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comparison csp2_snp.xml @ 59:d322910e773c

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"planemo upload"
author rliterman
date Thu, 19 Dec 2024 12:29:18 -0500
parents c8676ac8c6b7
children 5378cd1e3a39
comparison
equal deleted inserted replaced
58:c8676ac8c6b7 59:d322910e773c
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
12 #set query_fasta_input="" 11 #set query_fasta_input=""
13 #if $query_fasta.query_fasta_select == 'collection' 12 #set ref_fasta_input=""
13 #set query_reads_forward=""
14 #set query_reads_reverse=""
15 #set ref_reads_forward=""
16 #set ref_reads_reverse=""
17
18 #if "$query_fasta.query_fasta_select" == 'collection'
14 #set query_fasta_input=$query_fasta.coll.elements 19 #set query_fasta_input=$query_fasta.coll.elements
15 #elseif $query_fasta.query_fasta_select == 'history' 20 #elseif "$query_fasta.query_fasta_select" == 'history'
16 #set query_fasta_input=$query_fasta.list 21 #set query_fasta_input=$query_fasta.list
22 #end if
23
24 #if "$ref_fasta.ref_fasta_select" == 'collection'
25 #set ref_fasta_input=$ref_fasta.coll.elements
26 #elseif "$ref_fasta.ref_fasta_select" == 'history'
27 #set ref_fasta_input=$ref_fasta.list
28 #end if
29
30 #if "$query_reads.query_reads_select" == 'collection'
31 #set query_reads_forward=$query_reads.coll.forward
32 #set query_reads_reverse=$query_reads.coll.reverse
33 #elseif "$query_reads.query_reads_select" == 'history'
34 #set query_reads_forward=$query_reads.list
35 #set query_reads_reverse=""
36 #end if
37
38 #if "$ref_reads.ref_reads_select" == 'collection'
39 #set ref_reads_forward=$ref_reads.coll.forward
40 #set ref_reads_reverse=$ref_reads.coll.reverse
41 #elseif "$ref_reads.ref_reads_select" == 'history'
42 #set ref_reads_forward=$ref_reads.list
43 #set ref_reads_reverse=""
17 #end if 44 #end if
18 45
19 if [[ "$query_fasta.query_fasta_select" == "none" ]]; then 46 if [[ "$query_fasta.query_fasta_select" == "none" ]]; then
20 export QUERY_FASTA_ARG=""; 47 export QUERY_FASTA_ARG="";
21 else 48 else
23 ln -sf ${query} ./queries/${query.element_identifier}; 50 ln -sf ${query} ./queries/${query.element_identifier};
24 #end for 51 #end for
25 export QUERY_FASTA_ARG="--fasta ./queries"; 52 export QUERY_FASTA_ARG="--fasta ./queries";
26 fi; 53 fi;
27 54
28 #set ref_fasta_input=""
29 #if $ref_fasta.ref_fasta_select == 'collection'
30 #set ref_fasta_input=$ref_fasta.coll.elements
31 #elseif $ref_fasta.ref_fasta_select == 'history'
32 #set ref_fasta_input=$ref_fasta.list
33 #end if
34 55
35 if [[ "$ref_fasta.ref_fasta_select" == "none" ]]; then 56 if [[ "$ref_fasta.ref_fasta_select" == "none" ]]; then
36 export REF_FASTA_ARG=""; 57 export REF_FASTA_ARG="";
37 else 58 else
38 #for ref in $ref_fasta_input: 59 #for ref in $ref_fasta_input:
39 ln -sf ${ref} ./references/${ref.element_identifier}; 60 ln -sf ${ref} ./references/${ref.element_identifier};
40 #end for 61 #end for
41 export REF_FASTA_ARG="--fasta ./references"; 62 export REF_FASTA_ARG="--fasta ./references";
42 fi; 63 fi;
43 64
44 #set query_reads_forward=""
45 #set query_reads_reverse=""
46 #if $query_reads.query_reads_select == 'collection'
47 #set query_reads_forward=$query_reads.coll.forward
48 #set query_reads_reverse=$query_reads.coll.revese
49 #elseif $query_reads.query_reads_select == 'history'
50 #set query_reads_forward=$query_reads.list
51 #set query_reads_reverse=""
52 #end if
53
54 if [[ "$query_reads.query_reads_select" == "none" ]]; then 65 if [[ "$query_reads.query_reads_select" == "none" ]]; then
55 export QUERY_READS_ARG=""; 66 export QUERY_READS_ARG="";
56 else 67 else
57 #for query in $query_reads_forward $query_reads_reverse: 68 #for query in $query_reads_forward $query_reads_reverse:
