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comparison bio_hansel.xml @ 5:6396d043667b draft

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planemo upload for repository https://github.com/phac-nml/bio_hansel commit f9ecb9b31d5cace7e1a1ded13dd2e5eb8ef7759e-dirty
author nml
date Wed, 21 Feb 2018 12:13:32 -0500
parents c0d08ba0c6ee
children 5a42e475436e
comparison
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4:c0d08ba0c6ee 5:6396d043667b
1 <tool id="bio_hansel" name="Bio Hansel" version="1.0.1"> 1 <tool id="bio_hansel" name="Bio Hansel" version="1.2.0">
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="1.1.3">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>
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 ## Preparing file input. 8 ## Preparing file input.
9 #if $data_type.type == "paired": 9 #if $data_type.type == "paired":
10 10
11 ln -s '$data_type.fastq_input1' '$data_type.fastq_input1.name' && 11 ln -s '$data_type.fastq_input1' '$data_type.fastq_input1.name'.fastq &&
12 ln -s '$data_type.fastq_input2' '$data_type.fastq_input2.name' && 12 ln -s '$data_type.fastq_input2' '$data_type.fastq_input2.name'.fastq &&
13 13
14 #elif $data_type.type == "collection": 14 #elif $data_type.type == "collection":
15 15
16 ln -s '$data_type.fastq_input1.forward' '$data_type.fastq_input1.name'_1 && 16 ln -s '$data_type.fastq_input1.forward' '$data_type.fastq_input1.name'_1.fastq &&
17 ln -s '$data_type.fastq_input1.reverse' '$data_type.fastq_input1.name'_2 && 17 ln -s '$data_type.fastq_input1.reverse' '$data_type.fastq_input1.name'_2.fastq &&
18 18
19 #elif $data_type.type == "single": 19 #elif $data_type.type == "single":
20 20
21 #if $data_type.fastq_input1.is_of_type('fastqsanger') or $data_type.fastq_input1.is_of_type('fastq'): 21 #if $data_type.fastq_input1.is_of_type('fastqsanger') or $data_type.fastq_input1.is_of_type('fastq'):
22 ln -s '$data_type.fastq_input1' '$data_type.fastq_input1.name' && 22 ln -s '$data_type.fastq_input1' '$data_type.fastq_input1.name'.fastq &&
23 #end if 23 #end if
24 24
25 #if $data_type.fastq_input1.is_of_type('fasta'): 25 #if $data_type.fastq_input1.is_of_type('fasta'):
26 ln -s '$data_type.fastq_input1' '$data_type.fastq_input1.name' && 26 ln -s '$data_type.fastq_input1' '$data_type.fastq_input1.name'.fasta &&
27 #end if 27 #end if
28 28
29 #end if 29 #end if
30 30
31 31
49 enteritidis 49 enteritidis
50 #elif $type_of_scheme.scheme_type == "custom": 50 #elif $type_of_scheme.scheme_type == "custom":
51 '$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
55 #if $dev_args.use_json == "yes":
56 --json
57 #end if
54 58
55 #if $kmer_vals.kmer_min 59 #if $kmer_vals.kmer_min
56 --min-kmer-freq $kmer_vals.kmer_min 60 --min-kmer-freq $kmer_vals.kmer_min
57 #end if 61 #end if
58 62
81 85
82 86
83 ## Entering the file inputs 87 ## Entering the file inputs
84 88
85 #if $data_type.type == "single": 89 #if $data_type.type == "single":
86 '$data_type.fastq_input1.name' 90
91 #if $data_type.fastq_input1.is_of_type('fastqsanger') or $data_type.fastq_input1.is_of_type('fastq'):
92 '$data_type.fastq_input1.name'.fastq
93 #end if
94
95 #if $data_type.fastq_input1.is_of_type('fasta'):
96 '$data_type.fastq_input1.name'.fasta
97 #end if
87 98
88 #elif $data_type.type =="collection": 99 #elif $data_type.type =="collection":
89 -p '$data_type.fastq_input1.name'_1 '$data_type.fastq_input1.name'_2 100 -p '$data_type.fastq_input1.name'_1.fastq '$data_type.fastq_input1.name'_2.fastq
90 101
91 #elif $data_type.type =="paired": 102 #elif $data_type.type =="paired":
92 -p '$data_type.fastq_input1.name' '$data_type.fastq_input2.name' 103 -p '$data_type.fastq_input1.name'.fastq '$data_type.fastq_input2.name'.fastq
93 104
94 #end if 105 #end if
95 106
96 107
97 ]]></command> 108 ]]></command>
135 <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"/> 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"/>
136 <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"/> 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"/>
137 <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}"/> 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}"/>
138 <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}"/> 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}"/>
139 </section> 150 </section>
151 <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">
153 <option value="no">no</option>
154 <option value="yes">yes</option>
155 </param>
156 </section>
140 </inputs> 157 </inputs>
141 <outputs> 158 <outputs>
142 <data format="tabular" name="results.tab" from_work_dir="results.tab" label="results.tab"/> 159 <data format="tabular" name="results.tab" from_work_dir="results.tab" label="results.tab"/>
