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comparison csp2_snp.xml @ 54:d0a7dd5c900e

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"planemo upload"
author rliterman
date Thu, 19 Dec 2024 09:14:29 -0500
parents a21f63856acf
children 629a4fe7bb13
comparison
equal deleted inserted replaced
53:a21f63856acf 54:d0a7dd5c900e
7 <version_command>nextflow -version</version_command> 7 <version_command>nextflow -version</version_command>
8 <command detect_errors="aggressive"><![CDATA[ 8 <command detect_errors="aggressive"><![CDATA[
9 mkdir ./queries ./references; 9 mkdir ./queries ./references;
10 10
11 if [ -n "$query_fasta" ] && [ "$query_fasta" != "None" ]; then 11 if [ -n "$query_fasta" ] && [ "$query_fasta" != "None" ]; then
12 if [ -n "$query_fasta__collection_type" ]; then 12 if [ -n "$use_query_fasta_collection" == "true" ]; then
13 #for query in $query_fasta_ELEMENTS: 13 #for query in $query_fasta_ELEMENTS:
14 ln -sf ${query} ./queries/${query.element_identifier}; 14 ln -sf ${query} ./queries/${query.element_identifier};
15 #end for 15 #end for
16 else 16 else
17 #for query in $query_fasta: 17 #for query in $query_fasta:
21 else 21 else
22 export QUERY_FASTA_ARG=""; 22 export QUERY_FASTA_ARG="";
23 fi; 23 fi;
24 24
25 if [ -n "$query_reads" ] && [ "$query_reads" != "None" ]; then 25 if [ -n "$query_reads" ] && [ "$query_reads" != "None" ]; then
26 if [ -n "$query_reads__collection_type" ]; then 26 if [ -n "$use_query_reads_collection" == "true" ]; then
27 #for query in $query_reads_ELEMENTS: 27 #for query in $query_reads_ELEMENTS:
28 ln -sf ${query} ./queries/${query.element_identifier}; 28 ln -sf ${query} ./queries/${query.element_identifier};
29 #end for 29 #end for
30 else 30 else
31 #for query in $query_reads: 31 #for query in $query_reads:
35 else 35 else
36 export QUERY_READS_ARG=""; 36 export QUERY_READS_ARG="";
37 fi; 37 fi;
38 38
39 if [ -n "$ref_fasta" ] && [ "$ref_fasta" != "None" ]; then 39 if [ -n "$ref_fasta" ] && [ "$ref_fasta" != "None" ]; then
40 if [ -n "$ref_fasta__collection_type" ]; then 40 if [ -n "$use_ref_fasta_collection" == "true" ]; then
41 #for ref in $ref_fasta_ELEMENTS: 41 #for ref in $ref_fasta_ELEMENTS:
42 ln -sf ${ref} ./references/${ref.element_identifier}; 42 ln -sf ${ref} ./references/${ref.element_identifier};
43 #end for 43 #end for
44 else 44 else
45 #for ref in $ref_fasta: 45 #for ref in $ref_fasta:
49 else 49 else
50 export REF_FASTA_ARG=""; 50 export REF_FASTA_ARG="";
51 fi; 51 fi;
52 52
53 if [ -n "$ref_reads" ] && [ "$ref_reads" != "None" ]; then 53 if [ -n "$ref_reads" ] && [ "$ref_reads" != "None" ]; then
54 if [ -n "$ref_reads__collection_type" ]; then 54 if [ -n "$use_ref_reads_collection" == "true" ]; then
55 #for ref in $ref_reads_ELEMENTS: 55 #for ref in $ref_reads_ELEMENTS:
56 ln -sf ${ref} ./references/${ref.element_identifier}; 56 ln -sf ${ref} ./references/${ref.element_identifier};
57 #end for 57 #end for
58 else 58 else
59 #for ref in $ref_reads: 59 #for ref in $ref_reads:
84 84
85 ]]> 85 ]]>
86 </command> 86 </command>
87 <inputs> 87 <inputs>
88 <param name="query_fasta" type="data" format="fasta" value="" label="Query assemblies" multiple="true" optional="true" /> 88 <param name="query_fasta" type="data" format="fasta" value="" label="Query assemblies" multiple="true" optional="true" />
89 <param name="use_query_fasta_collection" type="boolean" value="false" label="Use a collection for query assemblies?" optional="true" />
89 <param name="ref_fasta" type="data" format="fasta" value="" label="Reference assemblies" multiple="true" optional="true" /> 90 <param name="ref_fasta" type="data" format="fasta" value="" label="Reference assemblies" multiple="true" optional="true" />
91 <param name="use_ref_fasta_collection" type="boolean" value="false" label="Use a collection for reference assemblies?" optional="true" />
90 <param name="query_reads" type="data" format="fastq,fastq.gz" value="" label="Query reads" multiple="true" optional="true" /> 92 <param name="query_reads" type="data" format="fastq,fastq.gz" value="" label="Query reads" multiple="true" optional="true" />
93 <param name="use_ref_reads_collection" type="boolean" value="false" label="Use a collection for query reads?" optional="true" />
91 <param name="ref_reads" type="data" format="fastq,fastq.gz" value="" label="Reference reads" multiple="true" optional="true" /> 94 <param name="ref_reads" type="data" format="fastq,fastq.gz" value="" label="Reference reads" multiple="true" optional="true" />
95 <param name="use_ref_reads_collection" type="boolean" value="false" label="Use a collection for reference reads?" optional="true" />
92 <param name="min_cov" type="float" value="85" label="Minimum reference genome coverage to proceed with distance estimation" optional="true" /> 96 <param name="min_cov" type="float" value="85" label="Minimum reference genome coverage to proceed with distance estimation" optional="true" />
93 <param name="min_iden" type="float" value="99" label="Minimum alignment percent identity to detect SNPs" optional="true" /> 97 <param name="min_iden" type="float" value="99" label="Minimum alignment percent identity to detect SNPs" optional="true" />
94 <param name="min_len" type="integer" value="500" label="Minimum alignment length to detect SNPs" optional="true" /> 98 <param name="min_len" type="integer" value="500" label="Minimum alignment length to detect SNPs" optional="true" />
95 <param name="ref_edge" type="integer" value="150" label="Prune SNPs within this many bases of reference contig edge" optional="true" /> 99 <param name="ref_edge" type="integer" value="150" label="Prune SNPs within this many bases of reference contig edge" optional="true" />
96 <param name="query_edge" type="integer" value="150" label="Prune SNPs within this many bases of query contig edge" optional="true" /> 100 <param name="query_edge" type="integer" value="150" label="Prune SNPs within this many bases of query contig edge" optional="true" />