Mercurial > repos > rliterman > csp2
changeset 55:629a4fe7bb13
"planemo upload"
| author | rliterman |
|---|---|
| date | Thu, 19 Dec 2024 10:43:45 -0500 |
| parents | d0a7dd5c900e |
| children | c8ca27626fa9 |
| files | csp2_snp.xml |
| diffstat | 1 files changed, 113 insertions(+), 53 deletions(-) [+] |
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--- a/csp2_snp.xml Thu Dec 19 09:14:29 2024 -0500 +++ b/csp2_snp.xml Thu Dec 19 10:43:45 2024 -0500 @@ -8,64 +8,69 @@ <command detect_errors="aggressive"><![CDATA[ mkdir ./queries ./references; -if [ -n "$query_fasta" ] && [ "$query_fasta" != "None" ]; then - if [ -n "$use_query_fasta_collection" == "true" ]; then - #for query in $query_fasta_ELEMENTS: - ln -sf ${query} ./queries/${query.element_identifier}; - #end for - else - #for query in $query_fasta: - ln -sf ${query} ./queries/${query.element_identifier}; - #end for +if [[ "$query_fasta.query_fasta_select" == "none" ]]; then + export QUERY_FASTA_ARG=""; +elif [[ "$query_fasta.query_fasta_select" == "history" ]]; then + #for query in $query_fasta.list: + ln -sf ${query} ./queries/${query.element_identifier}; + #end for export QUERY_FASTA_ARG="--fasta ./queries"; else - export QUERY_FASTA_ARG=""; + #for query in $query_fasta.elements: + ln -sf ${query} ./queries/${query.element_identifier}; + #end for + export QUERY_FASTA_ARG="--fasta ./queries"; fi; -if [ -n "$query_reads" ] && [ "$query_reads" != "None" ]; then - if [ -n "$use_query_reads_collection" == "true" ]; then - #for query in $query_reads_ELEMENTS: - ln -sf ${query} ./queries/${query.element_identifier}; - #end for - else - #for query in $query_reads: - ln -sf ${query} ./queries/${query.element_identifier}; - #end for - export QUERY_READS_ARG="--reads ./queries"; +if [[ "$ref_fasta.ref_fasta_select" == "none" ]]; then + export REF_FASTA_ARG=""; +elif [[ "$ref_fasta.ref_fasta_select" == "history" ]]; then + #for ref in $ref_fasta.list: + ln -sf ${ref} ./references/${ref.element_identifier}; + #end for + export REF_FASTA_ARG="--ref_fasta ./references"; else - export QUERY_READS_ARG=""; + #for ref in $ref_fasta.elements: + ln -sf ${ref} ./references/${ref.element_identifier}; + #end for + export REF_FASTA_ARG="--ref_fasta ./references"; fi; -if [ -n "$ref_fasta" ] && [ "$ref_fasta" != "None" ]; then - if [ -n "$use_ref_fasta_collection" == "true" ]; then - #for ref in $ref_fasta_ELEMENTS: - ln -sf ${ref} ./references/${ref.element_identifier}; - #end for - else - #for ref in $ref_fasta: - ln -sf ${ref} ./references/${ref.element_identifier}; - #end for - export REF_FASTA_ARG="--ref_fasta ./references"; +if [[ "$query_reads.query_reads_select" == "none" ]]; then + export QUERY_READS_ARG=""; +elif [[ "$query_reads.query_reads_select" == "history" ]]; then + #for query in $query_reads.list: + ln -sf ${query} ./queries/${query.element_identifier}; + #end for + export QUERY_READS_ARG="--reads ./queries"; else - export REF_FASTA_ARG=""; + #for query in $query_reads.coll.forward: + ln -sf ${query} ./queries/${query.element_identifier}; + #end for + #for query in $query_reads.coll.reverse: + ln -sf ${query} ./queries/${query.element_identifier}; + #end for + export QUERY_READS_ARG="--reads ./queries"; fi; -if [ -n "$ref_reads" ] && [ "$ref_reads" != "None" ]; then - if [ -n "$use_ref_reads_collection" == "true" ]; then - #for ref in $ref_reads_ELEMENTS: - ln -sf ${ref} ./references/${ref.element_identifier}; - #end for - else - #for ref in $ref_reads: - ln -sf ${ref} ./references/${ref.element_identifier}; - #end for +if [[ "$ref_reads.ref_reads_select" == "none" ]]; then + export REF_READS_ARG=""; +elif [[ "$ref_reads.ref_reads_select" == "history" ]]; then + #for ref in $ref_reads.list: + ln -sf ${ref} ./references/${ref.element_identifier}; + #end for export REF_READS_ARG="--ref_reads ./references"; else - export REF_READS_ARG=""; + #for ref in $ref_reads.coll.forward: + ln -sf ${ref} ./references/${ref.element_identifier}; + #end for + #for ref in $ref_reads.coll.reverse: + ln -sf ${ref} ./references/${ref.element_identifier}; + #end for + export REF_READS_ARG="--ref_reads ./references"; fi; - -if [ -n "$trim_name" ] && [ "$trim_name" != "None" ]; then +if [[ "$trim_name" != "DUMMYCSP2TRIM" ]]; then export TRIM_ARG="--trim_name $trim_name"; else export TRIM_ARG=""; @@ -85,14 +90,69 @@ ]]> </command> <inputs> - <param name="query_fasta" type="data" format="fasta" value="" label="Query assemblies" multiple="true" optional="true" /> - <param name="use_query_fasta_collection" type="boolean" value="false" label="Use a collection for query assemblies?" optional="true" /> - <param name="ref_fasta" type="data" format="fasta" value="" label="Reference assemblies" multiple="true" optional="true" /> - <param name="use_ref_fasta_collection" type="boolean" value="false" label="Use a collection for reference assemblies?" optional="true" /> - <param