58 ln -sf ${query} ./queries/${query.element_identifier}; 69 ln -sf ${query} ./queries/${query.element_identifier};
59 #end for 70 #end for
60 export QUERY_READS_ARG="--reads ./queries"; 71 export QUERY_READS_ARG="--reads ./queries";
61 fi; 72 fi;
62 73
63 #set ref_reads_forward=""
64 #set ref_reads_reverse=""
65 #if $ref_reads.ref_reads_select == 'collection'
66 #set ref_reads_forward=$ref_reads.coll.forward
67 #set ref_reads_reverse=$ref_reads.coll.revese
68 #elseif $ref_reads.ref_reads_select == 'history'
69 #set ref_reads_forward=$ref_reads.list
70 #set ref_reads_reverse=""
71 #end if
72
73 if [[ "$ref_reads.ref_reads_select" == "none" ]]; then 74 if [[ "$ref_reads.ref_reads_select" == "none" ]]; then
74 export QUERY_READS_ARG=""; 75 export QUERY_READS_ARG="";
75 else 76 else
76 #for ref in $ref_reads_forward $ref_reads_reverse: 77 #for ref in $ref_reads_forward $ref_reads_reverse:
77 ln -sf ${ref} ./references/${ref.element_identifier}; 78 ln -sf ${ref} ./references/${ref.element_identifier};
78 #end for 79 #end for
79 export QUERY_READS_ARG="--reads ./queries"; 80 export QUERY_READS_ARG="--reads ./queries";
80 fi; 81 fi;
81 82
82 if [[ "$trim_name" != "DUMMYCSP2TRIM" ]]; then 83 if [ -n "$trim_name" ] && [ "$trim_name" != "None" ]; then
83 export TRIM_ARG="--trim_name $trim_name"; 84 export TRIM_ARG="--trim_name $trim_name";
84 else 85 else
85 export TRIM_ARG=""; 86 export TRIM_ARG="";
86 fi; 87 fi;
87 88
170 <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" /> 171 <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" />
171 <param name="wsnps" type="text" value="3,2,1" label="Comma-separated list of maximum SNP counts per density window" optional="true" /> 172 <param name="wsnps" type="text" value="3,2,1" label="Comma-separated list of maximum SNP counts per density window" optional="true" />
172 <param name="readext" type="text" value="fastq.gz" label="Read extension format (e.g., fastq.gz)" optional="true" /> 173 <param name="readext" type="text" value="fastq.gz" label="Read extension format (e.g., fastq.gz)" optional="true" />
173 <param name="forward" type="text" value="_1.fastq.gz" label="Forward read suffix (e.g. _1.fastq.gz)" optional="true" /> 174 <param name="forward" type="text" value="_1.fastq.gz" label="Forward read suffix (e.g. _1.fastq.gz)" optional="true" />
174 <param name="reverse" type="text" value="_2.fastq.gz" label="Forward read suffix (e.g. _2.fastq.gz)" optional="true" /> 175 <param name="reverse" type="text" value="_2.fastq.gz" label="Forward read suffix (e.g. _2.fastq.gz)" optional="true" />
175 <param name="trim_name" type="text" value="DUMMYCSP2TRIM" label="Text to remove from all file names (e.g., _contigs_skesa)" optional="true" /> 176 <param name="trim_name" type="text" value="" label="Text to remove from all file names (e.g., _contigs_skesa)" optional="true" />
176 <param name="rescue" type="boolean" value="false" label="Enable SNP edge rescue mode" optional="true" /> 177 <param name="rescue" type="boolean" value="false" label="Enable SNP edge rescue mode" optional="true" />
177 <param name="max_missing" type="float" value="50" label="Maximum percent of isolates allowed to have missing data to retain a SNP" optional="true" /> 178 <param name="max_missing" type="float" value="50" label="Maximum percent of isolates allowed to have missing data to retain a SNP" optional="true" />
178 <param name="n_ref" type="integer" value="1" label="Number of reference genomes to select" optional="true" /> 179 <param name="n_ref" type="integer" value="1" label="Number of reference genomes to select" optional="true" />
179 180
180 </inputs> 181 </inputs>