Mercurial > repos > pimarin > abromics_galaxy_json_extractor

comparison abromics_galaxy_json_extractor.xml @ 3:73aea20004ff draft default tip

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planemo upload commit 8721cd95e02dd6b3a02e2eb549cd8ff6b1675ff8-dirty
author pimarin
date Sun, 23 Jul 2023 13:54:14 +0000
parents 421032d8dd5d
children
comparison
equal deleted inserted replaced
2:99499a61fa9e 3:73aea20004ff
68 --hypothetical_tabular_hid '$tool.select_tool.hypothetical_tabular_path.hid' 68 --hypothetical_tabular_hid '$tool.select_tool.hypothetical_tabular_path.hid'
69 #end if 69 #end if
70 #if str($tool.select_tool.plot_file_path) != 'None' 70 #if str($tool.select_tool.plot_file_path) != 'None'
71 --plot_file_path '$tool.select_tool.plot_file_path' 71 --plot_file_path '$tool.select_tool.plot_file_path'
72 --plot_file_hid '$tool.select_tool.plot_file_path.hid' 72 --plot_file_hid '$tool.select_tool.plot_file_path.hid'
73 #end if 73 #end if
74 #elif $tool.select_tool.tool_list == "bandage" 74 #elif $tool.select_tool.tool_list == "bandage"
75 #if str($tool.select_tool.bandage_plot_path) != 'None' 75 #if str($tool.select_tool.bandage_plot_path) != 'None'
76 --bandage_plot_path '$tool.select_tool.bandage_plot_path' 76 --bandage_plot_path '$tool.select_tool.bandage_plot_path'
77 --bandage_plot_hid '$tool.select_tool.bandage_plot_path.hid' 77 --bandage_plot_hid '$tool.select_tool.bandage_plot_path.hid'
78 #end if 78 #end if
79 #elif $tool.select_tool.tool_list == "bracken" 79 #elif $tool.select_tool.tool_list == "bracken"
80 #if str($tool.select_tool.kraken_report_path) != 'None' 80 #if str($tool.select_tool.kraken_report_path) != 'None'
81 --kraken_report_path "$tool.select_tool.kraken_report_path" 81 --kraken_report_path "$tool.select_tool.kraken_report_path"
82 --kraken_report_hid "$tool.select_tool.kraken_report_path.hid" 82 --kraken_report_hid "$tool.select_tool.kraken_report_path.hid"
83 #end if 83 #end if
124 --is_fna_hid "$tool.select_tool.is_fna_path.hid" 124 --is_fna_hid "$tool.select_tool.is_fna_path.hid"
125 #end if 125 #end if
126 #elif $tool.select_tool.tool_list == "kraken2" 126 #elif $tool.select_tool.tool_list == "kraken2"
127 #if str($tool.select_tool.seq_classification_file_path) != 'None' 127 #if str($tool.select_tool.seq_classification_file_path) != 'None'
128 --seq_classification_file_path "$tool.select_tool.seq_classification_file_path" 128 --seq_classification_file_path "$tool.select_tool.seq_classification_file_path"
129 --seq_classification_file_hid "$tool.select_tool.seq_classification_file_path.hid" 129 --seq_classification_file_hid "$tool.select_tool.seq_classification_file_path.hid"
130 #end if 130 #end if
131 #elif $tool.select_tool.tool_list == "plasmidfinder" 131 #elif $tool.select_tool.tool_list == "plasmidfinder"
132 #if str($tool.select_tool.genome_hit_path) != 'None' 132 #if str($tool.select_tool.genome_hit_path) != 'None'
133 --genome_hit_path "$tool.select_tool.genome_hit_path" 133 --genome_hit_path "$tool.select_tool.genome_hit_path"
134 --genome_hit_hid "$tool.select_tool.genome_hit_path.hid" 134 --genome_hit_hid "$tool.select_tool.genome_hit_path.hid"
184 | tee "$logfile" 184 | tee "$logfile"
185 #if $i < $counter 185 #if $i < $counter
186 && 186 &&
187 #end if 187 #end if
188 #end for 188 #end for
189 && ls abromics_extracted_folder 189 && ls abromics_extracted_folder
190 ]]> 190 ]]>
191 </command> 191 </command>
192 <inputs> 192 <inputs>
193 <section name="tool_section" title="Available tools" expanded="true"> 193 <section name="tool_section" title="Available tools" expanded="true">
194 <repeat name="tools" title="Tool" min="0"> 194 <repeat name="tools" title="Tool" min="0">
