| Previous changeset 1:ec3b8341f551 (2021-03-10) |
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Commit message:
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold commit 7777a0e34cc2ccd228183af74809ae0d5d9e9b85 |
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modified:
blastx_to_scaffold.xml |
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| diff -r ec3b8341f551 -r f03154ac4ed8 blastx_to_scaffold.xml --- a/blastx_to_scaffold.xml Wed Mar 10 19:11:14 2021 +0000 +++ b/blastx_to_scaffold.xml Wed Oct 11 13:03:33 2023 +0000 |
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| @@ -1,13 +1,14 @@ -<tool id="blastx2scaffold" name="blastx_to_scaffold" version="1.1.0"> +<tool id="blastx2scaffold" name="blastx_to_scaffold" version="1.1.1"> <description>Generate DNA scaffold from blastx alignment of Contigs</description> <requirements> <requirement type="package" version="3.7.6">python</requirement> </requirements> -<command interpreter="python"> - blastx_to_scaffold.py --sequences $sequences +<command detect_errors="exit_code"><![CDATA[ + python $__tool_directory__/blastx_to_scaffold.py + --sequences $sequences --blastx-tab $blastx_tab --output $output -</command> +]]></command> <inputs> <param name="sequences" type="data" format="fasta" label="Select a fasta contigs file"/> <param name="blastx_tab" type="data" format="tabular" label="Select a blastx output from your history" help="must have 13 columns with column 13 containing the subject lenght, other columns are standard"/> @@ -32,12 +33,17 @@ **What it Does** This tool starts from DNA contigs that aligned to a subject protein sequence through blastx. -The contigs must be provided in fasta format. The blastx output must be tabular, the 12 standard column plus column 13 with the length of the blastx subject. +The contigs must be provided in fasta format. The blastx output must be tabular, the 12 standard +columns plus column 13 with the length of the blastx subject. + The final scaffold is a DNA sequence. + Sequences of the subject protein which were not aligned to the contigs are replaced by Ns in this scaffold. -**Attribution** -This Galaxy tool was created by drosofff@gmail.com on 28/05/2015 </help> +<citations> + <citation type="doi">10.1186/s13742-015-0080-7</citation> +</citations> + </tool> |