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comparison csp2_snp.xml @ 66:90e29c1ddeca

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"planemo upload"
author rliterman
date Thu, 19 Dec 2024 15:55:32 -0500
parents c2a886313008
children 0e9998148a16
comparison
equal deleted inserted replaced
65:c2a886313008 66:90e29c1ddeca
38 38
39 #if (str($query_reads.query_reads_select) == "none"): 39 #if (str($query_reads.query_reads_select) == "none"):
40 export QUERY_READS_ARG=""; 40 export QUERY_READS_ARG="";
41 #elif (str($query_reads.query_reads_select) == "collection"): 41 #elif (str($query_reads.query_reads_select) == "collection"):
42 #for _, $pair in enumerate($query_reads.coll): 42 #for _, $pair in enumerate($query_reads.coll):
43 ln -sf ${pair.forward} ./queries/${pair.forward.element_identifier}; 43 ln -sf ${pair.forward} ./queries/${pair.forward.name};
44 ln -sf ${pair.reverse} ./queries/${pair.reverse.element_identifier}; 44 ln -sf ${pair.reverse} ./queries/${pair.reverse.name};
45 #end for 45 #end for
46 export QUERY_READS_ARG="--reads ./queries"; 46 export QUERY_READS_ARG="--reads ./queries";
47 #else 47 #else
48 #for _, $read_file in enumerate($query_reads.list): 48 #for _, $read_file in enumerate($query_reads.list):
49 ln -sf ${read_file} ./queries/${read_file.element_identifier}; 49 ln -sf ${read_file} ./queries/${read_file.element_identifier};
53 53
54 #if (str($ref_reads.ref_reads_select) == "none"): 54 #if (str($ref_reads.ref_reads_select) == "none"):
55 export REF_READS_ARG=""; 55 export REF_READS_ARG="";
56 #elif (str($ref_reads.ref_reads_select) == "collection"): 56 #elif (str($ref_reads.ref_reads_select) == "collection"):
57 #for _, $pair in enumerate($ref_reads.coll): 57 #for _, $pair in enumerate($ref_reads.coll):
58 ln -sf ${pair.forward} ./references/${pair.forward.element_identifier}; 58 ln -sf ${pair.forward} ./references/${pair.forward.name};
59 ln -sf ${pair.reverse} ./references/${pair.reverse.element_identifier}; 59 ln -sf ${pair.reverse} ./references/${pair.reverse.name};
60 #end for 60 #end for
61 export REF_READS_ARG="--ref_reads ./references"; 61 export REF_READS_ARG="--ref_reads ./references";
62 #else 62 #else
63 #for _, $read_file in enumerate($ref_reads.list): 63 #for _, $read_file in enumerate($ref_reads.list):
64 ln -sf ${read_file} ./references/${read_file.element_identifier}; 64 ln -sf ${read_file} ./references/${read_file.element_identifier};
160 <param name="forward" type="text" value="_1.fq.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" />
161 <param name="reverse" type="text" value="_2.fq.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" />
162 <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" />
163 <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" />
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" /> 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" />
165 <param name="n_ref" type="integer" value="2" label="Number of reference genomes to select" optional="true" /> 165 <param name="n_ref" type="integer" value="1" label="Number of reference genomes to select" optional="true" />
166 166
167 </inputs> 167 </inputs>
168 <outputs> 168 <outputs>
169 <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" />
170 <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" />