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comparison bio_hansel.xml @ 6:5a42e475436e draft

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planemo upload for repository https://github.com/phac-nml/bio_hansel commit e04f7d6043451f66946394d5a14582a1b39a6ec7-dirty
author nml
date Thu, 22 Feb 2018 12:21:08 -0500
parents 6396d043667b
children af59ac462926
comparison
equal deleted inserted replaced
5:6396d043667b 6:5a42e475436e
1 <tool id="bio_hansel" name="Bio Hansel" version="1.2.0"> 1 <tool id="bio_hansel" name="Bio Hansel" version="1.2.1">
2 <description>SNV Subtyping with genome assemblies or reads</description> 2 <description>SNV Subtyping with genome assemblies or reads</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.2.0">bio_hansel</requirement> 4 <requirement type="package" version="1.2.0">bio_hansel</requirement>
5 <requirement type="package" version="17.2.0">attrs</requirement> 5 <requirement type="package" version="17.2.0">attrs</requirement>
6 </requirements> 6 </requirements>
51 '$type_of_scheme.scheme_input.name' 51 '$type_of_scheme.scheme_input.name'
52 #end if 52 #end if
53 53
54 ## Use Json output 54 ## Use Json output
55 #if $dev_args.use_json == "yes": 55 #if $dev_args.use_json == "yes":
56 --json 56 --json
57 #end if 57 #end if
58 58
59 #if $kmer_vals.kmer_min 59 #if $kmer_vals.kmer_min
60 --min-kmer-freq $kmer_vals.kmer_min 60 --min-kmer-freq $kmer_vals.kmer_min
61 #end if 61 #end if
76 --min-ambiguous-tiles $qc_vals.min_ambiguous_tiles 76 --min-ambiguous-tiles $qc_vals.min_ambiguous_tiles
77 #end if 77 #end if
78 78
79 #if $qc_vals.max_intermediate_tiles 79 #if $qc_vals.max_intermediate_tiles
80 --max-intermediate-tiles $qc_vals.max_intermediate_tiles 80 --max-intermediate-tiles $qc_vals.max_intermediate_tiles
81 #end if
82
83 #if $qc_vals.low_coverage_warning
84 --low-cov-warning $qc_vals.low_coverage_warning
81 #end if 85 #end if
82 86
83 ## Adding more parameters to the command. 87 ## Adding more parameters to the command.
84 -vvv -t "\${GALAXY_SLOTS:-1}" -o results.tab -O match_results.tab -S tech_results.tab 88 -vvv -t "\${GALAXY_SLOTS:-1}" -o results.tab -O match_results.tab -S tech_results.tab
85 89
99 #elif $data_type.type =="collection": 103 #elif $data_type.type =="collection":
100 -p '$data_type.fastq_input1.name'_1.fastq '$data_type.fastq_input1.name'_2.fastq 104 -p '$data_type.fastq_input1.name'_1.fastq '$data_type.fastq_input1.name'_2.fastq
101 105
102 #elif $data_type.type =="paired": 106 #elif $data_type.type =="paired":
103 -p '$data_type.fastq_input1.name'.fastq '$data_type.fastq_input2.name'.fastq 107 -p '$data_type.fastq_input1.name'.fastq '$data_type.fastq_input2.name'.fastq
104 108 #end if
105 #end if
106
107 109
108 ]]></command> 110 ]]></command>
109 <inputs> 111 <inputs>
110 <conditional name="data_type"> 112 <conditional name="data_type">
111 <param name="type" type="select" label="Specify the read type."> 113 <param name="type" type="select" label="Specify the read type.">
145 <section name="qc_vals" title="Quality Checking Thresholds" expanded="False"> 147 <section name="qc_vals" title="Quality Checking Thresholds" expanded="False">
146 <param name="low_cov_depth_freq" argument="--low-cov-depth-freq" optional="True" type="integer" min="0" label="QC: Frequency below this coverage are considered low coverage" value="20" help="default = 20"/> 148 <param name="low_cov_depth_freq" argument="--low-cov-depth-freq" optional="True" type="integer" min="0" label="QC: Frequency below this coverage are considered low coverage" value="20" help="default = 20"/>
147 <param name="min_ambiguous_tiles" argument="--min-ambiguous-tiles" optional="True" type="integer" min="0" label="QC: Min number of tiles missing for Ambiguous Result" value="3" help="default = 3"/> 149 <param name="min_ambiguous_tiles" argument="--min-ambiguous-tiles" optional="True" type="integer" min="0" label="QC: Min number of tiles missing for Ambiguous Result" value="3" help="default = 3"/>
