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comparison p_chunks.xml @ 0:f45c65e3fd18 draft

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author greg
date Tue, 10 Jan 2023 20:40:45 +0000
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1 <tool id="p_chunks" name="p_chunks" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description></description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <command detect_errors="exit_code"><![CDATA[
8 #import os
9
10 #set plasmid_db_name = $os.path.join($plasmid_database.extra_files_path, 'blastdb')
11
12 mkdir 'output_dir' &&
13
14 export BLASTDB='$plasmid_database.extra_files_path' &&
15 Rscript '${__tool_directory__}/p_chunks.R'
16 --plasmid_psl '$plasmid_psl'
17 --plasmid_database '$plasmid_db_name'
18 --no_amr
19 --no_inc
20 --output 'output_dir'
21 --threads \${GALAXY_SLOTS:-4}
22 && cat `readlink output_dir/plasmids.tsv` > '$output_plasmids'
23 ]]></command>
24 <inputs>
25 <param argument="--plasmid_psl" type="data" format="psl" label="PSL file"/>
26 <param argument="--plasmid_database" type="data" format="blastdbn" label="BLAST database of the plasmid sequences" help="Plasmid sequences are typically contianed in file named plasmids_and_vectors.fasta"/>
27 </inputs>
28 <outputs>
29 <data name="output_plasmids" format="tsv" label="${tool.name} on ${on_string} (plasmids)"/>
30 </outputs>
31 <tests>
32 <!-- Tests are not possible due to file size requirements -->
33 </tests>
34 <help>
35 **What it does**
36
37 Accepts a PSL file and a BLAST database of the associated plasmid sequences and produces a tabular file containing query name,
38 plasmid name, plasmid accession, query size, aligned bases, plasmid size and missing plasmids.
39 </help>
40 <expand macro="citations"/>
41 </tool>
42