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comparison csp2_snp.xml @ 67:0e9998148a16

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"planemo upload"
author rliterman
date Thu, 19 Dec 2024 18:42:33 -0500
parents 90e29c1ddeca
children
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66:90e29c1ddeca 67:0e9998148a16
87 </command> 87 </command>
88 <inputs> 88 <inputs>
89 <conditional name="query_fasta"> 89 <conditional name="query_fasta">
90 <param name="query_fasta_select" type="select" label="Get query assemblies from a collection or your history"> 90 <param name="query_fasta_select" type="select" label="Get query assemblies from a collection or your history">
91 <option value="none" selected="true">Do not provide query assemblies</option> 91 <option value="none" selected="true">Do not provide query assemblies</option>
92 <option value="collection">Query assemblies from a collection_type</option> 92 <option value="collection">Query assemblies from a FASTA collection</option>
93 <option value="history">Query assemblies from your history</option> 93 <option value="history">Query assemblies from your history</option>
94 </param> 94 </param>
95 <when value="none"> 95 <when value="none">
96 </when> 96 </when>
97 <when value="collection"> 97 <when value="collection">
103 </conditional> 103 </conditional>
104 104
105 <conditional name="ref_fasta"> 105 <conditional name="ref_fasta">
106 <param name="ref_fasta_select" type="select" label="Get reference assemblies from a collection or your history"> 106 <param name="ref_fasta_select" type="select" label="Get reference assemblies from a collection or your history">
107 <option value="none" selected="true">Do not provide reference assemblies</option> 107 <option value="none" selected="true">Do not provide reference assemblies</option>
108 <option value="collection">Reference assemblies from a collection_type</option> 108 <option value="collection">Reference assemblies from a FASTA collection</option>
109 <option value="history">Reference assemblies from your history</option> 109 <option value="history">Reference assemblies from your history</option>
110 </param> 110 </param>
111 <when value="none"> 111 <when value="none">
112 </when> 112 </when>
113 <when value="collection"> 113 <when value="collection">
118 </when> 118 </when>
119 </conditional> 119 </conditional>
120 <conditional name="query_reads"> 120 <conditional name="query_reads">
121 <param name="query_reads_select" type="select" label="Get query reads from a paired-end collection or your history"> 121 <param name="query_reads_select" type="select" label="Get query reads from a paired-end collection or your history">
122 <option value="none" selected="true">Do not provide query reads</option> 122 <option value="none" selected="true">Do not provide query reads</option>
123 <option value="collection">Query reads from a collection_type</option> 123 <option value="collection">Paired-end query reads from a collection</option>
124 <option value="history">Query reads from your history</option> 124 <option value="history">Query reads from your history</option>
125 </param> 125 </param>
126 <when value="none"> 126 <when value="none">
127 </when> 127 </when>
128 <when value="collection"> 128 <when value="collection">
134 </conditional> 134 </conditional>
135 135
136 <conditional name="ref_reads"> 136 <conditional name="ref_reads">
137 <param name="ref_reads_select" type="select" label="Get reference reads from a paired-end collection or your history"> 137 <param name="ref_reads_select" type="select" label="Get reference reads from a paired-end collection or your history">
138 <option value="none" selected="true">Do not provide reference reads</option> 138 <option value="none" selected="true">Do not provide reference reads</option>
139 <option value="collection">Refrence reads from a collection_type</option> 139 <option value="collection">Paired-end reference reads from a collection_type</option>
140 <option value="history">Refrence reads from your history</option> 140 <option value="history">Reference reads from your history</option>
141 </param> 141 </param>
142 <when value="none"> 142 <when value="none">
143 </when> 143 </when>
144 <when value="collection"> 144 <when value="collection">
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" /> 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" />
154 <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" />
155 <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" />
156 <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" />
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" /> 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" />
158 <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" />
159 <param name="readext" type="text" value="fq.gz" label="Read extension format (e.g., fastq.gz)" optional="true" /> 159 <param name="readext" type="text" value="fastq.gz" label="Read extension format (e.g., 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" /> 160 <param name="forward" type="text" value="_1.fastq.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.fastq.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="1" 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 (disabled if reference reads/assemblies are provided)" 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" />