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comparison csp2_snp.xml @ 55:629a4fe7bb13

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"planemo upload"
author rliterman
date Thu, 19 Dec 2024 10:43:45 -0500
parents d0a7dd5c900e
children c8ca27626fa9
comparison
equal deleted inserted replaced
54:d0a7dd5c900e 55:629a4fe7bb13
6 </requirements> 6 </requirements>
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 [[ "$query_fasta.query_fasta_select" == "none" ]]; then
12 if [ -n "$use_query_fasta_collection" == "true" ]; then 12 export QUERY_FASTA_ARG="";
13 #for query in $query_fasta_ELEMENTS: 13 elif [[ "$query_fasta.query_fasta_select" == "history" ]]; then
14 ln -sf ${query} ./queries/${query.element_identifier}; 14 #for query in $query_fasta.list:
15 #end for 15 ln -sf ${query} ./queries/${query.element_identifier};
16 else 16 #end for
17 #for query in $query_fasta:
18 ln -sf ${query} ./queries/${query.element_identifier};
19 #end for
20 export QUERY_FASTA_ARG="--fasta ./queries"; 17 export QUERY_FASTA_ARG="--fasta ./queries";
21 else 18 else
22 export QUERY_FASTA_ARG=""; 19 #for query in $query_fasta.elements:
23 fi; 20 ln -sf ${query} ./queries/${query.element_identifier};
24 21 #end for
25 if [ -n "$query_reads" ] && [ "$query_reads" != "None" ]; then 22 export QUERY_FASTA_ARG="--fasta ./queries";
26 if [ -n "$use_query_reads_collection" == "true" ]; then 23 fi;
27 #for query in $query_reads_ELEMENTS: 24
28 ln -sf ${query} ./queries/${query.element_identifier}; 25 if [[ "$ref_fasta.ref_fasta_select" == "none" ]]; then
29 #end for 26 export REF_FASTA_ARG="";
30 else 27 elif [[ "$ref_fasta.ref_fasta_select" == "history" ]]; then
31 #for query in $query_reads: 28 #for ref in $ref_fasta.list:
32 ln -sf ${query} ./queries/${query.element_identifier}; 29 ln -sf ${ref} ./references/${ref.element_identifier};
33 #end for 30 #end for
34 export QUERY_READS_ARG="--reads ./queries"; 31 export REF_FASTA_ARG="--ref_fasta ./references";
35 else 32 else
33 #for ref in $ref_fasta.elements:
34 ln -sf ${ref} ./references/${ref.element_identifier};
35 #end for
36 export REF_FASTA_ARG="--ref_fasta ./references";
37 fi;
38
39 if [[ "$query_reads.query_reads_select" == "none" ]]; then
36 export QUERY_READS_ARG=""; 40 export QUERY_READS_ARG="";
37 fi; 41 elif [[ "$query_reads.query_reads_select" == "history" ]]; then
38 42 #for query in $query_reads.list:
39 if [ -n "$ref_fasta" ] && [ "$ref_fasta" != "None" ]; then 43 ln -sf ${query} ./queries/${query.element_identifier};
40 if [ -n "$use_ref_fasta_collection" == "true" ]; then 44 #end for
41 #for ref in $ref_fasta_ELEMENTS: 45 export QUERY_READS_ARG="--reads ./queries";
42 ln -sf ${ref} ./references/${ref.element_identifier}; 46 else
43 #end for 47 #for query in $query_reads.coll.forward:
44 else 48 ln -sf ${query} ./queries/${query.element_identifier};
45 #for ref in $ref_fasta: 49 #end for
46 ln -sf ${ref} ./references/${ref.element_identifier}; 50 #for query in $query_reads.coll.reverse:
47 #end for 51 ln -sf ${query} ./queries/${query.element_identifier};
48 export REF_FASTA_ARG="--ref_fasta ./references"; 52 #end for
49 else 53 export QUERY_READS_ARG="--reads ./queries";
50 export REF_FASTA_ARG=""; 54 fi;
51 fi; 55
52 56 if [[ "$ref_reads.ref_reads_select" == "none" ]]; then
53 if [ -n "$ref_reads" ] && [ "$ref_reads" != "None" ]; then 57 export REF_READS_ARG="";
54 if [ -n "$use_ref_reads_collection" == "true" ]; then 58 elif [[ "$ref_reads.ref_reads_select" == "history" ]]; then
55 #for ref in $ref_reads_ELEMENTS: 59 #for ref in $ref_reads.list:
56 ln -sf ${ref} ./references/${ref.element_identifier}; 60 ln -sf ${ref} ./references/${ref.element_identifier};
57 #end for 61 #end for
58 else
59 #for ref in $ref_reads:
60 ln -sf ${ref} ./references/${ref.element_identifier};
61 #end for
62 export REF_READS_ARG="--ref_reads ./references"; 62 export REF_READS_ARG="--ref_reads ./references";
63 else 63 else
64 export REF_READS_ARG=""; 64 #for ref in $ref_reads.coll.forward:
65 fi; 65 ln -sf ${ref} ./references/${ref.element_identifier};
66 66 #end for
67 67 #for ref in $ref_reads.coll.reverse:
68 if [ -n "$trim_name" ] && [ "$trim_name" != "None" ]; then 68 ln -sf ${ref} ./references/${ref.element_identifier};
