| Previous changeset 5:09424ec94e80 (2019-11-13) Next changeset 7:822575bf359f (2020-06-05) |
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Commit message:
"planemo upload for repository https://github.com/phac-nml/mob-suite commit dc6eaf2675bf842ab7a52c3fdf16d01028cddc9a" |
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modified:
mob_recon.xml mob_typer.xml |
| b |
| diff -r 09424ec94e80 -r 9424de64bfa8 mob_recon.xml --- 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 ${input.element_identifier}: Plasmids"> + <discover_datasets pattern="__name_and_ext__" directory="outdir/plasmids" /> </collection> </outputs> <tests> <test> - <param name="input" value="plasmid_476.fasta" ftype="fasta"/> - <section name="adv_param"> - <param name="unicycler_contigs" value="True"/> - <param name="run_circlator" value="True"/> - </section> - <output name="outfile1"> - <assert_contents> - <has_text text="NC_019097"/> - </assert_contents> - </output> + <param name="input" value="plasmid_476.fasta" ftype="fasta"/> + <section name="adv_param"> + <param name="unicycler_contigs" value="True"/> + <param name="run_circlator" value="True"/> + </section> + <output name="contig_report"> + <assert_contents> + <has_text text="NC_019097"/> + </assert_contents> + </output> </test> </tests> <help> |
| b |
| diff -r 09424ec94e80 -r 9424de64bfa8 mob_typer.xml --- a/mob_typer.xml Wed Nov 13 14:09:11 2019 -0500 +++ b/mob_typer.xml Wed Dec 11 19:17:11 2019 -0500 |
| [ |
| b'@@ -1,12 +1,14 @@\n-<tool id="mob_typer" name="MOB-Typer" version="1.4.9.1+galaxy0">\n+<tool id="mob_typer" name="MOB-Typer" version="2.0.5+galaxy0">\n <description>Get the plasmid type and mobility given its sequence</description>\n <requirements>\n- <requirement type="package" version="1.4.9.1">mob_suite</requirement>\n- </requirements> \n+ <requirement type="package" version="2.0.5">mob_suite</requirement>\n+ </requirements>\n+ <version_command>mob_typer --version</version_command>\n <command detect_errors="exit_code">\n <![CDATA[\n- ln -s "${input}" "${input.name}";\n- mob_typer --num_threads \\${GALAXY_SLOTS:-4} --infile "${input.name}" \n+ ln -s \'${input}\' \'${input.name}\' &&\n+ mob_typer --num_threads \\${GALAXY_SLOTS:-4} --infile \'${input.name}\'\n+ ${host_range_detailed}\n --min_rep_evalue \'$adv_param.min_rep_evalue_value\'\n --min_mob_evalue \'$adv_param.min_mob_evalue_value\'\n --min_con_evalue \'$adv_param.min_con_evalue_value\'\n@@ -16,11 +18,12 @@\n --min_mob_ident \'$adv_param.min_mob_ident\'\n --min_ori_ident \'$adv_param.min_ori_ident\'\n --min_mpf_ident \'$adv_param.min_mpf_ident\'\n- --outdir \'.\';\n+ --outdir \'outdir\';\n ]]>\n </command>\n <inputs>\n <param name="input" type="data" format="fasta" label="Input" help="FASTA file with contig(s)"/>\n+ <param name="host_range_detailed" type="boolean" truevalue="--host_range_detailed" falsevalue="" checked="true" label="Perform detailed host range analysis" />\n <section name="adv_param" title="Advanced parameters" expanded="False">\n <param name="min_rep_evalue_value" type="float" value="0.00001" min="0.00001" max="1" label="Minimum evalue threshold for replicon blastn"/> \n <param name="min_mob_evalue_value" type="float" value="0.00001" min="0.00001" max="1" label="Minimum evalue threshold for relaxase tblastn"/> \n@@ -31,19 +34,122 @@\n <param name="min_mob_ident" label="Minimum sequence identity for relaxases" type="integer" min="0" max="100" value="80"/>\n <param name="min_ori_ident" label="Minimum sequence identity for oriT elements" type="integer" min="0" max="100" value="90"/>\n <param name="min_mpf_ident" label="Minimum sequence identity for mpf elements" type="integer" min="0" max="100" value="80"/>\n- </section> \n+ </section>\n </inputs>\n <outputs>\n- <data name="outfile1" label="${tool.name}: Plasmid report on ${input.name}" format="tabular">\n- <discover_datasets pattern=".