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comparison pima_report.xml @ 29:1352b8aa5979 draft

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author greg
date Tue, 02 May 2023 13:40:06 +0000
parents 27485e70ed2b
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28:27485e70ed2b 29:1352b8aa5979
81 #set file_name = $i.file_name 81 #set file_name = $i.file_name
82 #set identifier = re.sub('[^\s\w\-\\.]', '_', str($i.element_identifier)) 82 #set identifier = re.sub('[^\s\w\-\\.]', '_', str($i.element_identifier))
83 ln -s $i 'mutation_regions_dir/$identifier' && 83 ln -s $i 'mutation_regions_dir/$identifier' &&
84 #end for 84 #end for
85 85
86 #if $lrn_risk_amr_collection: 86 #if str($lrn_risk_amr_files) != 'None':
87 #set lrn_risk_amr_file = 'lrn_risk_amr.tsv' 87 touch 'lrn_risk_amr.tsv' &&
88 touch $lrn_risk_amr_file && 88 #for $i in $lrn_risk_amr_files:
89 #for $i in $lrn_risk_amr_collection: 89 cat $i >> 'lrn_risk_amr.tsv' &&
90 cat $i >> $lrn_risk_amr_file &&
91 #end for 90 #end for
92 #end if 91 #end if
93 92
94 #if $lrn_risk_blacklist_collection: 93 #if str($lrn_risk_blacklist_files) != 'None':
95 #set lrn_risk_blacklist_file = 'lrn_risk_blacklist.tsv' 94 touch 'lrn_risk_blacklist.tsv' &&
96 touch $lrn_risk_blacklist_file && 95 #for $i in $lrn_risk_blacklist_files:
97 #for $i in $lrn_risk_blacklist_collection: 96 cat $i >> 'lrn_risk_blacklist.tsv' &&
98 cat $i >> $lrn_risk_blacklist_file &&
99 #end for 97 #end for
100 #end if 98 #end if
101 99
102 #if $lrn_risk_vf_collection: 100 #if str($lrn_risk_vf_files) != 'None':
103 #set lrn_risk_vf_file = 'lrn_risk_vf.tsv' 101 touch 'lrn_risk_vf.tsv' &&
104 touch $lrn_risk_vf_file && 102 #for $i in $lrn_risk_vf_files:
105 #for $i in $lrn_risk_vf_collection: 103 cat $i >> 'lrn_risk_vf.tsv' &&
106 cat $i >> $lrn_risk_vf_file &&
107 #end for 104 #end for
108 #end if 105 #end if
109 106
110 python '${__tool_directory__}/pima_report.py' 107 python '${__tool_directory__}/pima_report.py'
111 --amr_matrix_png_dir 'amr_matrix_png_dir' 108 --amr_matrix_png_dir 'amr_matrix_png_dir'
154 #end if 151 #end if
155 #if str($kraken2_report_file) not in ['None', '']: 152 #if str($kraken2_report_file) not in ['None', '']:
156 --kraken2_report_file '$kraken2_report_file' 153 --kraken2_report_file '$kraken2_report_file'
157 --kraken2_version '$kraken2_version' 154 --kraken2_version '$kraken2_version'
158 #end if 155 #end if
159 #if $lrn_risk_amr_collection: 156 --lrn_risk_amr_file 'lrn_risk_amr.tsv'
160 --lrn_risk_amr_file '$lrn_risk_amr_file' 157 --lrn_risk_blacklist_file 'lrn_risk_blacklist.tsv'
161 #end if 158 --lrn_risk_vf_file 'lrn_risk_vf.tsv'
162 #if $lrn_risk_blacklist_collection:
163 --lrn_risk_blacklist_file '$lrn_risk_blacklist_file'
164 #end if
165 #if $lrn_risk_vf_collection:
166 --lrn_risk_vf_file '$lrn_risk_vf_file'
167 #end if
168 #if str($minimap2_bam_file) not in ['None', '']: 159 #if str($minimap2_bam_file) not in ['None', '']:
169 --minimap2_version '$minimap2_version' 160 --minimap2_version '$minimap2_version'
170 #end if 161 #end if
171 --mutation_regions_dir 'mutation_regions_dir' 162 --mutation_regions_dir 'mutation_regions_dir'
172 --mutation_regions_bed_file '$mutation_regions_bed_file' 163 --mutation_regions_bed_file '$mutation_regions_bed_file'
198 <param name="features_bed" format="bed" type="data_collection" collection_type="list" label="Collection of best feature hits BED files"/> 189 <param name="features_bed" format="bed" type="data_collection" collection_type="list" label="Collection of best feature hits BED files"/>
199 <param name="features_png" format="png" type="data_collection" collection_type="list" label="Collection of best feature hits PNG files"/> 190 <param name="features_png" format="png" type="data_collection" collection_type="list" label="Collection of best feature hits PNG files"/>
200 <param name="assembler_version_file" type="data" format="fasta,tabular,tsv" optional="true" label="Assembly version file" help="Optional, ignored if not selected"/> 191 <param name="assembler_version_file" type="data" format="fasta,tabular,tsv" optional="true" label="Assembly version file" help="Optional, ignored if not selected"/>
201 <param name="genome_insertions_file" type="data" format="bed" label="Genome insertions BED file"/> 192 <param name="genome_insertions_file" type="data" format="bed" label="Genome insertions BED file"/>
202 <param name="kraken2_report_file" type="data" format="tabular,tsv" optional="true" label="Kraken2 report tabular file" help="Optional, ignored if not selected"/> 193 <param name="kraken2_report_file" type="data" format="tabular,tsv" optional="true" label="Kraken2 report tabular file" help="Optional, ignored if not selected"/>
203 <param name="lrn_risk_amr_collection" format="tsv" type="data_collection" collection_type="list" optional="true" label="LRN Risk AMR collection"/> 194 <param name="lrn_risk_amr_files" format="tsv" type="data" multiple="true" optional="true" label="LRN Risk AMR files"/>
204 <param name="lrn_risk_blacklist_collection" format="tsv" type="data_collection" collection_type="list" optional="true" label="LRN Risk blacklist collection"/> 195 <param name="lrn_risk_blacklist_files" format="tsv" type="data" multiple="true" optional="true" label="LRN Risk blacklist files"/>
205 <param name="lrn_risk_vf_collection" format="tsv" type="data_collection" collection_type="list" optional="true" label="LRN Risk virulence factors collection"/> 196 <param name="lrn_risk_vf_files" format="tsv" type="data" multiple="true" optional="true" label="LRN Risk virulence factors files"/>
206 <param name="minimap2_bam_file" type="data" format="bam" label="Minimap2 BAM file"/> 197 <param name="minimap2_bam_file" type="data" format="bam" label="Minimap2 BAM file"/>
207 <param name="mutation_regions" format="tabular,tsv" type="data_collection" collection_type="list" label="Collection of mutation regions tabular files"/> 198 <param name="mutation_regions" format="tabular,tsv" type="data_collection" collection_type="list" label="Collection of mutation regions tabular files"/>
208 <param name="mutation_regions_bed_file" type="data" format="mutations_regions,bed" label="Mutation regions BED file"/> 199 <param name="mutation_regions_bed_file" type="data" format="mutations_regions,bed" label="Mutation regions BED file"/>
209 <param name="quast_report_file" type="data" format="tabular" label="Quast report tabular file"/> 200 <param name="quast_report_file" type="data" format="tabular" label="Quast report tabular file"/>
210 <conditional name="read_type_cond"> 201 <conditional name="read_type_cond">