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comparison csp2_snp.xml @ 63:b87f07ac9edc

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"planemo upload"
author rliterman
date Thu, 19 Dec 2024 14:02:04 -0500
parents 0552b9528fc4
children 6f3b67127e44
comparison
equal deleted inserted replaced
62:0552b9528fc4 63:b87f07ac9edc
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 #set query_fasta_input="" 11 #if (str($query_fasta.query_fasta_select) == "none"):
12 #set ref_fasta_input=""
13 #set query_reads_forward=""
14 #set query_reads_reverse=""
15 #set ref_reads_forward=""
16 #set ref_reads_reverse=""
17
18 export QUERY_FASTA_SELECT="$query_fasta.query_fasta_select"
19 export QUERY_READS_SELECT="$query_reads.query_reads_select"
20 export REF_FASTA_SELECT="$ref_fasta.ref_fasta_select"
21 export REF_READS_SELECT="$ref_reads.ref_reads_select"
22
23 echo "Query Fasta: \$QUERY_FASTA_SELECT";
24 echo "Ref Fasta: \$REF_FASTA_SELECT";
25
26 echo "Query Reads: \$QUERY_READS_SELECT";
27 echo "Ref Reads: \$REF_READS_SELECT";
28
29 if [[ "\$QUERY_FASTA_SELECT" == 'collection' ]]; then
30 #set query_fasta_input=$query_fasta.coll.elements
31 elif [[ "\$QUERY_FASTA_SELECT" == 'history' ]]; then
32 #set query_fasta_input=$query_fasta.list
33 fi;
34
35 if [[ "\$REF_FASTA_SELECT" == 'collection' ]]; then
36 #set ref_fasta_input=$ref_fasta.coll.elements
37 elif [[ "\$REF_FASTA_SELECT" == 'history' ]]; then
38 #set ref_fasta_input=$ref_fasta.list
39 fi;
40
41 if [[ "\$QUERY_READS_SELECT" == 'collection' ]]; then
42 #set query_reads_forward=$query_reads.coll.forward
43 #set query_reads_reverse=$query_reads.coll.reverse
44 elif [[ "\$QUERY_READS_SELECT" == 'history' ]]; then
45 #set query_reads_forward=$query_reads.list
46 fi;
47
48 if [[ "\$REF_READS_SELECT" == 'collection' ]]; then
49 #set ref_reads_forward=$ref_reads.coll.forward
50 #set ref_reads_reverse=$ref_reads.coll.reverse
51 elif [[ "\$REF_READS_SELECT" == 'history' ]]; then
52 #set ref_reads_forward=$ref_reads.list
53 fi;
54
55 if [[ "\$QUERY_FASTA_SELECT" == 'none' ]]; then
56 export QUERY_FASTA_ARG=""; 12 export QUERY_FASTA_ARG="";
57 else 13 #elif (str($query_fasta.query_fasta_select) == "collection"):
58 #for query in $query_fasta_input: 14 #for _, $query_assembly in enumerate($query_fasta.coll):
59 ln -sf ${query} ./queries/${query.element_identifier}; 15 ln -sf ${query_assembly} ./queries/${query_assembly.element_identifier};
60 #end for 16 #end for
61 export QUERY_FASTA_ARG="--fasta ./queries"; 17 export QUERY_FASTA_ARG="--fasta ./queries";
62 fi; 18 #else
63 19 #for _, $query_assembly in enumerate($query_fasta.list):
64 if [[ "\$REF_FASTA_SELECT" == "none" ]]; then 20 ln -sf ${query_assembly} ./queries/${query_assembly.element_identifier};
21 #end for
22 export QUERY_FASTA_ARG="--fasta ./queries";
23 #end if
24
25 #if (str($ref_fasta.ref_fasta_select) == "none"):
65 export REF_FASTA_ARG=""; 26 export REF_FASTA_ARG="";
66 else 27 #elif (str($ref_fasta.ref_fasta_select) == "collection"):
67 #for ref in $ref_fasta_input: 28 #for _, $ref_assembly in enumerate($ref_fasta.coll):
68 ln -sf ${ref} ./references/${ref.element_identifier}; 29 ln -sf ${ref_assembly} ./references/${ref_assembly.element_identifier};
30 #end for
31 export REF_FASTA_ARG="--fasta ./queries";
32 else
33 #for _, $ref_assembly in enumerate($ref_fasta.list):
34 ln -sf ${ref_assembly} ./references/${ref_assembly.element_identifier};
69 #end for 35 #end for
70 export REF_FASTA_ARG="--fasta ./references"; 36 export REF_FASTA_ARG="--fasta ./references";
71 fi; 37 #end if
72 38
73 if [[ "\$QUERY_READS_SELECT" == "none" ]]; then 39 #if (str($query_reads.query_reads_select) == "none"):