+_report\\.txt" visible="true" format="tabular" assign_primary_output="true"/>\n- </data> \n+ <data name="plasmid_report" from_work_dir="outdir/mobtyper*_report.txt" label="${tool.name}: Plasmid report on ${input.element_identifier}" format="tabular" />\n+ <data name="refseq_hostrange_phylogeny_tree" from_work_dir="outdir/*_refseqhostrange_phylogeny_tree.nwk" label="${tool.name} on ${input.element_identifier}: RefSeq Host Range Phylogeny Tree" format="newick">\n+ <filter>host_range_detailed</filter>\n+ </data>\n+ <data name="literature_hostrange_phylogeny_tree" from_work_dir="outdir/*_literaturehostrange_phylogeny_tree.nwk" label="${tool.name} on ${input.element_identifier}: Literature Host Range Phylogeny Tree" format="newick">\n+ <filter>host_range_detailed</filter>\n+ </data>\n+ <data name="refseq_hostrange_ascii_tree" from_work_dir="outdir/*_refseqhostrange_asci_tree.txt" label="${tool.name} on ${input.element_identifier}: RefSeq Host Range ASCII Tree" format="txt">\n+ <filter>host_range_detailed</filter>\n+ </data>\n+ <data name="literature_hostrange_ascii_tree" from_work_dir="outdir/*_literaturehostrange_asci_tree.txt" label="${tool.name} on ${input.element_identifier}: Literature Host Range ASCII Tree" format="txt">\n+ <filter>host_range_detailed</filter>\n+ </data>\n+ <data name="literature_report" from_work_dir="outdir/*_literature_report.txt" label="${tool.name} on ${input.element_identifier}: Literature Report" format="tabular">\n+ <filter>host_range_deta'..b'on ${input.element_identifier}: RefSeq Host Range Phylogeny Stats" format="tabular">\n+ <filter>host_range_detailed</filter>\n+ </data>\n </outputs>\n <tests>\n <test>\n- <param name="input" value="plasmid_476.fasta" ftype="fasta"/>\n- <assert_stdout>\n- <has_text text="JN253636"/> \n- </assert_stdout>\n+ <param name="input" value="plasmid_476.fasta" ftype="fasta" />\n+ <param name="host_range_detailed" value="False" />\n+ <output name="plasmid_report">\n+ <assert_contents>\n+ <has_text text="000145__HE610900_00001"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <test>\n+ <param name="input" value="plasmid_476.fasta" ftype="fasta" />\n+ <param name="host_range_detailed" value="True" />\n+ <output name="refseq_hostrange_phylogeny_tree">\n+ <assert_contents>\n+ <has_text text="(624:1,984897:1)"/> \n+ </assert_contents>\n+ </output>\n+ </test>\n+ <test>\n+ <param name="input" value="plasmid_476.fasta" ftype="fasta" />\n+ <param name="host_range_detailed" value="True" />\n+ <output name="literature_hostrange_phylogeny_tree">\n+ <assert_contents>\n+ <has_text text="(90371:1,611:1,28144:1)"/> \n+ </assert_contents>\n+ </output>\n+ </test>\n+ <test>\n+ <param name="input" value="plasmid_476.fasta" ftype="fasta" />\n+ <param name="host_range_detailed" value="True" />\n+ <output name="refseq_hostrange_ascii_tree">\n+ <assert_contents>\n+ <has_text text="order, Enterobacterales"/>\n+ <has_text text="family, Enterobacteriaceae"/>\n+ <has_text text="genus, Shigella"/>\n+ <has_text text="species, Escherichia coli"/>\n+ <has_text text="genus, Serratia"/>\n+ <has_text text="species, Serratia marcescens"/>\n+ <has_text text="species, Klebsiella pneumoniae"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <test>\n+ <param name="input" value="plasmid_476.fasta" ftype="fasta" />\n+ <param name="host_range_detailed" value="True" />\n+ <output name="literature_hostrange_ascii_tree">\n+ <assert_contents>\n+ <has_text text="family, Enterobacteriaceae"/>\n+ <has_text text="species, Escherichia coli"/>\n+ <has_text text="species, Klebsiella pneumoniae"/>\n+ <has_text text="subspecies, Salmonella enterica subsp. enterica"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <test>\n+ <param name="input" value="plasmid_476.fasta" ftype="fasta" />\n+ <param name="host_range_detailed" value="True" />\n+ <output name="literature_report">\n+ <assert_contents>\n+ <has_text text="IncI1"/>\n+ <has_text text="R64"/>\n+ <has_text text="pHNRD174"/>\n+ <has_text text="pKHSB1"/>\n+ <has_text text="pCTXM1-MU2"/>\n+ <has_text_matching expression="family\\tEnterobacteriaceae"/>\n+ <has_text_matching expression="order\\tEnterobacteriales"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <test>\n+ <param name="input" value="plasmid_476.fasta" ftype="fasta" />\n+ <param name="host_range_detailed" value="True" />\n+ <output name="refseq_hostrange_report">\n+ <assert_contents>\n+ <has_text text="IncI1"/>\n+ <has_text text="Enterobacterales"/> \n+ </assert_contents>\n+ </output>\n+ </test>\n+ <test>\n+ <param name="input" value="plasmid_476.fasta" ftype="fasta" />\n+ <param name="host_range_detailed" value="True" />\n+ <output name="refseq_hostrange_phylostats">\n+ <assert_contents>\n+ <has_line_matching expression="rank\\tsci_name\\tdb_hits\\tconvergance_rank\\tconvergance_sci_name"/>\n+ <has_line_matching expression="family\\tEnterobacteriaceae\\t351"/>\n+ <has_line_matching expression="genus\\tSalmonella\\t113"/> \n+ </assert_contents>\n+ </output>\n </test>\n </tests>\n <help>\n' |