Mercurial > repos > nml > sistr_cmd
diff sistr_cmd.xml @ 0:ebee10be4297 draft
planemo upload commit 1ea98fb88a93a571beda5bbd56449c946860a258
| author | nml |
|---|---|
| date | Wed, 01 Mar 2017 12:35:39 -0500 |
| parents | |
| children | 9d7e381dfa5a |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sistr_cmd.xml Wed Mar 01 12:35:39 2017 -0500 @@ -0,0 +1,331 @@ +<tool id="sistr_cmd" name="sistr_cmd" version="0.3.4"> + <description> + Salmonella In Silico Typing Resource commandline tool for serovar prediction + </description> + <requirements> + <requirement type="package" version="0.3.4">sistr_cmd</requirement> + </requirements> + <stdio> + <exit_code range="1:" /> + </stdio> + <command><![CDATA[ + sistr + #for $fasta in $input_fastas + -i '$fasta' '${$fasta.name.replace("." + $fasta.ext, "")}' + #end for + -f $output_format + #if $output_format == "tab" + -o sistr-report.tab + #elif $output_format == "csv" + -o sistr-report.csv + #elif $output_format == "json" + -o sistr-report.json + #end if + -p $cgmlst_profiles + -n $novel_alleles + -a $alleles_output + $use_full_cgmlst_db + $no_cgmlst + $run_mash + $qc + --threads "\${GALAXY_SLOTS:-1}" + -T "\${TMPDIR:-/tmp}" + $keep_tmp + $verbosity + ]]></command> + <inputs> + <param + name="input_fastas" + type="data" + label="Input Genome(s)" + optional="false" + multiple="true" + format="fasta" + /> + <param + name="output_format" + type="select" + label="Results output format" + multiple="false"> + <option value="tab" selected="true"> + Tabular (tab-delimited values) + </option> + <option value="csv"> + CSV (Comma Separated Values) + </option> + <option value="json"> + JSON (JavaScript Object Notation) + </option> + </param> + <param + name="use_full_cgmlst_db" + type="boolean" + checked="false" + truevalue="--use-full-cgmlst-db" + falsevalue="" + label="Use full cgMLST database for serovar prediction. About 10X slower with equivalent results to reduced centroid allele database." + /> + <param + name="run_mash" + type="boolean" + checked="true" + truevalue="--run-mash" + falsevalue="" + label="Run Mash MinHash-based serovar prediction" + /> + <param + name="no_cgmlst" + type="boolean" + checked="false" + truevalue="--no-cgmlst" + falsevalue="" + label="Skip running cgMLST-based serovar prediction" + /> + <param + name="qc" + type="boolean" + checked="true" + truevalue="--qc" + falsevalue="" + label="Basic QC of results" + /> + <param + name="keep_tmp" + type="boolean" + checked="false" + falsevalue="" + truevalue="--keep-tmp" + label="Keep temporary analysis directory" + /> + <param + name="verbosity" + type="select" + label="Logging verbosity"> + <option value=""> + Error messages only + </option> + <option value="-v"> + Show warning messages + </option> + <option value="-vv" selected="true"> + Show info messages + </option> + <option value="-vvv"> + Show debug messages + </option> + </param> + </inputs> + <outputs> + <data + name="output_prediction_csv" + format="csv" + label="SISTR Results" + from_work_dir="sistr-report.csv"> + <filter>output_format == "csv"</filter> + </data> + <data + name="output_prediction_json" + format="json" + label="SISTR Results" + from_work_dir="sistr-report.json"> + <filter>output_format == "json"</filter> + </data> + <data + name="output_prediction_tab" + format="tabular" + label="SISTR Results" + from_work_dir="sistr-report.tab"> + <filter>output_format == "tab"</filter> + </data> + <data + name="cgmlst_profiles" + format="csv" + label="cgMLST results" /> + <data + name="novel_alleles" + format="fasta" + label="Novel cgMLST alleles" /> + <data + name="alleles_output" + format="json" + label="cgMLST allele match results" /> + </outputs> + <tests> + <test> + <param name="input_fastas" value="AE014613-699860.fasta"/> + <param name="output_format" value="tab"/> + <output + name="novel_alleles" + value="novel-alleles.fasta" + ftype="fasta" + compare="sim_size"/> + <output + name="cgmlst_profiles" + value="cgmlst-profiles.csv" + ftype="csv" + lines_diff="2"> + <assert_contents> + <has_text text=",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,3969539340,2545200385,225275747,2955003506,2353669245,2666669453,1672513023,3779563470,1301843222,2161147266,607954140,3680021500,2914087704,1062106200,3673111880,1314942441,1367997025,3293595301,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,1528212814,2110459436,4160823845,1648892875,2084418558,1638162324,469721942,1317894045,1973458150,926214622,2197498164,398274060,,,,,,,,,,1123870984,278162969,490843778,3950769715,,,,,,4203409135,3569491948,,,,,,,1052128508,,,1510445340,,,4065472468,,,,,,1495737522,,,,,,,,3076491138,712233770,3105746335,625241463,3016847250,1928860657,2229984332,1341416065,2978539204,1175502179,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,1328452594,2372254687,2640609716,3051501604,3258707132,,,,,,,,,,,,1007978530,,2019769394,1109678443,,,,,,,,,"/> + </assert_contents> + </output> + <output + name="output_prediction_tab" + value="sistr-results.tab" + ftype="tabular" + lines_diff="2"> + <assert_contents> + <has_text