Mercurial > repos > iuc > ncbi_acc_download
changeset 2:e063168e0a81 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 7077bbc8c1e416f717b545c5ac18b0c8b5a066b2
| author | iuc |
|---|---|
| date | Fri, 18 Nov 2022 18:21:57 +0000 |
| parents | 28587613264f |
| children | |
| files | macros.xml ncbi_acc_download.xml |
| diffstat | 2 files changed, 32 insertions(+), 1 deletions(-) [+] |
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--- a/macros.xml Tue Jul 20 12:18:01 2021 +0000 +++ b/macros.xml Fri Nov 18 18:21:57 2022 +0000 @@ -1,3 +1,3 @@ <macros> - <token name="@TOOL_VERSION@">0.2.7</token> + <token name="@TOOL_VERSION@">0.2.8</token> </macros>
--- a/ncbi_acc_download.xml Tue Jul 20 12:18:01 2021 +0000 +++ b/ncbi_acc_download.xml Fri Nov 18 18:21:57 2022 +0000 @@ -24,6 +24,9 @@ #if $molecule.format != 'featuretable' and $molecule.format != 'gff3': --extended-validation all #end if + #if $range != "" + --range $range + #end if \${accession}; failure=\$?; if [ \$failure -ne 0 ]; then @@ -73,6 +76,15 @@ </param> </when> </conditional> + <param argument="--range" type="text" label="Range" help="Region to subset accession. Start and end position separated by ':', '..', or '.'. Only for single accession"> + <sanitizer invalid_char=""> + <valid initial="string.digits"> + <add value=":" /> + <add value=".." /> + <add value="." /> + </valid> + </sanitizer> + </param> <param name="ignore_failed" type="select" display="radio" label="How to handle download failures"> <option value="0">Abort with error on first failure</option> @@ -296,6 +308,25 @@ </element> </output_collection> </test> + <test> + <conditional name="molecule"> + <param name="select" value="nucleotide"/> + <param name="format" value="genbank"/> + </conditional> + <conditional name="query_source"> + <param name="select" value="accession_list" /> + <param name="accession_list" value="NC_006666"/> + </conditional> + <param name="range" value="1697:2764"/> + <output_collection name="output" type="list"> + <element name="NC_006666" ftype="genbank"> + <assert_contents> + <has_text text="ND2" /> + <not_has_text text="tRNA-Ile" /> + </assert_contents> + </element> + </output_collection> + </test> </tests> <help><![CDATA[ **What it does**