Mercurial > repos > iuc > metaphlan

comparison metaphlan.xml @ 12:2e850e8ebc71 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaphlan commit 26cbf16569d13b7ddbbbd99fc49ec15ce312a992
author iuc
date Fri, 14 Nov 2025 13:45:33 +0000
parents 75c7ed7d4ff2
children
comparison
equal deleted inserted replaced
11:75c7ed7d4ff2 12:2e850e8ebc71
1 <tool id="metaphlan" name="MetaPhlAn" version="@TOOL_VERSION@+galaxy4" profile="@PROFILE@"> 1 <tool id="metaphlan" name="MetaPhlAn" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>to profile the composition of microbial communities</description> 2 <description>to profile the composition of microbial communities</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 <xml name="tax_lev"> 5 <xml name="tax_lev">
6 <conditional name="tax_lev"> 6 <conditional name="tax_lev">
146 #if $inputs.in.selector == "sam" 146 #if $inputs.in.selector == "sam"
147 --nreads \$(cat '$inputs.in.in' | grep -c -v '^@') 147 --nreads \$(cat '$inputs.in.in' | grep -c -v '^@')
148 #end if 148 #end if
149 #end if 149 #end if
150 #if $inputs.db.db_selector == "cached" 150 #if $inputs.db.db_selector == "cached"
151 --bowtie2db '$inputs.db.cached_db.fields.path' 151 --db_dir '$inputs.db.cached_db.fields.path'
152 --index '$inputs.db.cached_db.fields.dbkey' 152 --index '$inputs.db.cached_db.fields.dbkey'
153 #if $inputs.db.viral_analysis.profile_vsc
154 $inputs.db.viral_analysis.profile_vsc
155 --vsc_out '$vcs_breath_coverage'
156 --vsc_breadth $inputs.db.viral_analysis.vsc_breadth
157 #end if
153 #else 158 #else
154 --bowtie2db 'ref_db/' 159 --db_dir 'ref_db/'
155 --index 'custom_db' 160 --index 'custom_db'
156 #end if 161 #end if
157 -t '$analysis.analysis_type.t' 162 -t '$analysis.analysis_type.t'
158 #if $analysis.analysis_type.t == "rel_ab" or $analysis.analysis_type.t == "rel_ab_w_read_stats" 163 #if $analysis.analysis_type.t == "rel_ab" or $analysis.analysis_type.t == "rel_ab_w_read_stats"
159 --tax_lev '$analysis.analysis_type.tax_lev.tax_lev' 164 --tax_lev '$analysis.analysis_type.tax_lev.tax_lev'
160 #else if $analysis.analysis_type.t == "clade_specific_strain_tracker"
161 --clade '$analysis.analysis_type.clade'
162 #if str($analysis.analysis_type.min_ab) != ''
163 --min_ab $analysis.analysis_type.min_ab
164 #end if
165 #else if $analysis.analysis_type.t == "marker_ab_table" and str($analysis.analysis_type.nreads) != '' 165 #else if $analysis.analysis_type.t == "marker_ab_table" and str($analysis.analysis_type.nreads) != ''
166 --nreads $$analysis.analysis_type.nreads 166 --nreads $$analysis.analysis_type.nreads
167 #else if $analysis.analysis_type.t == "marker_pres_table" and str($analysis.analysis_type.pres_th) != '' 167 #else if $analysis.analysis_type.t == "marker_pres_table" and str($analysis.analysis_type.pres_th) != ''
168 --pres_th $analysis.analysis_type.pres_th 168 --pres_th $analysis.analysis_type.pres_th
169 #end if 169 #end if
170 --min_cu_len $analysis.min_cu_len
171 #if str($analysis.min_alignment_len) != '' 170 #if str($analysis.min_alignment_len) != ''
172 --min_alignment_len $analysis.min_alignment_len 171 --min_alignment_len $analysis.min_alignment_len
173 #end if 172 #end if
174 #if 'add_viruses' in $analysis.organism_profiling 173
175 --add_viruses 174 #echo " ".join(["--" + o for o in $analysis.organism_profiling])
176 #end if 175
177 #if 'ignore_eukaryotes' in $analysis.organism_profiling
178 --ignore_eukaryotes
179 #end if
180 #if 'ignore_bacteria' in $analysis.organism_profiling
181 --ignore_bacteria
182 #end if
183 #if 'ignore_archaea' in $analysis.organism_profiling
184 --ignore_archaea
185 #end if
186 --stat $analysis.stat 176 --stat $analysis.stat
187 --stat_q $analysis.stat_q 177 --stat_q $analysis.stat_q
188 --perc_nonzero $analysis.perc_nonzero 178 --perc_nonzero $analysis.perc_nonzero
189 #if $analysis.ignore_markers 179 #if $analysis.ignore_markers
190 --ignore_markers '$analysis.ignore_markers' 180 --ignore_markers '$analysis.ignore_markers'
191 #end if 181 #end if
192 $analysis.avoid_disqm 182 $analysis.avoid_disqm
193 --sample_id_key '$out.sample_id_key' 183 --sample_id_key '$out.sample_id_key'
194 --sample_id '$out.sample_id' 184 --sample_id '$out.sample_id'
195 $out.use_group_representative 185 $out.use_group_representative
196 $out.legacy_output
197 $out.CAMI_format_output 186 $out.CAMI_format_output
198 $out.unclassified_estimation 187 $out.skip_unclassified_estimation
199 -o '$output_file' 188 #if $out.biom_format_output
200 --bowtie2out 'bowtie2out' 189 $out.biom_format_output
190 -o '$biom_output_file'
191 #else
192 -o '$output_file'
193 #end if
194 --mapout 'mapout'
201 -s '$sam_output_file' 195 -s '$sam_output_file'
202 --biom '$biom_output_file'
203 --nproc \${GALAXY_SLOTS:-4} 196 --nproc \${GALAXY_SLOTS:-4}
204 #if $viral_analysis.profile_vsc
