Mercurial > repos > iuc > ivar_getmasked

comparison ivar_getmasked.xml @ 0:fafb3d685fa9 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
author iuc
date Mon, 30 Mar 2020 06:54:03 -0400
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1 <tool id="ivar_getmasked" name="ivar getmasked" version="@VERSION@+galaxy0">
2 <description>Detect primer mismatches and get primer indices for the amplicon to be masked</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <expand macro="version_command" />
8 <command detect_errors="exit_code"><![CDATA[
9 ivar getmasked
10 -i '$filtered_tsv'
11 -b '$primers_bed'
12 -f '$primers_tsv'
13 -p masked_primers
14 ]]> </command>
15 <inputs>
16 <param name="filtered_tsv" argument="-i" type="data" format="tabular,txt" label="Input filtered variants tsv generated from filtervariants"/>
17 <param name="primers_bed" argument="-b" type="data" format="bed" label="BED file with primer sequences and positions"/>
18 <param name="primers_tsv" argument="-f" type="data" format="tabular" label="Primer pair information file containing left and right primer names for the same amplicon"/>
19 </inputs>
20 <outputs>
21 <data name="masked" format="txt" label="${tool.name} on ${on_string} Output" from_work_dir="masked_primers.txt"/>
22 </outputs>
23 <tests>
24 <test>
25 <param name="filtered_tsv" value="zika/primers_Z52_consensus.tsv"/>
26 <param name="primers_bed" value="zika/db/zika_primers_consensus.bed"/>
27 <param name="primers_tsv" value="zika/db/pair_information.tsv"/>
28 <output name="masked" file="zika/primer_mismatchers_indices.txt"/>
29 </test>
30 </tests>
31 <help><![CDATA[
32 iVar uses a .tsv file with variants to get the zero based indices (based on
33 the BED file) of mismatched primers. This command requires another .tsv file
34 with each line containing the left and right primer names separated by a
35 tab. This is used to get both the primers for an amplicon with a single
36 mismatched primer. The output is a text file with the zero based primer
37 indices delimited by a space. The output is written to a a text file using
38 the prefix provided.
39
40 Documentation can be found at `<https://andersen-lab.github.io/ivar/html/manualpage.html>`_.
41 ]]> </help>
42 <expand macro="citations" />
43 </tool>