74 export QUERY_READS_ARG=""; 40 export QUERY_READS_ARG="";
75 else 41 #elif (str($query_reads.query_reads_select) == "collection"):
76 #for query in $query_reads_forward $query_reads_reverse: 42 #for _, $pair in enumerate($query_reads.coll):
77 ln -sf ${query} ./queries/${query.element_identifier}; 43 ln -sf '$pair.forward' ./queries/${pair.forward.element_identifier};
44 ln -sf '$pair.reverse' ./queries/${pair.reverse.element_identifier};
78 #end for 45 #end for
79 export QUERY_READS_ARG="--reads ./queries"; 46 export QUERY_READS_ARG="--reads ./queries";
80 fi; 47 else
81 48 #for _, $read_file in enumerate($query_reads.list):
82 if [[ "\$REF_READS_SELECT" == "none" ]]; then 49 ln -sf ${read_file} ./queries/${read_file.element_identifier};
83 export QUERY_READS_ARG=""; 50 #end for
84 else 51 export QUERY_FASTA_ARG="--reads ./queries";
85 #for ref in $ref_reads_forward $ref_reads_reverse: 52 #end if
86 ln -sf ${ref} ./references/${ref.element_identifier}; 53
87 #end for 54 #if (str($ref_reads.ref_reads_select) == "none"):
88 export QUERY_READS_ARG="--reads ./queries"; 55 export REF_READS_ARG="";
89 fi; 56 #elif (str($ref_reads.ref_reads_select) == "collection"):
57 #for _, $pair in enumerate($ref_reads.coll):
58 ln -sf '$pair.forward' ./references/${pair.forward.element_identifier};
59 ln -sf '$pair.reverse' ./references/${pair.reverse.element_identifier};
60 #end for
61 export REF_READS_ARG="--ref_reads ./references";
62 else
63 #for _, $read_file in enumerate($ref_reads.list):
64 ln -sf ${read_file} ./references/${read_file.element_identifier};
65 #end for
66 export REF_FASTA_ARG="--ref_reads ./references";
67 #end if
90 68
91 if [ -n "$trim_name" ] && [ "$trim_name" != "None" ]; then 69 if [ -n "$trim_name" ] && [ "$trim_name" != "None" ]; then
92 export TRIM_ARG="--trim_name $trim_name"; 70 export TRIM_ARG="--trim_name $trim_name";
93 else 71 else
94 export TRIM_ARG=""; 72 export TRIM_ARG="";
146 <option value="history">Query reads from your history</option> 124 <option value="history">Query reads from your history</option>
147 </param> 125 </param>
148 <when value="none"> 126 <when value="none">
149 </when> 127 </when>
150 <when value="collection"> 128 <when value="collection">
151 <param label="Query Reads Collection" name="coll" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" collection_type="paired" /> 129 <param label="Query Reads Collection" name="coll" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" collection_type="list:paired" />
152 </when> 130 </when>
153 <when value="history"> 131 <when value="history">
154 <param label="Query Reads List" type="data" name="list" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" multiple="true" /> 132 <param label="Query Reads List" type="data" name="list" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" multiple="true" />
155 </when> 133 </when>
156 </conditional> 134 </conditional>
162 <option value="history">Refrence reads from your history</option> 140 <option value="history">Refrence reads from your history</option>
163 </param> 141 </param>
164 <when value="none"> 142 <when value="none">
165 </when> 143 </when>
166 <when value="collection"> 144 <when value="collection">
167 <param label="Refrence Reads Collection" name="coll" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" collection_type="paired" /> 145 <param label="Refrence Reads Collection" name="coll" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" collection_type="list:paired" />
168 </when> 146 </when>
169 <when value="history"> 147 <when value="history">
170 <param label="Refrence Reads List" type="data" name="list" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" multiple="true" /> 148 <param label="Refrence Reads List" type="data" name="list" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" multiple="true" />
