Mercurial > repos > cpt > cpt_blasttab_dice_filter

comparison blasttab_dice_filter.xml @ 5:99baf3ee2a2b draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
author cpt
date Mon, 05 Jun 2023 02:40:11 +0000
parents
children f6d253d91757
comparison
equal deleted inserted replaced
4:2ed4d8ee01b9 5:99baf3ee2a2b
1 <tool id="edu.tamu.cpt.blast.blasttab_dice_filter" name="Blast Tabular Dice Filter" version="19.1.0.0">
2 <description>removes low-dice blast results</description>
3 <macros>
4 <import>macros.xml</import>
5 <import>cpt-macros.xml</import>
6 </macros>
7 <expand macro="requirements"/>
8 <command detect_errors="aggressive"><![CDATA[
9 '$__tool_directory__/blasttab_dice_filter.py'
10 @BLAST_TSV@
11 --min_dice '$min_dice'
12 > '$output']]></command>
13 <inputs>
14 <expand macro="blast_tsv"/>
15 <param label="Minimum dice score" help="Blast results with a dice score below this value will be removed" name="min_dice" type="float" value="0.5" min="0.0" max="1.0"/>
16 </inputs>
17 <outputs>
18 <data format="tabular" name="output"/>
19 </outputs>
20 <tests>
21 <test>
22 <param name="blast_tsv" value="T7_NT_BLAST.tabular"/>
23 <param name="min_dice" value="0.2"/>
24 <output name="output" file="T7_NT_BLAST_FILTERED.tabular"/>
25 </test>
26 <test>
27 <param name="blast_tsv" value="results.tsv"/>
28 <param name="min_dice" value="0.5"/>
29 <output name="output" file="results.diced.tsv"/>
30 </test>
31 </tests>
32 <help><![CDATA[
33 **What it does**
34
35 Filters your tabular BLAST results based on a dice score thresholding process.
36
37 **How it works**
38
39 The tool processes BLAST results line by line, at each line calculating the dice score.
40 The equation for the dice score is as follows::
41
42 2 * number of identical matches / (query sequence length + subject sequence length)
43
44 The denominator normalizes the score by accounting for the length of both sequences. A
45 pairwise alignment is required to have between 50-100% identity.
46
47 ]]></help>
48 <expand macro="citations"/>
49 </tool>