Mercurial > repos > nml > mob_suite
changeset 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 |
files | mob_recon.xml mob_typer.xml |
diffstat | 2 files changed, 146 insertions(+), 38 deletions(-) [+] |
line wrap: on
line diff
--- 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 ${input.element_identifier}: Plasmids"> + <discover_datasets pattern="__name_and_ext__" directory="outdir/plasmids" /> </collection> </outputs> <tests> <test> - <param name="input" value="plasmid_476.fasta" ftype="fasta"/> - <section name="adv_param"> - <param name="unicycler_contigs" value="True"/> - <param name="run_circlator" value="True"/> - </section> - <output name="outfile1"> - <assert_contents> - <has_text text="NC_019097"/> - </assert_contents> - </output> + <param name="input" value="plasmid_476.fasta" ftype="fasta"/> + <section name="adv_param"> + <param name="unicycler_contigs" value="True"/> + <param name="run_circlator" value="True"/> + </section> + <output name="contig_report"> + <assert_contents> + <has_text text="NC_019097"/> + </assert_contents> + </output> </test> </tests> <help>
--- a/mob_typer.xml Wed Nov 13 14:09:11 2019 -0500 +++ b/mob_typer.xml Wed Dec 11 19:17:11 2019 -0500 @@ -1,12 +1,14 @@ -<tool id="mob_typer" name="MOB-Typer" version="1.4.9.1+galaxy0"> +<tool id="mob_typer" name="MOB-Typer" version="2.0.5+galaxy0"> <description>Get the plasmid type and mobility given its sequence</description> <requirements> - <requirement type="package" version="1.4.9.1">mob_suite</requirement> - </requirements> + <requirement type="package" version="2.0.5">mob_suite</requirement> + </requirements> + <version_command>mob_typer --version</version_command> <command detect_errors="exit_code"> <![CDATA[ - ln -s "${input}" "${input.name}"; - mob_typer --num_threads \${GALAXY_SLOTS:-4} --infile "${input.name}" + ln -s '${input}' '${input.name}' && + mob_typer --num_threads \${GALAXY_SLOTS:-4} --infile '${input.name}' + ${host_range_detailed} --min_rep_evalue '$adv_param.min_rep_evalue_value' --min_mob_evalue '$adv_param.min_mob_evalue_value' --min_con_evalue '$adv_param.min_con_evalue_value' @@ -16,11 +18,12 @@ --min_mob_ident '$adv_param.min_mob_ident' --min_ori_ident '$adv_param.min_ori_ident' --min_mpf_ident '$adv_param.min_mpf_ident' - --outdir '.'; + --outdir 'outdir'; ]]> </command> <inputs> <param name="input" type="data" format="fasta" label="Input" help="FASTA file with contig(s)"/> + <param name="host_range_detailed" type="boolean" truevalue="--host_range_detailed" falsevalue="" checked="true" label="Perform detailed host range analysis" /> <section name="adv_param" title="Advanced parameters" expanded="False"> <param name="min_rep_evalue_value" type="float" value="0.00001" min="0.00001" max="1" label="Minimum evalue threshold for replicon blastn"/> <param name="min_mob_evalue_value" type="float" value="0.00001" min="0.00001" max="1" label="Minimum evalue threshold for relaxase tblastn"/> @@ -31,19 +34,122 @@ <param name="min_mob_ident" label="Minimum sequence identity for relaxases" type="integer" min="0" max="100" value="80"/> <param name="min_ori_ident" label="Minimum sequence identity for oriT elements" type="integer" min="0" max="100" value="90"/> <param name="min_mpf_ident" label="Minimum sequence identity for mpf elements" type="integer" min="0" max="100" value="80"/> - </section> + </section> </inputs> <outputs> - <data name="outfile1" label="${tool.name}: Plasmid report on ${input.name}" format="tabular"> - <discover_datasets pattern=".+_report\.txt" visible="true" format="tabular" assign_primary_output="true"/> - </data> + <data name="plasmid_report" from_work_dir="outdir/mobtyper*_report.txt" label="${tool.name}: Plasmid report on ${input.element_identifier}" format="tabular" /> + <data name="refseq_hostrange_phylogeny_tree" from_work_dir="outdir/*_refseqhostrange_phylogeny_tree.nwk" label="${tool.name} on ${input.element_identifier}: RefSeq Host Range Phylogeny Tree" format="newick"> + <filter>host_range_detailed</filter> + </data> + <data name="literature_hostrange_phylogeny_tree" from_work_dir="outdir/*_literaturehostrange_phylogeny_tree.nwk" label="${tool.name} on ${input.element_identifier}: Literature Host Range Phylogeny Tree" format="newick"> + <filter>host_range_detailed</filter> + </data> + <data name="refseq_hostrange_ascii_tree" from_work_dir="outdir/*_refseqhostrange_asci_tree.txt" label="${tool.name} on ${input.element_identifier}: RefSeq Host Range ASCII Tree" format="txt"> + <filter>host_range_detailed</filter> + </data> + <data name="literature_hostrange_ascii_tree" from_work_dir="outdir/*_literaturehostrange_asci_tree.txt" label="${tool.name} on ${input.element_identifier}: Literature Host Range ASCII Tree" format="txt"> + <filter>host_range_detailed</filter> + </data> + <data name="literature_report" from_work_dir="outdir/*_literature_report.txt" label="${tool.name} on ${input.element_identifier}: Literature Report" format="tabular"> + <filter>host_range_detailed</filter> + </data> + <data name="refseq_hostrange_report" from_work_dir="outdir/*_refseqhostrange_report.txt" label="${tool.name} on ${input.element_identifier}: RefSeq Host Range Report" format="tabular"> + <filter>host_range_detailed</filter> + </data> + <data name="refseq_hostrange_phylostats" from_work_dir="outdir/*_refseqhostrange_phylostats.txt" label="${tool.name} on ${input.element_identifier}: RefSeq Host Range Phylogeny Stats" format="tabular"> + <filter>host_range_detailed</filter> + </data> </outputs> <tests> <test> - <param name="input" value="plasmid_476.fasta" ftype="fasta"/> - <assert_stdout> - <has_text text="JN253636"/> - </assert_stdout> + <param name="input" value="plasmid_476.fasta" ftype="fasta" /> + <param name="host_range_detailed" value="False" /> + <output name="plasmid_report"> + <assert_contents> + <has_text text="000145__HE610900_00001"/> + </assert_contents> + </output> + </test> + <test> + <param name="input" value="plasmid_476.fasta" ftype="fasta" /> + <param name="host_range_detailed" value="True" /> + <output name="refseq_hostrange_phylogeny_tree"> + <assert_contents> + <has_text text="(624:1,984897:1)"/> + </assert_contents> + </output> + </test> + <test> + <param name="input" value="plasmid_476.fasta" ftype="fasta" /> + <param name="host_range_detailed" value="True" /> + <output name="literature_hostrange_phylogeny_tree"> + <assert_contents> + <has_text text="(90371:1,611:1,28144:1)"/> + </assert_contents> + </output> + </test> + <test> + <param name="input" value="plasmid_476.fasta" ftype="fasta" /> + <param name="host_range_detailed" value="True" /> + <output name="refseq_hostrange_ascii_tree"> + <assert_contents> + <has_text text="order, Enterobacterales"/> + <has_text text="family, Enterobacteriaceae"/> + <has_text text="genus, Shigella"/> + <has_text text="species, Escherichia coli"/> + <has_text text="genus, Serratia"/> + <has_text text="species, Serratia marcescens"/> + <has_text text="species, Klebsiella pneumoniae"/> + </assert_contents> + </output> + </test> + <test> + <param name="input" value="plasmid_476.fasta" ftype="fasta" /> + <param name="host_range_detailed" value="True" /> + <output name="literature_hostrange_ascii_tree"> + <assert_contents> + <has_text text="family, Enterobacteriaceae"/> + <has_text text="species, Escherichia coli"/> + <has_text text="species, Klebsiella pneumoniae"/> + <has_text text="subspecies, Salmonella enterica subsp. enterica"/> + </assert_contents> + </output> + </test> + <test> + <param name="input" value="plasmid_476.fasta" ftype="fasta" /> + <param name="host_range_detailed" value="True" /> + <output name="literature_report"> + <assert_contents> + <has_text text="IncI1"/> + <has_text text="R64"/> + <has_text text="pHNRD174"/> + <has_text text="pKHSB1"/> + <has_text text="pCTXM1-MU2"/> + <has_text_matching expression="family\tEnterobacteriaceae"/> + <has_text_matching expression="order\tEnterobacteriales"/> + </assert_contents> + </output> + </test> + <test> + <param name="input" value="plasmid_476.fasta" ftype="fasta" /> + <param name="host_range_detailed" value="True" /> + <output name="refseq_hostrange_report"> + <assert_contents> + <has_text text="IncI1"/> + <has_text text="Enterobacterales"/> + </assert_contents> + </output> + </test> + <test> + <param name="input" value="plasmid_476.fasta" ftype="fasta" /> + <param name="host_range_detailed" value="True" /> + <output name="refseq_hostrange_phylostats"> + <assert_contents> + <has_line_matching expression="rank\tsci_name\tdb_hits\tconvergance_rank\tconvergance_sci_name"/> + <has_line_matching expression="family\tEnterobacteriaceae\t351"/> + <has_line_matching expression="genus\tSalmonella\t113"/> + </assert_contents> + </output> </test> </tests> <help>