text="AE014613-699860" /> + <has_text text="Typhi" /> + <has_text text="enterica" /> + <has_text text="-:-:-" /> + <has_n_columns n="19" /> + </assert_contents> + </output> + <output + name="alleles_output" + value="alleles-output.json" + ftype="json" + compare="sim_size"/> + </test> + <test> + <param name="input_fastas" value="13-1101-Paratyphi_B.fasta"/> + <param name="output_format" value="tab"/> + <output + name="novel_alleles" + value="novel-alleles-13-1101.fasta" + ftype="fasta" + compare="sim_size"/> + <output + name="cgmlst_profiles" + value="cgmlst-profiles-13-1101.csv" + ftype="csv" + lines_diff="2"> + </output> + <output + name="output_prediction_tab" + value="sistr-results-13-1101.tab" + ftype="tabular" + lines_diff="2"> + <assert_contents> + <has_text text="13-1101-Paratyphi_B" /> + <has_text text="Paratyphi B var. Java" /> + <has_text text="enterica" /> + <has_text text="1,4,[5],12" /> + <has_text text="PASS" /> + <has_text text="2375035975"/> + <has_n_columns n="21" /> + </assert_contents> + </output> + <output + name="alleles_output" + value="alleles-output-13-1101.json" + ftype="json" + compare="sim_size"/> + </test> + <test> + <param name="input_fastas" value="13-1101 Paratyphi_B.fasta"/> + <param name="output_format" value="tab"/> + <output + name="novel_alleles" + value="novel-alleles-13-1101.fasta" + ftype="fasta" + compare="sim_size"/> + <output + name="cgmlst_profiles" + value="cgmlst-profiles-13-1101.csv" + ftype="csv" + lines_diff="2"> + </output> + <output + name="output_prediction_tab" + value="sistr-results-13-1101.tab" + ftype="tabular" + lines_diff="2"> + <assert_contents> + <has_text text="13-1101 Paratyphi_B" /> + <has_text text="Paratyphi B var. Java" /> + <has_text text="enterica" /> + <has_text text="1,4,[5],12" /> + <has_text text="PASS" /> + <has_text text="2375035975"/> + <has_n_columns n="21" /> + </assert_contents> + </output> + <output + name="alleles_output" + value="alleles-output-13-1101.json" + ftype="json" + compare="sim_size"/> + </test> + </tests> + <help> + <![CDATA[ + +Usage:: + + usage: sistr_cmd [-h] [-i fasta_path genome_name] [-f OUTPUT_FORMAT] + [-o OUTPUT_PREDICTION] [-p CGMLST_PROFILES] + [-n NOVEL_ALLELES] [-a ALLELES_OUTPUT] [-T TMP_DIR] [-K] + [--use-full-cgmlst-db] [--no-cgmlst] [-m] [--qc] [-t THREADS] + [-v] [-V] + [F [F ...]] + + SISTR (Salmonella In Silico Typing Resource) Command-line Tool + ============================================================== + Serovar predictions from whole-genome sequence assemblies by determination of antigen gene and cgMLST gene alleles using BLAST. + + Note about using the "--use-full-cgmlst-db" flag: + The "centroid" allele database is ~10% the size of the full set so analysis is much quicker with the "centroid" vs "full" set of alleles. Results between 2 cgMLST allele sets should not differ. + + If you find this program useful in your research, please cite as: + + The Salmonella In Silico Typing Resource (SISTR): an open web-accessible tool for rapidly typing and subtyping draft Salmonella genome assemblies. + Catherine Yoshida, Peter Kruczkiewicz, Chad R. Laing, Erika J. Lingohr, Victor P.J. Gannon, John H.E. Nash, Eduardo N. Taboada. + PLoS ONE 11(1): e0147101. doi: 10.1371/journal.pone.0147101 + + positional arguments: + F Input genome FASTA file + + optional arguments: + -h, --help show this help message and exit + -i fasta_path genome_name, --input-fasta-genome-name fasta_path genome_name + fasta file path to genome name pair + -f OUTPUT_FORMAT, --output-format OUTPUT_FORMAT + Output format (json, csv, pickle) + -o OUTPUT_PREDICTION, --output-prediction OUTPUT_PREDICTION + SISTR serovar prediction output path + -p CGMLST_PROFILES, --cgmlst-profiles CGMLST_PROFILES + Output CSV file destination for cgMLST allelic + profiles + -n NOVEL_ALLELES, --novel-alleles NOVEL_ALLELES + Output FASTA file destination of novel cgMLST alleles + from input genomes + -a ALLELES_OUTPUT, --alleles-output ALLELES_OUTPUT + Output path of allele sequences and info to JSON + -T TMP_DIR, --tmp-dir TMP_DIR + Base temporary working directory for intermediate + analysis files. + -K, --keep-tmp Keep temporary analysis files. + --use-full-cgmlst-db Use the full set of cgMLST alleles which can include + highly similar alleles. By default the smaller + "centroid" alleles or representative alleles are used + for each marker. + --no-cgmlst Do not run cgMLST serovar prediction + -m, --run-mash Determine Mash MinHash genomic distances to Salmonella + genomes with trusted serovar designations. Mash binary + must be in accessible via $PATH (e.g. /usr/bin). + --qc Perform basic QC to provide level of confidence in + serovar prediction results. + -t THREADS, --threads THREADS + Number of parallel threads to run sistr_cmd analysis. + -v, --verbose Logging verbosity level (-v == show warnings; -vvv == + show debug info) + -V, --version show program's version number and exit +]]> + + </help> + <citations> + <!-- Citation for SISTR PLOS ONE paper --> + <citation type="doi">10.1371/journal.pone.0147101</citation> + </citations> +</tool>