name="query_reads" type="data" format="fastq,fastq.gz" value="" label="Query reads" multiple="true" optional="true" /> - <param name="use_ref_reads_collection" type="boolean" value="false" label="Use a collection for query reads?" optional="true" /> - <param name="ref_reads" type="data" format="fastq,fastq.gz" value="" label="Reference reads" multiple="true" optional="true" /> - <param name="use_ref_reads_collection" type="boolean" value="false" label="Use a collection for reference reads?" optional="true" /> + <conditional name="query_fasta"> + <param name="query_fasta_select" type="select" label="Get query assemblies from a collection or your history"> + <option value="none" selected="true">Do not provide query assemblies</option> + <option value="collection">Query assemblies from a collection_type</option> + <option value="history">Query assemblies from your history</option> + </param> + <when value="none"> + </when> + <when value="collection"> + <param label="Query Assembly Collection" name="coll" type="data_collection" format="fasta" collection_type="list" /> + </when> + <when value="history"> + <param label="Query Assembly List" type="data" name="list" format="fasta" multiple="true" /> + </when> + </conditional> + + <conditional name="ref_fasta"> + <param name="ref_fasta_select" type="select" label="Get reference assemblies from a collection or your history"> + <option value="none" selected="true">Do not provide reference assemblies</option> + <option value="collection">Reference assemblies from a collection_type</option> + <option value="history">Reference assemblies from your history</option> + </param> + <when value="none"> + </when> + <when value="collection"> + <param label="Reference Assembly Collection" name="coll" type="data_collection" format="fasta" collection_type="list" /> + </when> + <when value="history"> + <param label="Reference Assembly List" type="data" name="list" format="fasta" multiple="true" /> + </when> + </conditional> + <conditional name="query_reads"> + <param name="query_reads_select" type="select" label="Get query reads from a paired-end collection or your history"> + <option value="none" selected="true">Do not provide query reads</option> + <option value="collection">Query reads from a collection_type</option> + <option value="history">Query reads from your history</option> + </param> + <when value="none"> + </when> + <when value="collection"> + <param label="Query Reads Collection" name="coll" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" collection_type="paired" /> + </when> + <when value="history"> + <param label="Query Reads List" type="data" name="list" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" multiple="true" /> + </when> + </conditional> + + <conditional name="ref_reads"> + <param name="ref_reads_select" type="select" label="Get reference reads from a paired-end collection or your history"> + <option value="none" selected="true">Do not provide reference reads</option> + <option value="collection">Refrence reads from a collection_type</option> + <option value="history">Refrence reads from your history</option> + </param> + <when value="none"> + </when> + <when value="collection"> + <param label="Refrence Reads Collection" name="coll" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" collection_type="paired" /> + </when> + <when value="history"> + <param label="Refrence Reads List" type="data" name="list" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" multiple="true" /> + </when> + </conditional> + <param name="min_cov" type="float" value="85" label="Minimum reference genome coverage to proceed with distance estimation" optional="true" /> <param name="min_iden" type="float" value="99" label="Minimum alignment percent identity to detect SNPs" optional="true" /> <param name="min_len" type="integer" value="500" label="Minimum alignment length to detect SNPs" optional="true" /> @@ -103,7 +163,7 @@ <param name="readext" type="text" value="fastq.gz" label="Read extension format (e.g., fastq.gz)" optional="true" /> <param name="forward" type="text" value="_1.fastq.gz" label="Forward read suffix (e.g. _1.fastq.gz)" optional="true" /> <param name="reverse" type="text" value="_2.fastq.gz" label="Forward read suffix (e.g. _2.fastq.gz)" optional="true" /> - <param name="trim_name" type="text" value="" label="Text to remove from all file names (e.g., _contigs_skesa)" optional="true" /> + <param name="trim_name" type="text" value="DUMMYCSP2TRIM" label="Text to remove from all file names (e.g., _contigs_skesa)" optional="true" /> <param name="rescue" type="boolean" value="false" label="Enable SNP edge rescue mode" optional="true" /> <param name="max_missing" type="float" value="50" label="Maximum percent of isolates allowed to have missing data to retain a SNP" optional="true" /> <param name="n_ref" type="integer" value="1" label="Number of reference genomes to select" optional="true" />