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Commit message:
"planemo upload" |
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modified:
csp2_screen.xml |
| csp2_screen.xml |
| diff -r 757b7dcd0ee6 -r 1f407d5f5899 csp2_screen.xml |
| csp2_screen.xml |
| --- a/csp2_screen.xml Mon Dec 02 15:44:29 2024 -0500 +++ b/csp2_screen.xml Mon Dec 02 16:44:52 2024 -0500 @@ -1,130 +1,132 @@ - <tool id="csp2-screen" name="CSP2 (Screening Mode)" version="0.9.7"> +<tool id="csp2-screen" name="CSP2 (Screening Mode)" version="0.9.7"> <description>Screen query assemblies against reference assemblies</description> <requirements> - <requirement type="package" version="24.10.1">nextflow</requirement> - <requirement type="package" version="1.5.8">micromamba</requirement> + <requirement type="package" version="24.10.1">nextflow</requirement> + <requirement type="package" version="1.5.8">micromamba</requirement> </requirements> <version_command>nextflow -version</version_command> <command detect_errors="aggressive"><![CDATA[ - export CSP2_DIR=\$PWD; - mkdir -p \$CSP2_DIR/queries \$CSP2_DIR/references; + export CSP2_DIR=\$PWD; + mkdir -p \$CSP2_DIR/queries \$CSP2_DIR/references; - if [ -n "$query_fasta" ] && [ "$query_fasta" != "None" ]; then - #for query in $query_fasta: - ln -sf ${query} \$CSP2_DIR/queries/${query.element_identifier}; - #end for - export QUERY_FASTA_ARG="--fasta \$CSP2_DIR/queries"; - else - export QUERY_FASTA_ARG=""; - fi; + if [ -n "$query_fasta" ] && [ "$query_fasta" != "None" ]; then + #for query in $query_fasta: + ln -sf ${query} \$CSP2_DIR/queries/${query.element_identifier}; + #end for + export QUERY_FASTA_ARG="--fasta \$CSP2_DIR/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}; - #end for - export QUERY_READS_ARG="--reads \$CSP2_DIR/queries"; - else - export QUERY_READS_ARG=""; - fi; + if [ -n "$query_reads" ] && [ "$query_reads" != "None" ]; then + #for query in $query_reads: + ln -sf ${query} \$CSP2_DIR/queries/${query.element_identifier}; + #end for + export QUERY_READS_ARG="--reads \$CSP2_DIR/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}; - #end for - export REF_FASTA_ARG="--ref_fasta \$CSP2_DIR/references"; - else - export REF_FASTA_ARG=""; - fi; + if [ -n "$ref_fasta" ] && [ "$ref_fasta" != "None" ]; then + #for ref in $ref_fasta: + ln -sf ${ref} \$CSP2_DIR/references/${ref.element_identifier}; + #end for + export REF_FASTA_ARG="--ref_fasta \$CSP2_DIR/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}; - #end for - export REF_READS_ARG="--ref_reads \$CSP2_DIR/references"; - else - export REF_READS_ARG=""; - fi; + if [ -n "$ref_reads" ] && [ "$ref_reads" != "None" ]; then + #for ref in $ref_reads: + ln -sf ${ref} \$CSP2_DIR/references/${ref.element_identifier}; + #end for + export REF_READS_ARG="--ref_reads \$CSP2_DIR/references"; + else + export REF_READS_ARG=""; + fi; - if [ -n "$trim_name" ] && [ "$trim_name" != "None" ]; then - export TRIM_ARG="--trim_name $trim_name"; - else - export TRIM_ARG=""; - fi; + if [ -n "$trim_name" ] && [ "$trim_name" != "None" ]; then + export TRIM_ARG="--trim_name $trim_name"; + else + export TRIM_ARG=""; + fi; - if [ -n "$ref_id" ] && [ "$ref_id" != "None" ]; then - export REF_ID_ARG="--ref_id $ref_id"; - else - export REF_ID_ARG=""; - ..emblies/Sample_J.fasta" /> - <element name="Sample_K" value="assemblies/Sample_K.fasta" /> - <element name="Sample_L" value="assemblies/Sample_L.fasta" /> - <element