Mercurial > repos > rliterman > csp2
changeset 51:2a36d0ebb408
"planemo upload"
| author | rliterman |
|---|---|
| date | Fri, 13 Dec 2024 08:49:33 -0500 |
| parents | 16b103443761 |
| children | 44cbdce84814 |
| files | csp2_snp.xml |
| diffstat | 1 files changed, 29 insertions(+), 20 deletions(-) [+] |
line wrap: on
line diff
--- a/csp2_snp.xml Thu Dec 12 18:30:42 2024 -0500 +++ b/csp2_snp.xml Fri Dec 13 08:49:33 2024 -0500 @@ -6,41 +6,40 @@ </requirements> <version_command>nextflow -version</version_command> <command detect_errors="aggressive"><![CDATA[ -export CSP2_DIR=\$PWD; -mkdir -p \$CSP2_DIR/queries \$CSP2_DIR/references; +mkdir ./queries ./references; if [ -n "$query_fasta" ] && [ "$query_fasta" != "None" ]; then #for query in $query_fasta: - ln -sf ${query} \$CSP2_DIR/queries/${query.element_identifier}; + ln -sf ${query} ./queries/${query.element_identifier}; #end for - export QUERY_FASTA_ARG="--fasta \$CSP2_DIR/queries"; + export QUERY_FASTA_ARG="--fasta ./queries"; else export QUERY_FASTA_ARG=""; fi; if [ -n "$query_reads" ] && [ "$query_reads" != "None" ]; then #for query in $query_reads: - ln -sf ${query} \$CSP2_DIR/queries/${query.element_identifier}; + ln -sf ${query} ./queries/${query.element_identifier}; #end for - export QUERY_READS_ARG="--reads \$CSP2_DIR/queries"; + export QUERY_READS_ARG="--reads ./queries"; else export QUERY_READS_ARG=""; fi; if [ -n "$ref_fasta" ] && [ "$ref_fasta" != "None" ]; then #for ref in $ref_fasta: - ln -sf ${ref} \$CSP2_DIR/references/${ref.element_identifier}; + ln -sf ${ref} ./references/${ref.element_identifier}; #end for - export REF_FASTA_ARG="--ref_fasta \$CSP2_DIR/references"; + export REF_FASTA_ARG="--ref_fasta ./references"; else export REF_FASTA_ARG=""; fi; if [ -n "$ref_reads" ] && [ "$ref_reads" != "None" ]; then #for ref in $ref_reads: - ln -sf ${ref} \$CSP2_DIR/references/${ref.element_identifier}; + ln -sf ${ref} ./references/${ref.element_identifier}; #end for - export REF_READS_ARG="--ref_reads \$CSP2_DIR/references"; + export REF_READS_ARG="--ref_reads ./references"; else export REF_READS_ARG=""; fi; @@ -57,9 +56,12 @@ export RESCUE_ARG=""; fi; -nextflow run ${__tool_directory__}/CSP2/CSP2.nf -profile csp2_galaxy --runmode snp \$QUERY_FASTA_ARG \$REF_FASTA_ARG \$QUERY_READS_ARG \$REF_READS_ARG \$TRIM_ARG \$RESCUE_ARG --readext $readext --forward $forward --reverse $reverse --ref_readext $readext --ref_forward $forward --ref_reverse $reverse --min_cov $min_cov --min_iden $min_iden --min_len $min_len --ref_edge $ref_edge --query_edge $query_edge --dwin $dwin --wsnps $wsnps --max_missing $max_missing --out \$CSP2_DIR/CSP2_SNP_Output > Nextflow_Log.txt 2>&1; +nextflow run ${__tool_directory__}/CSP2/CSP2.nf -profile csp2_galaxy --runmode snp \$QUERY_FASTA_ARG \$REF_FASTA_ARG \$QUERY_READS_ARG \$REF_READS_ARG \$TRIM_ARG \$RESCUE_ARG --readext $readext --forward $forward --reverse $reverse --ref_readext $readext --ref_forward $forward --ref_reverse $reverse --min_cov $min_cov --min_iden $min_iden --min_len $min_len --ref_edge $ref_edge --query_edge $query_edge --dwin $dwin --wsnps $wsnps --max_missing $max_missing --out ./CSP2_SNP_Output > Nextflow_Log.txt 2>&1 && +ls -la CSP2_SNP_Output/SNP_Analysis/* && +mkdir