Mercurial > repos > nml > mob_suite
diff mob_recon.xml @ 6:9424de64bfa8 draft
"planemo upload for repository https://github.com/phac-nml/mob-suite commit dc6eaf2675bf842ab7a52c3fdf16d01028cddc9a"
author | nml |
---|---|
date | Wed, 11 Dec 2019 19:17:11 -0500 |
parents | 09424ec94e80 |
children | 822575bf359f |
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--- a/mob_recon.xml Wed Nov 13 14:09:11 2019 -0500 +++ b/mob_recon.xml Wed Dec 11 19:17:11 2019 -0500 @@ -1,17 +1,18 @@ -<tool id="mob_recon" name="MOB-Recon" version="1.4.9.1+galaxy0"> +<tool id="mob_recon" name="MOB-Recon" version="2.0.5+galaxy0"> <description>Type contigs and extract plasmid sequences</description> <requirements> - <requirement type="package" version="1.4.9.1">mob_suite</requirement> - </requirements> + <requirement type="package" version="2.0.5">mob_suite</requirement> + </requirements> + <version_command>mob_recon --version</version_command> <command detect_errors="exit_code"> <![CDATA[ #import re #import os.path - #set $named_input = re.sub(r'(\s|\(|\)|:|!)', '_', str($input.element_identifier)+".fasta") - ln -s "$input" $named_input && + #set $named_input = re.sub(r'(\s|\(|\)|:|!)', '_', str($input.element_identifier)+'.fasta') + ln -s '$input' '$named_input' && - mob_recon --num_threads \${GALAXY_SLOTS:-4} --infile "${named_input}" + mob_recon --num_threads \${GALAXY_SLOTS:-4} --infile '${named_input}' #if str($adv_param.unicycler_contigs) == "True": --unicycler_contigs #end if @@ -19,7 +20,7 @@ --run_circlator #end if #if str($adv_param.min_length_condition.min_length_param) == "True": - --min_length ${adv_param.min_length_condition.min_length_value} + --min_length '${adv_param.min_length_condition.min_length_value}' #end if --run_typer --min_rep_evalue '${adv_param.min_rep_evalue}' --min_rep_evalue '${adv_param.min_rep_evalue}' @@ -29,8 +30,8 @@ --min_mob_ident '${adv_param.min_mob_ident}' --min_con_ident '${adv_param.min_con_ident}' --min_rpp_ident '${adv_param.min_rpp_ident}' - --outdir '.' && - mkdir ./sequences && (cp plasmid*.fasta chromosome.fasta ./sequences 2> /dev/null || true) + --outdir 'outdir' && + mkdir ./outdir/plasmids && (mv outdir/plasmid*.fasta ./outdir/plasmids 2> /dev/null || true) ]]> </command> <inputs> @@ -65,25 +66,26 @@ </section> </inputs> <outputs> - <data name="outfile1" format="tabular" from_work_dir="contig_report.txt" label="${tool.name} on ${on_string}: Overall contig MOB-recon report"/> - <data name="outfile2" format="tabular" from_work_dir="repetitive_blast_report.txt" label="${tool.name} on ${on_string}: Repetitive elements BLAST report"/> - <data name="outfile3" format="tabular" from_work_dir="mobtyper_aggregate_report.txt" label="${tool.name} on ${on_string}: Aggregate MOB-typer report for all contigs"/> - <collection name="seqhits" type="list" label="${tool.name} on ${on_string}: Extracted sequences (plasmids,chromosome(s))"> - <discover_datasets pattern="__name_and_ext__" directory="sequences" /> + <data name="contig_report" format="tabular" from_work_dir="outdir/contig_report.txt" label="${tool.name} on ${input.element_identifier}: Overall contig MOB-recon report"/> + <data name="repetitive_blast_report" format="tabular" from_work_dir="outdir/repetitive_blast_report.txt" label="${tool.name} on ${input.element_identifier}: Repetitive elements BLAST report"/> + <data name="mobtyper_aggregate_report" format="tabular" from_work_dir="outdir/mobtyper_aggregate_report.txt" label="${tool.name} on ${input.element_identifier}: Aggregate MOB-typer report for all contigs"/> + <data name="chromosome" format="fasta" from_work_dir="outdir/chromosome.fasta" label="${tool.name} on ${input.element_identifier}: Chromosomal sequences"/> + <collection name="plasmids" type="list" label="${tool.name} on ${input.element_identifier}: Plasmids"> + <discover_datasets pattern="__name_and_ext__" directory="outdir/plasmids" /> </collection> </outputs> <tests> <test> - <param name="input" value="plasmid_476.fasta" ftype="fasta"/> - <section name="adv_param"> - <param name="unicycler_contigs" value="True"/> - <param name="run_circlator" value="True"/> - </section> - <output name="outfile1"> - <assert_contents> - <has_text text="NC_019097"/> - </assert_contents> - </output> + <param name="input" value="plasmid_476.fasta" ftype="fasta"/> + <section name="adv_param"> + <param name="unicycler_contigs" value="True"/> + <param name="run_circlator" value="True"/> + </section> + <output name="contig_report"> + <assert_contents> + <has_text text="NC_019097"/> + </assert_contents> + </output> </test> </tests> <help>