Mercurial > repos > cpt > cpt_blastn_to_gff
diff cpt_blastn_to_gff/blastn_to_gff3.xml @ 0:54c3aabcb3e7 draft
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author | cpt |
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date | Fri, 13 May 2022 04:42:45 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cpt_blastn_to_gff/blastn_to_gff3.xml Fri May 13 04:42:45 2022 +0000 @@ -0,0 +1,60 @@ +<tool id="edu.tamu.cpt.blastn_to_gff3" name="BlastN Results to GFF3" version="19.1.0.0"> + <description>converts blast xml or tabular results to a JBrowse-compatible file</description> + <macros> + <import>macros.xml</import> + <import>cpt-macros.xml</import> + </macros> + <expand macro="requirements"/> + <command detect_errors="aggressive"><![CDATA[ +$__tool_directory__/blast_to_gff3.py +$input_type.blast_input +#if $input_type.input_type_selector == "xml": + --blastxml +#elif $input_type.input_type_selector == "tsv": + --blasttab +#end if +> $output]]></command> + <inputs> + <conditional name="input_type"> + <param name = "input_type_selector" type="select" label="Choose BlastN File Format"> + <option value="xml" selected="true">BlastXML</option> + <option value="tsv">Blast 25 Column Table"</option> + </param> + <when value="xml"> + <param name="blast_input" type="data" format="xml" label="BlastXML Input"/> + </when> + <when value="tsv"> + <param name="blast_input" type="data" format="tabular" label="Blast 25 Column Table"/> + </when> + </conditional> + </inputs> + <outputs> + <data format="gff3" name="output"/> + </outputs> + <tests> + <test> + <param name="input_type_selector" value="xml"/> + <param name="blast_input" value="BlastnXmlToGff_In.blastxml" /> + <output name="output" file="BlastnXmlToGff_Out.gff3" /> + </test> + <test> + <param name="input_type_selector" value="tsv"/> + <param name="blast_input" value="BlastnTsvToGff_In.tabular" ftype="tabular"/> + <output name="output" ftype="gff3" > + <assert_contents> + <has_line line="##gff-version 3"/> + <has_n_lines n="3152"/> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ +**What it does** + +Convert BlastN XML or tabular results into GFF3 format for visualization within JBrowse, please be sure to select the correct input option for your data. +This is critical for displaying the position of high-scoring pairs of the Target aligned against the Query. If you need to convert BlastP results, please use the "BlastP Results to GFF3" tool. + +]]></help> + <expand macro="citations" /> +</tool> +