CSP2_Output && +cat CSP2_SNP_Output/logs/Reference_IDs.txt | while read line; do cp 'CSP2_SNP_Output/SNP_Analysis/'\$line'/CSP2_SNP_Pipeline.log' 'CSP2_Output/'\$line'_CSP2_SNP_Pipeline.log'; cp 'CSP2_SNP_Output/SNP_Analysis/'\$line'/Reference_Screening.tsv' 'CSP2_Output/'\$line'_Reference_Screening.tsv'; cp 'CSP2_SNP_Output/SNP_Analysis/'\$line'/snp_distance_matrix_preserved.tsv' 'CSP2_Output/'\$line'_snp_distance_matrix_preserved.tsv'; cp 'CSP2_SNP_Output/SNP_Analysis/'\$line'/snp_distance_pairwise_preserved.tsv' 'CSP2_Output/'\$line'_snp_distance_pairwise_preserved.tsv'; cp 'CSP2_SNP_Output/SNP_Analysis/'\$line'/snpma_preserved.fasta' 'CSP2_Output/'\$line'_snpma_preserved.fasta';done && +ls -la CSP2_Output; -zip -r CSP2_Output.zip CSP2_SNP_Output; ]]> </command> <inputs> @@ -82,16 +84,23 @@ <param name="max_missing" type="float" value="50" label="Maximum percent of isolates allowed to have missing data to retain a SNP" optional="true" /> </inputs> <outputs> - <data name="nextflow_log" format="txt" label="Nextflow Log" from_work_dir="Nextflow_Log.txt" /> <data name="isolate_data" format="tabular" label="Isolate Data" from_work_dir="CSP2_SNP_Output/Isolate_Data.tsv" /> <data name="raw_mummer" format="tabular" label="Raw MUMmer Output" from_work_dir="CSP2_SNP_Output/Raw_MUMmer_Summary.tsv" /> - <data name="csp2_zip" format="zip" label="Zipped Output" from_work_dir="CSP2_Output.zip" /> - <collection name="reference_results" type="list:list"> - <discover_datasets pattern="*/CSP2_SNP_Pipeline.log" format="txt" visible="true" directory="./CSP2_SNP_Output/SNP_Analysis" /> - <discover_datasets pattern="*/Reference_Screening.tsv" format="tabular" visible="true" directory="./CSP2_SNP_Output/SNP_Analysis" /> - <discover_datasets pattern="*/snp_distance_matrix_preserved.tsv" format="tabular" visible="true" directory="./CSP2_SNP_Output/SNP_Analysis" /> - <discover_datasets pattern="*/snp_distance_pairwise_preserved.tsv" format="tabular" visible="true" directory="./CSP2_SNP_Output/SNP_Analysis" /> - <discover_datasets pattern="*/snpma_preserved.fasta" format="fasta" visible="true" directory="./CSP2_SNP_Output/SNP_Analysis" /> + + <collection name="csp2_logs" type='list' label="CSP2 Log"> + <discover_datasets pattern="(?P<designation>.+)_CSP2_SNP_Pipeline\.log" directory="CSP2_Output" format='txt'/> + </collection> + <collection name="csp2_alignments" type='list' label="CSP2 Alignment"> + <discover_datasets pattern="(?P<designation>.+)_snpma_preserved\.fasta" directory="CSP2_Output" format='fasta'/> + </collection> + <collection name="csp2_matrices" type='list' label="CSP2 Matrices"> + <discover_datasets pattern="(?P<designation>.+)_snp_distance_matrix_preserved\.tsv" directory="CSP2_Output" format='tabular'/> + </collection> + <collection name="csp2_pairwise" type='list' label="CSP2 Pairwise Distances"> + <discover_datasets pattern="(?P<designation>.+)_snp_distance_pairwise_preserved\.tsv" directory="CSP2_Output" format='tabular'/> + </collection> + <collection name="csp2_ref_screening" type='list' label="CSP2 Reference Screening"> + <discover_datasets pattern="(?P<designation>.+)_Reference_Screening\.tsv" directory="CSP2_Output" format='tabular'/> </collection> </outputs> <tests>