171 </when> 149 </when>
172 </conditional> 150 </conditional>
176 <param name="min_len" type="integer" value="500" label="Minimum alignment length to detect SNPs" optional="true" /> 154 <param name="min_len" type="integer" value="500" label="Minimum alignment length to detect SNPs" optional="true" />
177 <param name="ref_edge" type="integer" value="150" label="Prune SNPs within this many bases of reference contig edge" optional="true" /> 155 <param name="ref_edge" type="integer" value="150" label="Prune SNPs within this many bases of reference contig edge" optional="true" />
178 <param name="query_edge" type="integer" value="150" label="Prune SNPs within this many bases of query contig edge" optional="true" /> 156 <param name="query_edge" type="integer" value="150" label="Prune SNPs within this many bases of query contig edge" optional="true" />
179 <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" /> 157 <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" />
180 <param name="wsnps" type="text" value="3,2,1" label="Comma-separated list of maximum SNP counts per density window" optional="true" /> 158 <param name="wsnps" type="text" value="3,2,1" label="Comma-separated list of maximum SNP counts per density window" optional="true" />
181 <param name="readext" type="text" value="fastq.gz" label="Read extension format (e.g., fastq.gz)" optional="true" /> 159 <param name="readext" type="text" value="fq.gz" label="Read extension format (e.g., fastq.gz)" optional="true" />
182 <param name="forward" type="text" value="_1.fastq.gz" label="Forward read suffix (e.g. _1.fastq.gz)" optional="true" /> 160 <param name="forward" type="text" value="_1.fq.gz" label="Forward read suffix (e.g. _1.fastq.gz)" optional="true" />
183 <param name="reverse" type="text" value="_2.fastq.gz" label="Forward read suffix (e.g. _2.fastq.gz)" optional="true" /> 161 <param name="reverse" type="text" value="_2.fq.gz" label="Forward read suffix (e.g. _2.fastq.gz)" optional="true" />
184 <param name="trim_name" type="text" value="" label="Text to remove from all file names (e.g., _contigs_skesa)" optional="true" /> 162 <param name="trim_name" type="text" value="" label="Text to remove from all file names (e.g., _contigs_skesa)" optional="true" />
185 <param name="rescue" type="boolean" value="false" label="Enable SNP edge rescue mode" optional="true" /> 163 <param name="rescue" type="boolean" value="false" label="Enable SNP edge rescue mode" optional="true" />
186 <param name="max_missing" type="float" value="50" label="Maximum percent of isolates allowed to have missing data to retain a SNP" optional="true" /> 164 <param name="max_missing" type="float" value="50" label="Maximum percent of isolates allowed to have missing data to retain a SNP" optional="true" />
187 <param name="n_ref" type="integer" value="1" label="Number of reference genomes to select" optional="true" /> 165 <param name="n_ref" type="integer" value="2" label="Number of reference genomes to select" optional="true" />
188 166
189 </inputs> 167 </inputs>
190 <outputs> 168 <outputs>
191 <data name="isolate_data" format="tabular" label="Isolate Data" from_work_dir="CSP2_SNP_Output/Isolate_Data.tsv" /> 169 <data name="isolate_data" format="tabular" label="Isolate Data" from_work_dir="CSP2_SNP_Output/Isolate_Data.tsv" />
192 <data name="raw_mummer" format="tabular" label="Raw MUMmer Output" from_work_dir="CSP2_SNP_Output/Raw_MUMmer_Summary.tsv" /> 170 <data name="raw_mummer" format="tabular" label="Raw MUMmer Output" from_work_dir="CSP2_SNP_Output/Raw_MUMmer_Summary.tsv" />