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comparison pima_report.xml @ 28:27485e70ed2b draft

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Uploaded
author greg
date Fri, 28 Apr 2023 19:40:58 +0000
parents 46edd7435555
children 1352b8aa5979
comparison
equal deleted inserted replaced
27:ddc056cf16bf 28:27485e70ed2b
80 #for $i in $mutation_regions: 80 #for $i in $mutation_regions:
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
86 #if $lrn_risk_amr_collection:
87 #set lrn_risk_amr_file = 'lrn_risk_amr.tsv'
88 touch $lrn_risk_amr_file &&
89 #for $i in $lrn_risk_amr_collection:
90 cat $i >> $lrn_risk_amr_file &&
91 #end for
92 #end if
93
94 #if $lrn_risk_blacklist_collection:
95 #set lrn_risk_blacklist_file = 'lrn_risk_blacklist.tsv'
96 touch $lrn_risk_blacklist_file &&
97 #for $i in $lrn_risk_blacklist_collection:
98 cat $i >> $lrn_risk_blacklist_file &&
99 #end for
100 #end if
101
102 #if $lrn_risk_vf_collection:
103 #set lrn_risk_vf_file = 'lrn_risk_vf.tsv'
104 touch $lrn_risk_vf_file &&
105 #for $i in $lrn_risk_vf_collection:
106 cat $i >> $lrn_risk_vf_file &&
107 #end for
108 #end if
85 109
86 python '${__tool_directory__}/pima_report.py' 110 python '${__tool_directory__}/pima_report.py'
87 --amr_matrix_png_dir 'amr_matrix_png_dir' 111 --amr_matrix_png_dir 'amr_matrix_png_dir'
88 --amr_deletions_file '$amr_deletions_file' 112 --amr_deletions_file '$amr_deletions_file'
89 --analysis_name '$analysis_name' 113 --analysis_name '$analysis_name'
129 --illumina_reverse_read_file '$read_type_cond.illumina_reverse_read' 153 --illumina_reverse_read_file '$read_type_cond.illumina_reverse_read'
130 #end if 154 #end if
131 #if str($kraken2_report_file) not in ['None', '']: 155 #if str($kraken2_report_file) not in ['None', '']:
132 --kraken2_report_file '$kraken2_report_file' 156 --kraken2_report_file '$kraken2_report_file'
133 --kraken2_version '$kraken2_version' 157 --kraken2_version '$kraken2_version'
158 #end if
159 #if $lrn_risk_amr_collection:
160 --lrn_risk_amr_file '$lrn_risk_amr_file'
161 #end if
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'
134 #end if 167 #end if
135 #if str($minimap2_bam_file) not in ['None', '']: 168 #if str($minimap2_bam_file) not in ['None', '']:
136 --minimap2_version '$minimap2_version' 169 --minimap2_version '$minimap2_version'
137 #end if 170 #end if
138 --mutation_regions_dir 'mutation_regions_dir' 171 --mutation_regions_dir 'mutation_regions_dir'
165 <param name="features_bed" format="bed" type="data_collection" collection_type="list" label="Collection of best feature hits BED files"/> 198 <param name="features_bed" format="bed" type="data_collection" collection_type="list" label="Collection of best feature hits BED files"/>
166 <param name="features_png" format="png" type="data_collection" collection_type="list" label="Collection of best feature hits PNG files"/> 199 <param name="features_png" format="png" type="data_collection" collection_type="list" label="Collection of best feature hits PNG files"/>
167 <param name="assembler_version_file" type="data" format="fasta,tabular,tsv" optional="true" label="Assembly version file" help="Optional, ignored if not selected"/> 200 <param name="assembler_version_file" type="data" format="fasta,tabular,tsv" optional="true" label="Assembly version file" help="Optional, ignored if not selected"/>
168 <param name="genome_insertions_file" type="data" format="bed" label="Genome insertions BED file"/> 201 <param name="genome_insertions_file" type="data" format="bed" label="Genome insertions BED file"/>
169 <param name="kraken2_report_file" type="data" format="tabular,tsv" optional="true" label="Kraken2 report tabular file" help="Optional, ignored if not selected"/> 202 <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"/>
204 <param name="lrn_risk_blacklist_collection" format="tsv" type="data_collection" collection_type="list" optional="true" label="LRN Risk blacklist collection"/>
205 <param name="lrn_risk_vf_collection" format="tsv" type="data_collection" collection_type="list" optional="true" label="LRN Risk virulence factors collection"/>
170 <param name="minimap2_bam_file" type="data" format="bam" label="Minimap2 BAM file"/> 206 <param name="minimap2_bam_file" type="data" format="bam" label="Minimap2 BAM file"/>
171 <param name="mutation_regions" format="tabular,tsv" type="data_collection" collection_type="list" label="Collection of mutation regions tabular files"/> 207 <param name="mutation_regions" format="tabular,tsv" type="data_collection" collection_type="list" label="Collection of mutation regions tabular files"/>
172 <param name="mutation_regions_bed_file" type="data" format="mutations_regions,bed" label="Mutation regions BED file"/> 208 <param name="mutation_regions_bed_file" type="data" format="mutations_regions,bed" label="Mutation regions BED file"/>
173 <param name="quast_report_file" type="data" format="tabular" label="Quast report tabular file"/> 209 <param name="quast_report_file" type="data" format="tabular" label="Quast report tabular file"/>
174 <conditional name="read_type_cond"> 210 <conditional name="read_type_cond">