Mercurial > repos > iuc > sra_tools
changeset 31:734abc7ac21d draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 3a7f854e8ebfb2bed11198fb83181f305af633f7
| author | iuc |
|---|---|
| date | Thu, 14 Sep 2023 07:38:02 +0000 |
| parents | 4317d3cb6cba |
| children | fb723c531be5 |
| files | fasterq_dump.xml fastq_dump.xml macros.xml |
| diffstat | 3 files changed, 70 insertions(+), 1 deletions(-) [+] |
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--- a/fasterq_dump.xml Mon Sep 11 08:37:23 2023 +0000 +++ b/fasterq_dump.xml Thu Sep 14 07:38:02 2023 +0000 @@ -187,6 +187,30 @@ </element> </output_collection> </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"/> + <section name="adv"> + <param name="seq_defline" value="@$ac.$si/$ri $sn length=$rl"/> + </section> + <output_collection name="list_paired" type="list:paired" count="1"> + <element name="SRR11953971"> + <element name="forward" ftype="fastqsanger.gz" decompress="True"> + <assert_contents> + <!-- TODO replace has_size by has_line --> + <has_size min="56206"/> + <!-- <has_line line="@SRR11953971.2053/1 2053 length=101"/> --> + </assert_contents> + </element> + <element name="reverse" ftype="fastqsanger.gz" decompress="True"> + <assert_contents> + <has_size min="59843"/> + <!-- <has_line line="@SRR11953971.2053/2 2053 length=101"/> --> + </assert_contents> + </element> + </element> + </output_collection> + </test> </tests> <help><![CDATA[ **What it does?**
--- a/fastq_dump.xml Mon Sep 11 08:37:23 2023 +0000 +++ b/fastq_dump.xml Thu Sep 14 07:38:02 2023 +0000 @@ -226,6 +226,49 @@ </element> </output_collection> </test> + <test expect_num_outputs="2"> + <param name="input_select" value="accession_number"/> + <param name="outputformat" value="fastqsanger.gz"/> + <param name="accession" value="ERR086330, SRR11953971"/> + <section name="adv"> + <param name="defline_seq" value="@$ac.$si/$ri $sn length=$rl"/> + </section> + <output_collection name="list_paired" type="list:paired" count="2"> + <element name="ERR086330"> + <element name="forward" ftype="fastqsanger.gz" decompress="True"> + <assert_contents> + <!-- decompressed content assertions only work from 23.1 + therefore we test for size being at least one byte + larger than the results of the previous test which + uses the shorter default deflines + TODO replace has_size by has_line--> + <has_size min="147"/> + <!-- <has_line line="@ERR086330.1/1 1 length=76"/> --> + </assert_contents> + </element> + <element name="reverse" ftype="fastqsanger.gz" decompress="True"> + <assert_contents> + <has_size min="141"/> + <!-- <has_line line="@ERR086330.1/2 1 length=76"/> --> + </assert_contents> + </element> + </element> + <element name="SRR11953971"> + <element name="forward" ftype="fastqsanger.gz" decompress="True"> + <assert_contents> + <has_size min="56206"/> + <!-- <has_line line="@SRR11953971.1/1 1 length=101"/> --> + </assert_contents> + </element> + <element name="reverse" ftype="fastqsanger.gz" decompress="True"> + <assert_contents> + <has_size min="59843"/> + <!-- <has_line line="@SRR11953971.1/2 1 length=101"/> --> + </assert_contents> + </element> + </element> + </output_collection> + </test> </tests> <help><![CDATA[ **What it does?**
--- a/macros.xml Mon Sep 11 08:37:23 2023 +0000 +++ b/macros.xml Thu Sep 14 07:38:02 2023 +0000 @@ -1,6 +1,6 @@ <macros> <token name="@TOOL_VERSION@">3.0.5</token> - <token name="@VERSION_SUFFIX@">1</token> + <token name="@VERSION_SUFFIX@">3</token> <token name="@PROFILE@">22.01</token> <xml name="edam_ontology"> <edam_topics> @@ -144,6 +144,8 @@ <add value=":" /> <add value="/" /> <add value="?" /> + <add value=" " /> + <add value="=" /> </valid> </sanitizer> <validator type="regex" message="Must start with @">^.*</validator>