Mercurial > repos > cpt_testbed > suite_work2
diff transterm.xml @ 0:d5c3354c166d draft default tip
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| author | cpt_testbed |
|---|---|
| date | Fri, 29 Apr 2022 10:33:36 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/transterm.xml Fri Apr 29 10:33:36 2022 +0000 @@ -0,0 +1,47 @@ +<tool id="TransTermHP" name="TransTermHP" version="19.1.0.0"> + <description>predicts transcription terminators</description> + <macros> + <import>macros.xml</import> + <import>cpt-macros.xml</import> + </macros> + <requirements> + <requirement type="package" version="3.7.9">python</requirement> + <requirement type="package" version="1.77">biopython</requirement> + <requirement type="package" version="2.09">transtermhp</requirement> + <requirement type="package" version="1.1.3">cpt_gffparser</requirement> + <requirement type="package" version="1.5">bcftools</requirement> + </requirements> + <command detect_errors="aggressive"><![CDATA[ +@GENOME_SELECTOR_PRE@ + +$__tool_directory__/transterm.py +@GENOME_SELECTOR@ +$gff3_data + +> $output + +]]> + </command> + <inputs> + <expand macro="genome_selector" /> + <expand macro="gff3_input" /> + </inputs> + <outputs> + <data name="output" label="Terminators from ${gff3_data.name}" format="gff3" /> + </outputs> + <tests> + <test> + <param name="genome_fasta" value="Transterm_In.fa" /> + <param name="gff3_data" value="Transterm_In.gff3" /> + <output name="output" file="Transterm_Out.gff3" /> + </test> + </tests> + <help> +*TransTermHP* finds rho-independent transcription terminators in bacterial +genomes. Each terminator found by the program is assigned a confidence +value that estimates its probability of being a true terminator. + </help> + <citations> + <citation type="doi">10.1186/gb-2007-8-2-r22</citation> + </citations> +</tool>