240 </when> 240 </when>
241 <when value="bracken"> 241 <when value="bracken">
242 <param name="input" type="data" format="txt,tabular" multiple="false" label="Bracken report file" help="Tabular file from bracken output"/> 242 <param name="input" type="data" format="txt,tabular" multiple="false" label="Bracken report file" help="Tabular file from bracken output"/>
243 <expand macro="analysis_software_version"/> 243 <expand macro="analysis_software_version"/>
244 <expand macro="reference_database_version"/> 244 <expand macro="reference_database_version"/>
245 <param argument="--kraken_report_path" type="data" format="txt,tabular" multiple="false" label="Kraken re-estimated report" help="New kraken report from bracken tool"/> 245 <param argument="--kraken_report_path" type="data" format="txt,tabular" multiple="false" optional="true" label="Kraken re-estimated report" help="New kraken report from bracken tool"/>
246 <param argument="--threshold" type="integer" min="0" optional="true" label="PRIOR on read numbers" help="Prior of read for estimation, default is 0"/> 246 <param argument="--threshold" type="integer" min="0" optional="true" label="PRIOR on read numbers" help="Prior of read for estimation, default is 0"/>
247 <param argument="--read_len" type="integer" min="0" optional="true" label="Read length"/> 247 <param argument="--read_len" type="integer" min="0" optional="true" label="Read length"/>
248 <param argument="--level" type="select" label="Taxonomic level estimation" help="Level of final abundance (from Domain to subspecies, default on species)"> 248 <param argument="--level" type="select" label="Taxonomic level estimation" optional="true" help="Level of final abundance (from Domain to subspecies, default on species)">
249 <option value="D">Domain</option> 249 <option value="D">Domain</option>
250 <option value="P">Phylum</option> 250 <option value="P">Phylum</option>
251 <option value="C">Class</option> 251 <option value="C">Class</option>
252 <option value="O">Order</option> 252 <option value="O">Order</option>
253 <option value="F">Family</option> 253 <option value="F">Family</option>
258 </when> 258 </when>
259 <when value="fastp"> 259 <when value="fastp">
260 <param name="input" type="data" format="json" multiple="false" label="Fastp report file" help="Fastp result in json format"/> 260 <param name="input" type="data" format="json" multiple="false" label="Fastp report file" help="Fastp result in json format"/>
261 <param argument="--trimmed_forward_R1_path" type="data" format="fastq,fastq.gz" optional="true" multiple="false" label="Fastp trimmed R1" help="trimmed file R1"/> 261 <param argument="--trimmed_forward_R1_path" type="data" format="fastq,fastq.gz" optional="true" multiple="false" label="Fastp trimmed R1" help="trimmed file R1"/>
262 <param argument="--trimmed_reverse_R2_path" type="data" format="fastq,fastq.gz" optional="true" multiple="false" label="Fastp trimmed R2" help="trimmed file R2"/> 262 <param argument="--trimmed_reverse_R2_path" type="data" format="fastq,fastq.gz" optional="true" multiple="false" label="Fastp trimmed R2" help="trimmed file R2"/>
263 <param argument="--html_report_path" type="data" format="html" multiple="false" label="Fastp report html" help="Fastp result in html format"/> 263 <param argument="--html_report_path" type="data" format="html" multiple="false" optional="true" label="Fastp report html" help="Fastp result in html format"/>
264 <expand macro="analysis_software_version"/> 264 <expand macro="analysis_software_version"/>
265 <expand macro="reference_database_version"/> 265 <expand macro="reference_database_version"/>
266 </when> 266 </when>
267 <when value="integronfinder2"> 267 <when value="integronfinder2">
