| Previous changeset 1:9d7e381dfa5a (2017-03-03) Next changeset 3:5c8ff92e38a9 (2017-06-14) |
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Commit message:
planemo upload commit c190273bbf3bfd1efb6e14135601d746b748daab |
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modified:
sistr_cmd.xml test-data/sistr-results.tab |
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| diff -r 9d7e381dfa5a -r 13632190a0ff sistr_cmd.xml --- a/sistr_cmd.xml Fri Mar 03 14:31:21 2017 -0500 +++ b/sistr_cmd.xml Thu Apr 20 14:33:38 2017 -0400 |
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| @@ -1,9 +1,9 @@ -<tool id="sistr_cmd" name="sistr_cmd" version="0.3.4"> +<tool id="sistr_cmd" name="sistr_cmd" version="0.3.6"> <description> Salmonella In Silico Typing Resource commandline tool for serovar prediction </description> <requirements> - <requirement type="package" version="0.3.4">sistr_cmd</requirement> + <requirement type="package" version="0.3.6">sistr_cmd</requirement> </requirements> <stdio> <exit_code range="1:" /> @@ -25,6 +25,8 @@ --threads "\${GALAXY_SLOTS:-1}" -T "\${TMPDIR:-/tmp}" $keep_tmp + $full_output + $report_blast_results $verbosity ]]></command> <inputs> @@ -84,6 +86,22 @@ label="Basic QC of results" /> <param + name="report_blast_results" + type="boolean" + checked="false" + truevalue="--report-blast-results" + falsevalue="" + label="Report all blastn results from antigen search" + /> + <param + name="full_output" + type="boolean" + checked="false" + truevalue="--full-output" + falsevalue="" + label="Report detailed results" + /> + <param name="keep_tmp" type="boolean" checked="false" @@ -172,7 +190,7 @@ <has_text text="Typhi" /> <has_text text="enterica" /> <has_text text="-:-:-" /> - <has_n_columns n="19" /> + <has_n_columns n="21" /> </assert_contents> </output> <output @@ -206,7 +224,6 @@ <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> @@ -241,7 +258,6 @@ <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> @@ -258,7 +274,8 @@ Usage:: usage: sistr_cmd [-h] [-i fasta_path genome_name] [-f OUTPUT_FORMAT] - [-o OUTPUT_PREDICTION] [-p CGMLST_PROFILES] + [-o OUTPUT_PREDICTION] [--full-output] + [--report-blast-results] [-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] @@ -288,6 +305,9 @@ Output format (json, csv, pickle) -o OUTPUT_PREDICTION, --output-prediction OUTPUT_PREDICTION SISTR serovar prediction output path + --full-output Produce full detailed output + --report-blast-results + Report blastn results for each antigen gene -p CGMLST_PROFILES, --cgmlst-profiles CGMLST_PROFILES Output CSV file destination for cgMLST allelic profiles |
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| diff -r 9d7e381dfa5a -r 13632190a0ff test-data/sistr-results.tab --- a/test-data/sistr-results.tab Fri Mar 03 14:31:21 2017 -0500 +++ b/test-data/sistr-results.tab Thu Apr 20 14:33:38 2017 -0400 |
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| @@ -1,2 +1,2 @@ -cgmlst_distance cgmlst_genome_match cgmlst_matching_alleles cgmlst_subspecies fasta_filepath genome h1 h2 mash_distance mash_genome mash_match mash_serovar o_antigen qc_messages qc_status serogroup serovar serovar_antigen serovar_cgmlst -0.827272727273 73530 57 enterica /mnt/ssd240/work/repos/galaxy_tools/tools/sistr_cmd/test-data/AE014613-699860.fasta AE014613-699860 - - 0.0637124 60369 151 Typhi - FAIL: Large number of cgMLST330 loci missing (n=272 > 30) | FAIL: Wzx/Wzy genes missing. Cannot determine O-antigen group/serogroup. Cannot accurately predict serovar from antigen genes. | WARNING: H1 antigen gene (fliC) missing. Cannot determine H1 antigen. Cannot accurately predict serovar from antigen genes. | WARNING: Input genome size (699860 bp) not within expected range of 4000000-6000000 (bp) for Salmonella | WARNING: Only matched 57 cgMLST330 loci. Min threshold for confident serovar prediction from cgMLST is 297.0 FAIL - -:-:- -:-:- Typhi +cgmlst_ST cgmlst_distance cgmlst_genome_match cgmlst_matching_alleles cgmlst_subspecies fasta_filepath genome h1 h2 mash_distance mash_genome mash_match mash_serovar mash_subspecies o_antigen qc_messages qc_status serogroup serovar serovar_antigen serovar_cgmlst + 0.8272727272727273 73530 57 enterica /mnt/ssd240/work/repos/galaxy_tools/tools/sistr_cmd/test-data/AE014613-699860.fasta AE014613-699860 - - 0.0637124 60369 151 Typhi - FAIL: Large number of cgMLST330 loci missing (n=272 > 30) | FAIL: Wzx/Wzy genes missing. Cannot determine O-antigen group/serogroup. Cannot accurately predict serovar from antigen genes. | WARNING: H1 antigen gene (fliC) missing. Cannot determine H1 antigen. Cannot accurately predict serovar from antigen genes. | WARNING: Input genome size (699860 bp) not within expected range of 4000000-6000000 (bp) for Salmonella | WARNING: Only matched 57 cgMLST330 loci. Min threshold for confident serovar prediction from cgMLST is 297.0 FAIL - -:-:- -:-:- Typhi |