| Previous changeset 24:e08a7ad4378b (2021-02-01) Next changeset 26:83c7d564b128 (2021-09-03) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit a464017f4a599697101dbd26cf5eb902588359b5" |
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modified:
fasterq_dump.xml sra_macros.xml test-data/SRR522874.sra_1.fastq.gz test-data/SRR522874.sra_2.fastq.gz test-data/SRR522874.sra_3.fastq.gz test-data/SRR522874.sra_4.fastq.gz |
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| diff -r e08a7ad4378b -r 69ebb7f46e45 fasterq_dump.xml --- a/fasterq_dump.xml Mon Feb 01 20:03:42 2021 +0000 +++ b/fasterq_dump.xml Tue Apr 27 08:55:34 2021 +0000 |
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| @@ -106,10 +106,10 @@ </collection> </outputs> <tests> - <test> + <test expect_num_outputs="4"> <param name="input_select" value="accession_number"/> <param name="accession" value="ERR086330"/> - <output_collection name="list_paired" type="list:paired"> + <output_collection name="list_paired" type="list:paired" count="1"> <element name="ERR086330"> <element name="forward" file="ERR086330_1.fastq.gz" decompress="True"> </element> @@ -118,22 +118,22 @@ </element> </output_collection> </test> - <test> + <test expect_num_outputs="4"> <param name="input_select" value="accession_number"/> <param name="accession" value="SRR002702"/> <param name="split" value="--split-files"/> <param name="skip_technical" value="False"/> - <output_collection name="output_collection_other" type="list"> + <output_collection name="output_collection_other" type="list" count="2"> <element name="SRR002702_1" file="SRR002702_1.fastq.gz" ftype="fastqsanger.gz" decompress="True"/> <element name="SRR002702_2" file="SRR002702_2.fastq.gz" ftype="fastqsanger.gz" decompress="True"/> </output_collection> </test> - <test> + <test expect_num_outputs="4"> <param name="input_select" value="file"/> <param name="file" value="SRR522874.sra"/> <param name="split" value="--split-files"/> <param name="skip_technical" value="True"/> - <output_collection name="list_paired" type="list:paired"> + <output_collection name="list_paired" type="list:paired" count="1"> <element name="SRR522874.sra"> <element name="forward" file="SRR522874.sra_2.fastq.gz" decompress="True"> </element> @@ -142,64 +142,50 @@ </element> </output_collection> </test> - <test> + <test expect_num_outputs="4"> <param name="input_select" value="file"/> <param name="file" value="SRR522874.sra"/> <param name="split" value="--split-files"/> <param name="skip_technical" value="False"/> - <output_collection name="output_collection_other" type="list"> - <element name="SRR522874.sra_1" file="SRR522874.sra_1.fastq.gz" ftype="fastqsanger.gz" decompress="True"/> - <element name="SRR522874.sra_2" file="SRR522874.sra_2.fastq.gz" ftype="fastqsanger.gz" decompress="True"/> - <element name="SRR522874.sra_3" file="SRR522874.sra_3.fastq.gz" ftype="fastqsanger.gz" decompress="True"/> - <element name="SRR522874.sra_4" file="SRR522874.sra_4.fastq.gz" ftype="fastqsanger.gz" decompress="True"/> + <output_collection name="output_collection_other" type="list" count="4"> + <element name="SRR522874_1" file="SRR522874.sra_1.fastq.gz" ftype="fastqsanger.gz" decompress="True"/> + <element name="SRR522874_2" file="SRR522874.sra_2.fastq.gz" ftype="fastqsanger.gz" decompress="True"/> + <element name="SRR522874_3" file="SRR522874.sra_3.fastq.gz" ftype="fastqsanger.gz" decompress="True"/> + <element name="SRR522874_4" file="SRR522874.sra_4.fastq.gz" ftype="fastqsanger.gz" decompress="True"/> </output_collection> </test> - <test> + <test expect_num_outputs="4"> <param name="input_select" value="file_list"/> <param name="file_list" value="list_sra"/> <param name="minlen" value="21"/> <output_collection name="output_collection_other" type="list"> <element name="SRR522874__single" file="SRR522874.fastq.gz" ftype="fastqsanger.gz" decompress="True"/> </output_collection> - <output_collection name="list_paired" type="list:paired"> + <output_collection name="list_paired" type="list:paired" count="1"> <element name="SRR522874"> - <element name="forward" file="SRR522874_1.fastq.gz" decompress="True"> - </element> - <element name="reverse" file="SRR522874_2.fastq.gz" decompress="True"> - </element> + <element name="forward" file="SRR522874_1.fastq.gz" decompress="True"/> + <element name="reverse" file="SRR522874_2.fastq.gz" decompress="True"/> </element> </output_collection> <output_collection name="output_collection" type="list"> <element name="SRR002702" file="SRR002702_2.fastq.gz" ftype="fastqsanger.gz" decompress="True"/> </output_collection> </test> - <test> + <test expect_num_outputs="4"> <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"> + <output_collection name="list_paired" type="list:paired" count="1"> <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> - <test> + <test expect_num_outputs="4"> <!-- test accession downloaded from public bucket --> <param name="input_select" value="accession_number"/> <param name="accession" value="SRR11859153"/> - <output_collection name="output_collection" type="list"> + <output_collection name="output_collection" type="list" count="1"> <element name="SRR11859153" file="SRR11859153.fastq.gz" decompress="True"/> </output_collection> <output name="log"> |
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| diff -r e08a7ad4378b -r 69ebb7f46e45 sra_macros.xml --- a/sra_macros.xml Mon Feb 01 20:03:42 2021 +0000 +++ b/sra_macros.xml Tue Apr 27 08:55:34 2021 +0000 |
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| @@ -1,5 +1,5 @@ <macros> - <token name="@VERSION@">2.10.9</token> + <token name="@VERSION@">2.11.0</token> <token name="@ACCESSIONS_FROM_FILE@"> grep '^[[:space:]]*[E|S|D]RR[0-9]\{1,\}[[:space:]]*$' </token> |
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| diff -r e08a7ad4378b -r 69ebb7f46e45 test-data/SRR522874.sra_1.fastq.gz |
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| diff -r e08a7ad4378b -r 69ebb7f46e45 test-data/SRR522874.sra_2.fastq.gz |
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| diff -r e08a7ad4378b -r 69ebb7f46e45 test-data/SRR522874.sra_3.fastq.gz |
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| diff -r e08a7ad4378b -r 69ebb7f46e45 test-data/SRR522874.sra_4.fastq.gz |
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