69 #end for
70 export REF_READS_ARG="--ref_reads ./references";
71 fi;
72
73 if [[ "$trim_name" != "DUMMYCSP2TRIM" ]]; then
69 export TRIM_ARG="--trim_name $trim_name"; 74 export TRIM_ARG="--trim_name $trim_name";
70 else 75 else
71 export TRIM_ARG=""; 76 export TRIM_ARG="";
72 fi; 77 fi;
73 78
83 ls -la CSP2_Output; 88 ls -la CSP2_Output;
84 89
85 ]]> 90 ]]>
86 </command> 91 </command>
87 <inputs> 92 <inputs>
88 <param name="query_fasta" type="data" format="fasta" value="" label="Query assemblies" multiple="true" optional="true" /> 93 <conditional name="query_fasta">
89 <param name="use_query_fasta_collection" type="boolean" value="false" label="Use a collection for query assemblies?" optional="true" /> 94 <param name="query_fasta_select" type="select" label="Get query assemblies from a collection or your history">
90 <param name="ref_fasta" type="data" format="fasta" value="" label="Reference assemblies" multiple="true" optional="true" /> 95 <option value="none" selected="true">Do not provide query assemblies</option>
91 <param name="use_ref_fasta_collection" type="boolean" value="false" label="Use a collection for reference assemblies?" optional="true" /> 96 <option value="collection">Query assemblies from a collection_type</option>
92 <param name="query_reads" type="data" format="fastq,fastq.gz" value="" label="Query reads" multiple="true" optional="true" /> 97 <option value="history">Query assemblies from your history</option>
93 <param name="use_ref_reads_collection" type="boolean" value="false" label="Use a collection for query reads?" optional="true" /> 98 </param>
94 <param name="ref_reads" type="data" format="fastq,fastq.gz" value="" label="Reference reads" multiple="true" optional="true" /> 99 <when value="none">
95 <param name="use_ref_reads_collection" type="boolean" value="false" label="Use a collection for reference reads?" optional="true" /> 100 </when>
101 <when value="collection">
102 <param label="Query Assembly Collection" name="coll" type="data_collection" format="fasta" collection_type="list" />
103 </when>
104 <when value="history">
105 <param label="Query Assembly List" type="data" name="list" format="fasta" multiple="true" />
106 </when>
107 </conditional>
108
109 <conditional name="ref_fasta">
110 <param name="ref_fasta_select" type="select" label="Get reference assemblies from a collection or your history">
111 <option value="none" selected="true">Do not provide reference assemblies</option>
112 <option value="collection">Reference assemblies from a collection_type</option>
113 <option value="history">Reference assemblies from your history</option>
114 </param>
115 <when value="none">
116 </when>
117 <when value="collection">
118 <param label="Reference Assembly Collection" name="coll" type="data_collection" format="fasta" collection_type="list" />
119 </when>
120 <when value="history">
121 <param label="Reference Assembly List" type="data" name="list" format="fasta" multiple="true" />
122 </when>
123 </conditional>
124 <conditional name="query_reads">
125 <param name="query_reads_select" type="select" label="Get query reads from a paired-end collection or your history">
126 <option value="none" selected="true">Do not provide query reads</option>
127 <option value="collection">Query reads from a collection_type</option>
128 <option value="history">Query reads from your history</option>
129 </param>
130 <when value="none">
131 </when>
132 <when value="collection">
133 <param label="Query Reads Collection" name="coll" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" collection_type="paired" />
134 </when>
135 <when value="history">
136 <param label="Query Reads List" type="data" name="list" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" multiple="true" />
137 </when>
138 </conditional>
139
140 <conditional name="ref_reads">
141 <param name="ref_reads_select" type="select" label="Get reference reads from a paired-end collection or your history">
142 <option value="none" selected="true">Do not provide reference reads</option>
143 <option value="collection">Refrence reads from a collection_type</option>
