| Previous changeset 25:69ebb7f46e45 (2021-04-27) Next changeset 27:9a776b080193 (2023-01-22) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 21f935ba50d3e4b455246c681e54d5c57c67032f" |
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modified:
fasterq_dump.xml fastq_dump.xml sam_dump.xml sra_macros.xml |
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| diff -r 69ebb7f46e45 -r 83c7d564b128 fasterq_dump.xml --- a/fasterq_dump.xml Tue Apr 27 08:55:34 2021 +0000 +++ b/fasterq_dump.xml Fri Sep 03 16:17:53 2021 +0000 |
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| @@ -1,5 +1,6 @@ -<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> + <expand macro="bio_tools"/> <macros> <import>sra_macros.xml</import> </macros> @@ -14,11 +15,8 @@ ln -s '${input.file}' "\$acc" && #end if @CONFIGURE_RETRY@ - ## fetch from public s3 bucket if we can - export acc_or_path="\$acc" && - aws s3 cp --no-sign-request "s3://sra-pub-sars-cov2/run/\$acc/\$acc" "\$acc.sra" 2>&1 | tee '$log' && export acc_or_path="\$acc.sra"|| true && while [ \$SRA_PREFETCH_ATTEMPT -le \$SRA_PREFETCH_RETRIES ] ; do - fasterq-dump "\$acc_or_path" -e \${GALAXY_SLOTS:-1} + fasterq-dump "\$acc" -e \${GALAXY_SLOTS:-1} $adv.split #if str( $adv.minlen ) != "": --min-read-len "$adv.minlen" @@ -181,19 +179,6 @@ </element> </output_collection> </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" count="1"> - <element name="SRR11859153" file="SRR11859153.fastq.gz" decompress="True"/> - </output_collection> - <output name="log"> - <assert_contents> - <has_text text="download: s3://sra-pub-sars-cov2/"/> - </assert_contents> - </output> - </test> </tests> <help><![CDATA[ **What it does?** @@ -259,7 +244,7 @@ .. _fastq: https://en.wikipedia.org/wiki/FASTQ_format -.. _fastq-dump: https://ncbi.github.io/sra-tools/fastq-dump.html +.. _fastq-dump: https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=toolkit_doc&f=fastq-dump .. _fasterq-dump: https://github.com/ncbi/sra-tools/wiki/HowTo:-fasterq-dump .. _collection: https://galaxyproject.org/tutorials/collections/ .. _link: https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies |
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| diff -r 69ebb7f46e45 -r 83c7d564b128 fastq_dump.xml --- a/fastq_dump.xml Tue Apr 27 08:55:34 2021 +0000 +++ b/fastq_dump.xml Fri Sep 03 16:17:53 2021 +0000 |
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| @@ -1,5 +1,6 @@ <tool id="fastq_dump" name="Download and Extract Reads in FASTA/Q" version="@VERSION@+galaxy0" profile="18.01"> <description>format from NCBI SRA</description> + <expand macro="bio_tools"/> <macros> <import>sra_macros.xml</import> </macros> @@ -335,7 +336,7 @@ .. _fastq: https://en.wikipedia.org/wiki/FASTQ_format -.. _fastq-dump: https://ncbi.github.io/sra-tools/fastq-dump.html +.. _fastq-dump: https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=toolkit_doc&f=fastq-dump .. _collection: https://galaxyproject.org/tutorials/collections/ .. _link: https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies |
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| diff -r 69ebb7f46e45 -r 83c7d564b128 sam_dump.xml --- a/sam_dump.xml Tue Apr 27 08:55:34 2021 +0000 +++ b/sam_dump.xml Fri Sep 03 16:17:53 2021 +0000 |
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| @@ -1,5 +1,6 @@ <tool id="sam_dump" name="Download and Extract Reads in BAM" version="@VERSION@+galaxy0" profile="18.01"> <description>format from NCBI SRA</description> + <expand macro="bio_tools"/> <macros> <import>sra_macros.xml</import> </macros> @@ -167,7 +168,7 @@ ----- .. _BAM: https://samtools.github.io/hts-specs/SAMv1.pdf -.. _sam-dump: https://ncbi.github.io/sra-tools/sam-dump.html +.. _sam-dump: https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=toolkit_doc&f=sam-dump .. _collection: https://galaxyproject.org/tutorials/collections/ .. _link: https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies |
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| diff -r 69ebb7f46e45 -r 83c7d564b128 sra_macros.xml --- a/sra_macros.xml Tue Apr 27 08:55:34 2021 +0000 +++ b/sra_macros.xml Fri Sep 03 16:17:53 2021 +0000 |
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| @@ -8,6 +8,11 @@ export SRA_PREFETCH_RETRIES=3 && export SRA_PREFETCH_ATTEMPT=1 && ]]></token> + <xml name="bio_tools"> + <xrefs> + <xref type="bio.tools">sra-tools</xref> + </xrefs> + </xml> <token name="@COPY_CONFIGFILE@"><![CDATA[ mkdir -p ~/.ncbi && cp '$user_settings_mkfg' ~/.ncbi/user-settings.mkfg && @@ -35,7 +40,6 @@ <macro name="requirements"> <requirements> <requirement type="package" version="@VERSION@">sra-tools</requirement> - <requirement type="package" version="1.18.222">awscli</requirement> <requirement type="package" version="2.5">pigz</requirement> <yield/> </requirements> |