dump.xml
--- a/sam_dump.xml Mon Jun 08 05:49:21 2020 -0400
+++ b/sam_dump.xml Tue Jun 23 17:18:45 2020 -0400
b
@@ -1,4 +1,4 @@
-<tool id="sam_dump" name="Download and Extract Reads in BAM" version="@VERSION@+galaxy0" profile="18.01">
+<tool id="sam_dump" name="Download and Extract Reads in BAM" version="@VERSION@+galaxy1" profile="18.01">
     <description>format from NCBI SRA</description>
     <macros>
         <import>sra_macros.xml</import>
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diff -r 7068f48d0ef9 -r 248f85ff0733 sra_macros.xml
--- a/sra_macros.xml Mon Jun 08 05:49:21 2020 -0400
+++ b/sra_macros.xml Tue Jun 23 17:18:45 2020 -0400
[
@@ -19,7 +19,13 @@
     ]]></token>
     <token name="@SET_ACCESSIONS@"><![CDATA[
         #if $input.input_select=="file_list":
-            for acc in `@ACCESSIONS_FROM_FILE@ '$input.file_list'` ;
+            #if $input.file_list.is_of_type('sra_manifest.tabular'):
+                #set $column = $input.file_list.unsanitized.metadata.column_names.index('Run') + 1
+                cut -f $column '$input.file_list'| tail -n +2 > "manifest" &&
+            #else
+                ln -s '$input.file_list' > manifest &&
+            #end if
+            for acc in `@ACCESSIONS_FROM_FILE@ manifest` ;
             do (
         #elif $input.input_select=="accession_number":
             acc='${input.accession}' && [ ""\$acc" =~ ^[E|S|D]RR[0-9]{1,}$" ] && (
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diff -r 7068f48d0ef9 -r 248f85ff0733 test-data/SRR11953971_1.fastq.gz
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Binary file test-data/SRR11953971_1.fastq.gz has changed
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diff -r 7068f48d0ef9 -r 248f85ff0733 test-data/SRR11953971_2.fastq.gz
b
Binary file test-data/SRR11953971_2.fastq.gz has changed
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diff -r 7068f48d0ef9 -r 248f85ff0733 test-data/sra_manifest.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sra_manifest.tabular Tue Jun 23 17:18:45 2020 -0400
b
@@ -0,0 +1,2 @@
+Run Assay Type BioProject BioSample Center Name Consent DATASTORE filetype DATASTORE provider DATASTORE region Experiment Instrument LibraryLayout LibrarySelection LibrarySource Organism Platform Sample Name SRA Study Bytes ReleaseDate Library Name Collection_Date isolate AvgSpotLen Bases BioSampleModel Host geo_loc_name_country geo_loc_name_country_continent geo_loc_name host_disease collected_by isolation_source lat_lon host_sex passage_history strain host_age host_subject_id ENA-FIRST-PUBLIC (run) ENA-FIRST-PUBLIC ENA-LAST-UPDATE (run) ENA-LAST-UPDATE geographic_location_(country_and/or_sea) host_health_state collecting_institution collector_name geographic_location_(region_and_locality) host_common_name host_scientific_name gisaid_id isolation_source_host-associated sample_capture_status isolate (run) ARTIC_barcode_identifiers host_tissue_sampled library_id AssemblyName GEO_Accession (exp) source_name tissue barcode_identifiers Cell_type host_description sample_type age_event Age Biomaterial_provider cell_number cell_processing_protocol cell_quality disease disease_stage ETHNICITY health_state sex single_cell synthetic tissue_processing cell_subsets patient_group disease_state subject_status tissue/cell_type sample_origin organ host_disease_stage stock_production_date culture_collection COUNTRY Extraction-method host_disease_outcome identification_method Laboratory_Host link_addit_analys ref_biomaterial datatype (run)
+SRR11953971 RNA-Seq PRJNA622837 SAMN14938999 BROAD INSTITUTE OF HARVARD AND MIT public bam,sra gs,ncbi,s3 gs.US,ncbi.public,s3.us-east-1 SRX8498148 Illumina NovaSeq 6000 PAIRED cDNA VIRAL RNA Severe acute respiratory syndrome coronavirus 2 ILLUMINA MA_MGH_00524 SRP266465 207470 2020-06-08T00:00:00Z SAMN14938999_ERCC-00040_RandomHexamer_NexteraXT 2020-03-17 not applicable 202 415514 Pathogen.cl Homo sapiens USA North America USA: Massachusetts COVID-19 Massachusetts General Hospital nasopharyngeal swab missing not applicable not applicable MA_MGH_00524