144 <option value="history">Refrence reads from your history</option>
145 </param>
146 <when value="none">
147 </when>
148 <when value="collection">
149 <param label="Refrence Reads Collection" name="coll" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" collection_type="paired" />
150 </when>
151 <when value="history">
152 <param label="Refrence Reads List" type="data" name="list" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" multiple="true" />
153 </when>
154 </conditional>
155
96 <param name="min_cov" type="float" value="85" label="Minimum reference genome coverage to proceed with distance estimation" optional="true" /> 156 <param name="min_cov" type="float" value="85" label="Minimum reference genome coverage to proceed with distance estimation" optional="true" />
97 <param name="min_iden" type="float" value="99" label="Minimum alignment percent identity to detect SNPs" optional="true" /> 157 <param name="min_iden" type="float" value="99" label="Minimum alignment percent identity to detect SNPs" optional="true" />
98 <param name="min_len" type="integer" value="500" label="Minimum alignment length to detect SNPs" optional="true" /> 158 <param name="min_len" type="integer" value="500" label="Minimum alignment length to detect SNPs" optional="true" />
99 <param name="ref_edge" type="integer" value="150" label="Prune SNPs within this many bases of reference contig edge" optional="true" /> 159 <param name="ref_edge" type="integer" value="150" label="Prune SNPs within this many bases of reference 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" /> 160 <param name="query_edge" type="integer" value="150" label="Prune SNPs within this many bases of query contig edge" optional="true" />
101 <param name="dwin" type="text" value="1000,125,15" label="Comma-separated set of window sizes for SNP density filtration (Set to 0 to disable density filtration)" optional="true" /> 161 <param name="dwin" type="text" value="1000,125,15" label="Comma-separated set of window sizes for SNP density filtration (Set to 0 to disable density filtration)" optional="true" />
102 <param name="wsnps" type="text" value="3,2,1" label="Comma-separated list of maximum SNP counts per density window" optional="true" /> 162 <param name="wsnps" type="text" value="3,2,1" label="Comma-separated list of maximum SNP counts per density window" optional="true" />
103 <param name="readext" type="text" value="fastq.gz" label="Read extension format (e.g., fastq.gz)" optional="true" /> 163 <param name="readext" type="text" value="fastq.gz" label="Read extension format (e.g., fastq.gz)" optional="true" />
104 <param name="forward" type="text" value="_1.fastq.gz" label="Forward read suffix (e.g. _1.fastq.gz)" optional="true" /> 164 <param name="forward" type="text" value="_1.fastq.gz" label="Forward read suffix (e.g. _1.fastq.gz)" optional="true" />
105 <param name="reverse" type="text" value="_2.fastq.gz" label="Forward read suffix (e.g. _2.fastq.gz)" optional="true" /> 165 <param name="reverse" type="text" value="_2.fastq.gz" label="Forward read suffix (e.g. _2.fastq.gz)" optional="true" />
106 <param name="trim_name" type="text" value="" label="Text to remove from all file names (e.g., _contigs_skesa)" optional="true" /> 166 <param name="trim_name" type="text" value="DUMMYCSP2TRIM" label="Text to remove from all file names (e.g., _contigs_skesa)" optional="true" />
107 <param name="rescue" type="boolean" value="false" label="Enable SNP edge rescue mode" optional="true" /> 167 <param name="rescue" type="boolean" value="false" label="Enable SNP edge rescue mode" optional="true" />
108 <param name="max_missing" type="float" value="50" label="Maximum percent of isolates allowed to have missing data to retain a SNP" optional="true" /> 168 <param name="max_missing" type="float" value="50" label="Maximum percent of isolates allowed to have missing data to retain a SNP" optional="true" />
109 <param name="n_ref" type="integer" value="1" label="Number of reference genomes to select" optional="true" /> 169 <param name="n_ref" type="integer" value="1" label="Number of reference genomes to select" optional="true" />
110 170
111 </inputs> 171 </inputs>