268 <param name="input" type="data" format="txt,tabular" multiple="false" label="Integronfinder report" help="Integron file from integronfinder2"/> 268 <param name="input" type="data" format="txt,tabular" multiple="false" label="Integronfinder report" help="Integron file from integronfinder2"/>
269 <param argument="--summary_file_path" type="data" format="txt,tabular" multiple="false" label="Summary report" help="Summary file from integronfinder2"/> 269 <param argument="--summary_file_path" type="data" format="txt,tabular" multiple="false" optional="true" label="Summary report" help="Summary file from integronfinder2"/>
270 <expand macro="analysis_software_version"/> 270 <expand macro="analysis_software_version"/>
271 <expand macro="reference_database_version"/> 271 <expand macro="reference_database_version"/>
272 </when> 272 </when>
273 <when value="isescan"> 273 <when value="isescan">
274 <param name="input" type="data" format="txt,tabular" multiple="false" label="Isescan report" help="IseScan file from integronfinder2"/> 274 <param name="input" type="data" format="txt,tabular" multiple="false" label="Isescan report" help="IseScan file from integronfinder2"/>
298 <expand macro="analysis_software_version"/> 298 <expand macro="analysis_software_version"/>
299 <expand macro="reference_database_version"/> 299 <expand macro="reference_database_version"/>
300 </when> 300 </when>
301 <when value="quast"> 301 <when value="quast">
302 <param name="input" type="data" format="txt,tabular" multiple="false" label="Quast report" help="Tabular Quast report"/> 302 <param name="input" type="data" format="txt,tabular" multiple="false" label="Quast report" help="Tabular Quast report"/>
303 <param argument="--quast_html_path" type="data" format="html" multiple="false" label="Quast html report" help="Quast html report"/> 303 <param argument="--quast_html_path" type="data" format="html" multiple="false" optional="true" label="Quast html report" help="Quast html report"/>
304 <expand macro="analysis_software_version"/> 304 <expand macro="analysis_software_version"/>
305 <expand macro="reference_database_version"/> 305 <expand macro="reference_database_version"/>
306 </when> 306 </when>
307 <when value="recentrifuge"> 307 <when value="recentrifuge">
308 <param name="input" type="data" format="txt,tabular" multiple="false" label="Recentrifuge data file"/> 308 <param name="input" type="data" format="txt,tabular" multiple="false" label="Recentrifuge data file"/>
332 <expand macro="analysis_software_version"/> 332 <expand macro="analysis_software_version"/>
333 <expand macro="reference_database_version"/> 333 <expand macro="reference_database_version"/>
334 </when> 334 </when>
335 <when value="tabular_file"> 335 <when value="tabular_file">
336 <param name="input" type="data" format="txt,tabular" multiple="false" label="Tabular file type" help="Generic result file in tabular format with header"/> 336 <param name="input" type="data" format="txt,tabular" multiple="false" label="Tabular file type" help="Generic result file in tabular format with header"/>
337 <param argument="--analysis_software_name" type="text" multiple="false" label="Tool name" help="Tool name which generated the result file"/> 337 <param argument="--analysis_software_name" type="text" multiple="false" optional="true" label="Tool name" help="Tool name which generated the result file"/>
338 <expand macro="analysis_software_version"/> 338 <expand macro="analysis_software_version"/>
339 <expand macro="reference_database_version"/> 339 <expand macro="reference_database_version"/>
340 </when> 340 </when>
341 </conditional> 341 </conditional>
342 </repeat> 342 </repeat>