143 <data format="tabular" name="match_results.tab" from_work_dir="match_results.tab" label="match_results.tab"/> 160 <data format="tabular" name="match_results.tab" from_work_dir="match_results.tab" label="match_results.tab"/>
144 <data format="tabular" name="tech_results.tab" from_work_dir="tech_results.tab" label="tech_results.tab"/> 161 <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">
163 <filter>dev_args['use_json'] == "yes"</filter>
164 </data>
165 <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>
167 </data>
168 <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>
170 </data>
145 </outputs> 171 </outputs>
146 <tests> 172 <tests>
147 <test> 173 <test>
148 <param name="type" value="single"/> 174 <param name="type" value="single"/>
149 <param name="type_of_scheme" value="heidelberg"/> 175 <param name="type_of_scheme" value="heidelberg"/>
150 <param name="fastq_input1" value="SRR1002850_SMALL.fasta"/> 176 <param name="fastq_input1" value="SRR1002850_SMALL.fasta"/>
151 <output name="results.tab"> 177 <output name="results.tab">
152 <assert_contents> 178 <assert_contents>
153 <has_text_matching expression="sample\s+scheme\s+scheme_version\s+subtype\s+all_subtypes\s+tiles_matching_subtype\s+are_subtypes_consistent\s+inconsistent_subtypes\s+n_tiles_matching_all\s+n_tiles_matching_all_expected\s+n_tiles_matching_positive\s+n_tiles_matching_positive_expected\s+n_tiles_matching_subtype\s+n_tiles_matching_subtype_expected\s+file_path\s+qc_status\s+qc_message"/> 179 <has_text_matching expression="sample\s+scheme\s+scheme_version\s+subtype\s+all_subtypes\s+tiles_matching_subtype\s+are_subtypes_consistent\s+n_tiles_matching_all\s+n_tiles_matching_all_expected\s+n_tiles_matching_positive\s+n_tiles_matching_positive_expected\s+n_tiles_matching_subtype\s+n_tiles_matching_subtype_expected\s+file_path\s+qc_status\s+qc_message"/>
154 </assert_contents> 180 </assert_contents>
155 </output> 181 </output>
156 <output name="match_results.tab"> 182 <output name="match_results.tab">
157 <assert_contents> 183 <assert_contents>
158 <has_text_matching expression="tilename\s+seq\s+is_revcomp\s+contig_id\s+match_index\s+refposition\s+subtype\s+is_pos_tile\s+sample\s+file_path\s+scheme\s+scheme_version\s+qc_status\s+qc_message"/> 184 <has_text_matching expression="tilename\s+seq\s+is_revcomp\s+contig_id\s+match_index\s+refposition\s+subtype\s+is_pos_tile\s+sample\s+file_path\s+scheme\s+scheme_version\s+qc_status\s+qc_message"/>
169 <param name="type_of_scheme" value="heidelberg"/> 195 <param name="type_of_scheme" value="heidelberg"/>
170 <param name="fastq_input1" value="SRR5646583_SMALL_1.fastq"/> 196 <param name="fastq_input1" value="SRR5646583_SMALL_1.fastq"/>
171 <param name="fastq_input2" value="SRR5646583_SMALL_2.fastq"/> 197 <param name="fastq_input2" value="SRR5646583_SMALL_2.fastq"/>
172 <output name="results.tab"> 198 <output name="results.tab">
173 <assert_contents> 199 <assert_contents>
174 <has_text_matching expression="sample\s+scheme\s+scheme_version\s+subtype\s+all_subtypes\s+tiles_matching_subtype\s+are_subtypes_consistent\s+inconsistent_subtypes\s+n_tiles_matching_all\s+n_tiles_matching_all_expected\s+n_tiles_matching_positive\s+n_tiles_matching_positive_expected\s+n_tiles_matching_subtype\s+n_tiles_matching_subtype_expected\s+file_path\s+qc_status\s+qc_message"/> 200 <has_text_matching expression="sample\s+scheme\s+scheme_version\s+subtype\s+all_subtypes\s+tiles_matching_subtype\s+are_subtypes_consistent\s+n_tiles_matching_all\s+n_tiles_matching_all_expected\s+n_tiles_matching_positive\s+n_tiles_matching_positive_expected\s+n_tiles_matching_subtype\s+n_tiles_matching_subtype_expected\s+file_path"/>
175 </assert_contents> 201 </assert_contents>
176 </output> 202 </output>
177 <output name="match_results.tab"> 203 <output name="match_results.tab">
178 <assert_contents> 204 <assert_contents>
179 <has_text_matching expression="tilename\s+seq\s+freq\s+refposition\s+subtype\s+is_pos_tile\s+is_kmer_freq_okay\s+sample\s+scheme\s+scheme_version\s+qc_status\s+qc_message"/> 205 <has_text_matching expression="tilename\s+seq\s+freq\s+refposition\s+subtype\s+is_pos_tile\s+is_kmer_freq_okay\s+sample\s+scheme\s+scheme_version\s+qc_status\s+qc_message"/>
180 </assert_contents> 206 </assert_contents>
181 </output> 207 </output>
182 <output name="tech_results.tab"> 208 <output name="tech_results.tab">
183 <assert_contents> 209 <assert_contents>
184 <has_text_matching expression="sample\s+subtype\s+qc_status\s+qc_message"/> 210 <has_text_matching expression="sample\s+subtype\s+avg_tile_coverage\s+qc_status\s+qc_message"/>
185 </assert_contents> 211 </assert_contents>
186 </output> 212 </output>
187 </test> 213 </test>
188 </tests> 214 </tests>
189 <help><![CDATA[ 215 <help><![CDATA[