name="Sample_M" value="assemblies/Sample_M.fasta" /> - <element name="Sample_N" value="assemblies/Sample_N.fasta" /> - <element name="Sample_O" value="assemblies/Sample_O.fasta" /> - </collection> - </param> - <param name="query_reads"> - <collection type="list"> - <element name="Forward" value="reads/Week_42_Reads_1.fq.gz" /> - <element name="Reverse" value="reads/Week_42_Reads_2.fq.gz" /> - </collection> - </param> + <tests> + <test> + <param name="query_fasta"> + <collection type="list"> + <element name="Sample_A" value="assemblies/Sample_A.fasta" /> + <element name="Sample_B" value="assemblies/Sample_B.fasta" /> + <element name="Sample_C" value="assemblies/Sample_C.fasta" /> + <element name="Sample_D" value="assemblies/Sample_D.fasta" /> + <element name="Sample_E" value="assemblies/Sample_E.fasta" /> + <element name="Sample_F" value="assemblies/Sample_F.fasta" /> + <element name="Sample_G" value="assemblies/Sample_G.fasta" /> + <element name="Sample_H" value="assemblies/Sample_H.fasta" /> + <element name="Sample_I" value="assemblies/Sample_I.fasta" /> + <element name="Sample_J" value="assemblies/Sample_J.fasta" /> + <element name="Sample_K" value="assemblies/Sample_K.fasta" /> + <element name="Sample_L" value="assemblies/Sample_L.fasta" /> + <element name="Sample_M" value="assemblies/Sample_M.fasta" /> + <element name="Sample_N" value="assemblies/Sample_N.fasta" /> + <element name="Sample_O" value="assemblies/Sample_O.fasta" /> + </collection> + </param> + <param name="query_reads"> + <collection type="list"> + <element name="Forward" value="reads/Week_42_Reads_1.fq.gz" /> + <element name="Reverse" value="reads/Week_42_Reads_2.fq.gz" /> + </collection> + </param> - <param name="ref_id" value="Sample_A,Sample_B" /> - <param name="readext" value="fq.gz" /> - <param name="forward" value="_1.fq.gz" /> - <param name="reverse" value="_2.fq.gz" /> + <param name="ref_id" value="Sample_A,Sample_B" /> + <param name="readext" value="fq.gz" /> + <param name="forward" value="_1.fq.gz" /> + <param name="reverse" value="_2.fq.gz" /> - <output name="screening_results" value="Screening_Results.tsv" /> - <output name="isolate_data" value="Isolate_Data.tsv" /> - </test> -</tests> + <output name="screening_results" value="Screening_Results.tsv" /> + <output name="isolate_data" value="Isolate_Data.tsv" /> + </test> + </tests> <help> - This tool takes query assemblies and reference assemblies and calculates the pairwise distance between each query/reference combination. If no reference is provided, all queries are compared to all other queries. + This tool takes query assemblies and reference assemblies and calculates the pairwise distance between each query/reference combination. If no reference is provided, all queries are compared to all other queries. </help> <citations> - <citation type="doi">10.XXXX/placeholder.doi</citation> - <citation type="bibtex">@article{example2024,title={CFSAN SNP Pipeline 2 (CSP2): a pipeline for fast and accurate SNP distance estimation from bacterial genome assemblies.},author={Doe, John and Smith, Jane},journal={Submitted},year={2024}} - </citation> + <citation type="doi">10.XXXX/placeholder.doi</citation> + <citation type="bibtex">@article{example2024,title={CFSAN SNP Pipeline 2 (CSP2): a pipeline for fast and accurate SNP distance estimation from bacterial genome assemblies.},author={Doe, John and Smith, Jane},journal={Submitted},year={2024}} + </citation> </citations> - </tool> +</tool> + |