148 <param name="max_missing_tiles" argument="--max-missing-tiles" optional="True" type="float" min="0" max="1" label="QC: Decimal Proportion of max allowed missing tiles" value="0.05" help="default = 0.05, valid values {0.0 - 1.0}"/> 150 <param name="max_missing_tiles" argument="--max-missing-tiles" optional="True" type="float" min="0" max="1" label="QC: Decimal Proportion of max allowed missing tiles" value="0.05" help="default = 0.05, valid values {0.0 - 1.0}"/>
149 <param name="max_intermediate_tiles" argument="--max-intermediate-tiles" optional="True" type="float" min="0" max="1" label="QC: Decimal Proportion of max allowed missing tiles for an intermediate subtype" value="0.05" help="default = 0.05, valid values {0.0 - 1.0}"/> 151 <param name="max_intermediate_tiles" argument="--max-intermediate-tiles" optional="True" type="float" min="0" max="1" label="QC: Decimal Proportion of max allowed missing tiles for an intermediate subtype" value="0.05" help="default = 0.05, valid values {0.0 - 1.0}"/>
152 <param name="low_coverage_warning" argument="--low-cov-warning" optional="True" type="integer" min="0" label="QC: Overall tile coverage below this value will trigger a low coverage warning" value="20" help="default = 20"/>
150 </section> 153 </section>
151 <section name="dev_args" title="Developer Options" expanded="False"> 154 <section name="dev_args" title="Developer Options" expanded="False">
152 <param name="use_json" type="select" label="Enable JSON output" help="Use this option of you need json representations of analysis' details"> 155 <param name="use_json" type="select" label="Enable JSON output" help="Use this option of you need json representations of analysis' details">
153 <option value="no">no</option> 156 <option value="no">no</option>
154 <option value="yes">yes</option> 157 <option value="yes">yes</option>
155 </param> 158 </param>
156 </section> 159 </section>
157 </inputs> 160 </inputs>
158 <outputs> 161 <outputs>
159 <data format="tabular" name="results.tab" from_work_dir="results.tab" label="results.tab"/> 162 <data format="tabular" name="results.tab" from_work_dir="results.tab" label="results.tab"/>
160 <data format="tabular" name="match_results.tab" from_work_dir="match_results.tab" label="match_results.tab"/> 163 <data format="tabular" name="match_results.tab" from_work_dir="match_results.tab" label="match_results.tab"/>
161 <data format="tabular" name="tech_results.tab" from_work_dir="tech_results.tab" label="tech_results.tab"/> 164 <data format="tabular" name="tech_results.tab" from_work_dir="tech_results.tab" label="tech_results.tab"/>
162 <data format="json" name="results.json" from_work_dir="results.tab.json" label="results.json"> 165 <data format="json" name="results.json" from_work_dir="results.tab.json" label="results.json">
163 <filter>dev_args['use_json'] == "yes"</filter> 166 <filter>dev_args['use_json'] == "yes"</filter>
164 </data> 167 </data>
165 <data format="json" name="match_results.json" from_work_dir="match_results.tab.json" label="match_results.json"> 168 <data format="json" name="match_results.json" from_work_dir="match_results.tab.json" label="match_results.json">
166 <filter>dev_args['use_json'] == "yes"</filter> 169 <filter>dev_args['use_json'] == "yes"</filter>
167 </data> 170 </data>
168 <data format="json" name="tech_results.json" from_work_dir="tech_results.tab.json" label="tech_results.json"> 171 <data format="json" name="tech_results.json" from_work_dir="tech_results.tab.json" label="tech_results.json">
169 <filter>dev_args['use_json'] == "yes"</filter> 172 <filter>dev_args['use_json'] == "yes"</filter>
170 </data> 173 </data>
171 </outputs> 174 </outputs>
172 <tests> 175 <tests>
173 <test> 176 <test>
174 <param name="type" value="single"/> 177 <param name="type" value="single"/>