Previous changeset 31:734abc7ac21d (2023-09-14) Next changeset 33:6591f049cf7e (2023-10-25) |
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit ac10fe34f1b2d5e8109dcaaf42b7870bee57827b |
modified:
fastq_dump.xml macros.xml |
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diff -r 734abc7ac21d -r fb723c531be5 fastq_dump.xml --- a/fastq_dump.xml Thu Sep 14 07:38:02 2023 +0000 +++ b/fastq_dump.xml Wed Oct 25 07:10:06 2023 +0000 |
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@@ -12,7 +12,7 @@ @SET_ACCESSIONS@ #if $input.input_select == "sra_file": - fastq-dump --log-level fatal --accession '${input.file.name}' + fastq-dump --log-level fatal --accession "\$acc" #else: ## Do not use prefetch if region is specified, to avoid downloading ## the complete sra file. @@ -20,8 +20,8 @@ prefetch -X 200000000 "\$acc" && #end if fastq-dump --accession "\$acc" - --split-files #end if + --split-files --defline-seq '$adv.defline_seq' --defline-qual '+' @@ -269,6 +269,21 @@ </element> </output_collection> </test> + <test expect_num_outputs="2"> + <param name="input_select" value="sra_file"/> + <param name="sra_file" value="SRR522874.sra"/> + <param name="split" value="True"/> + <param name="skip_technical" value="True"/> + <section name="adv"> + <param name="defline_seq" value="@$sn/$ri"/> + </section> + <output_collection name="list_paired" type="list:paired" count="1"> + <element name="SRR522874.sra"> + <element name="forward" file="SRR522874.sra_2.fastq.gz" ftype="fastqsanger.gz" decompress="True"/> + <element name="reverse" file="SRR522874.sra_4.fastq.gz" ftype="fastqsanger.gz" decompress="True"/> + </element> + </output_collection> + </test> </tests> <help><![CDATA[ **What it does?** |
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diff -r 734abc7ac21d -r fb723c531be5 macros.xml --- a/macros.xml Thu Sep 14 07:38:02 2023 +0000 +++ b/macros.xml Wed Oct 25 07:10:06 2023 +0000 |
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@@ -1,6 +1,6 @@ <macros> - <token name="@TOOL_VERSION@">3.0.5</token> - <token name="@VERSION_SUFFIX@">3</token> + <token name="@TOOL_VERSION@">3.0.8</token> + <token name="@VERSION_SUFFIX@">0</token> <token name="@PROFILE@">22.01</token> <xml name="edam_ontology"> <edam_topics> @@ -15,8 +15,8 @@ <macro name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">sra-tools</requirement> - <requirement type="package" version="2.6">pigz</requirement> - <requirement type="package" version="1.17">samtools</requirement> + <requirement type="package" version="2.8">pigz</requirement> + <requirement type="package" version="1.18">samtools</requirement> <yield/> </requirements> </macro> |