| Previous changeset 53:a21f63856acf (2024-12-19) Next changeset 55:629a4fe7bb13 (2024-12-19) |
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Commit message:
"planemo upload" |
|
modified:
csp2_snp.xml |
| csp2_snp.xml |
| diff -r a21f63856acf -r d0a7dd5c900e csp2_snp.xml |
| csp2_snp.xml |
| --- a/csp2_snp.xml Thu Dec 19 08:53:33 2024 -0500 +++ b/csp2_snp.xml Thu Dec 19 09:14:29 2024 -0500 @@ -9,7 +9,7 @@ mkdir ./queries ./references; if [ -n "$query_fasta" ] && [ "$query_fasta" != "None" ]; then - if [ -n "$query_fasta__collection_type" ]; then + if [ -n "$use_query_fasta_collection" == "true" ]; then #for query in $query_fasta_ELEMENTS: ln -sf ${query} ./queries/${query.element_identifier}; #end for @@ -23,7 +23,7 @@ fi; if [ -n "$query_reads" ] && [ "$query_reads" != "None" ]; then - if [ -n "$query_reads__collection_type" ]; then + if [ -n "$use_query_reads_collection" == "true" ]; then #for query in $query_reads_ELEMENTS: ln -sf ${query} ./queries/${query.element_identifier}; #end for @@ -37,7 +37,7 @@ fi; if [ -n "$ref_fasta" ] && [ "$ref_fasta" != "None" ]; then - if [ -n "$ref_fasta__collection_type" ]; then + if [ -n "$use_ref_fasta_collection" == "true" ]; then #for ref in $ref_fasta_ELEMENTS: ln -sf ${ref} ./references/${ref.element_identifier}; #end for @@ -51,7 +51,7 @@ fi; if [ -n "$ref_reads" ] && [ "$ref_reads" != "None" ]; then - if [ -n "$ref_reads__collection_type" ]; then + if [ -n "$use_ref_reads_collection" == "true" ]; then #for ref in $ref_reads_ELEMENTS: ln -sf ${ref} ./references/${ref.element_identifier}; #end for @@ -86,9 +86,13 @@ </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" /> <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" /> |