205 $viral_analysis.profile_vsc
206 --vsc_out '$vcs_breath_coverage'
207 --vsc_breadth $viral_analysis.vsc_breadth
208 #end if
209 197
210 #if $subsample.selector != "no" 198 #if $subsample.selector != "no"
211 #if $subsample.selector == "single" 199 #if $subsample.selector == "single"
212 --subsampling $subsample.subsampling 200 --subsampling $subsample.subsampling
213 #else 201 #else
224 --offline 212 --offline
225 #end if 213 #end if
226 214
227 #if $inputs.in.selector == "raw" 215 #if $inputs.in.selector == "raw"
228 && 216 &&
229 mv 'bowtie2out' '$bowtie2out' 217 mv 'mapout' '$mapout'
230 #end if 218 #end if
231 219
232 220
233 #if $analysis.analysis_type.t in ['rel_ab', 'rel_ab_w_read_stats'] 221 #if $analysis.analysis_type.t in ['rel_ab', 'rel_ab_w_read_stats']
234 #if $analysis.analysis_type.tax_lev.tax_lev == 'a' and $analysis.analysis_type.tax_lev.split_levels 222 #if $analysis.analysis_type.tax_lev.tax_lev == 'a' and $analysis.analysis_type.tax_lev.split_levels
237 && 225 &&
238 python '$__tool_directory__/formatoutput.py' 226 python '$__tool_directory__/formatoutput.py'
239 split_levels 227 split_levels
240 --metaphlan_output '$output_file' 228 --metaphlan_output '$output_file'
241 --outdir 'split_levels' 229 --outdir 'split_levels'
242 $out.legacy_output
243 #end if 230 #end if
244 #end if 231 #end if
245 232
246 #if $out.krona_output 233 #if $out.krona_output
247 && 234 &&
255 <section name="inputs" title="Inputs" expanded="true"> 242 <section name="inputs" title="Inputs" expanded="true">
256 <conditional name="in"> 243 <conditional name="in">
257 <param name="selector" type="select" label="Input(s)"> 244 <param name="selector" type="select" label="Input(s)">
258 <option value="raw" selected="true">Fasta/FastQ file(s) with microbiota reads</option> 245 <option value="raw" selected="true">Fasta/FastQ file(s) with microbiota reads</option>
259 <option value="sam">Externally BowTie2-mapped SAM file</option> 246 <option value="sam">Externally BowTie2-mapped SAM file</option>
260 <option value="bowtie2out">Intermediary mapping file of the microbiota generated by a previous MetaPhlAn run</option> 247 <option value="mapout">Intermediary mapping file of the microbiota generated by a previous MetaPhlAn run</option>
261 </param> 248 </param>
262 <when value="raw"> 249 <when value="raw">
263 <conditional name="raw_in"> 250 <conditional name="raw_in">
264 <param name="selector" type="select" label="Fasta/FastQ file(s) with microbiota reads"> 251 <param name="selector" type="select" label="Fasta/FastQ file(s) with microbiota reads">
265 <option value="single" selected="true">One single-end file</option> 252 <option value="single" selected="true">One single-end file</option>
293 </section> 280 </section>
294 </when> 281 </when>
295 <when value="sam"> 282 <when value="sam">
296 <param name="in" type="data" format="sam" label="Externally BowTie2-mapped SAM file" help="BowTie2 needs to be used first to map microbiota reads"/> 283 <param name="in" type="data" format="sam" label="Externally BowTie2-mapped SAM file" help="BowTie2 needs to be used first to map microbiota reads"/>
297 </when> 284 </when>
298 <when value="bowtie2out"> 285 <when value="mapout">
299 <param name="in" type="data" format="tabular" label="Intermediary mapping file of the microbiota generated by a previous MetaPhlAn run" help="File needs to be generated with MetaPhlAn versions &gt;3.0"/> 286 <param name="in" type="data" format="tabular" label="Intermediary mapping file of the microbiota generated by a previous MetaPhlAn run" help="File needs to be generated with MetaPhlAn versions &gt;3.0"/>
300 </when> 287 </when>
301 </conditional> 288 </conditional>
302 <conditional name="db"> 289 <conditional name="db">
303 <param name="db_selector" type="select" label="Database with clade-specific marker genes"> 290 <param name="db_selector" type="select" label="Database with clade-specific marker genes">
309 <options from_data_table="@IDX_DATA_TABLE@"> 296 <options from_data_table="@IDX_DATA_TABLE@">
310 <filter type="static_value" column="4" value="@IDX_VERSION@"/> 297 <filter type="static_value" column="4" value="@IDX_VERSION@"/>
311 <validator message="No compatible MetaPhlAn database is available" type="no_options"/> 298 <validator message="No compatible MetaPhlAn database is available" type="no_options"/>
312 </options> 299 </options>
313 </param> 300 </param>
301 <conditional name="viral_analysis">
302 <param argument="--profile_vsc" type="select" label="Profile Viruses with VSCs approach">
303 <option value="--profile_vsc">Yes (requires FASTQ input and reference data with VSG fasta)</option>
304 <option value="" selected="true">No</option>
305 </param>
306 <when value="--profile_vsc">
307 <param argument="--vsc_breadth" type="float" min="0" max="1" value="0.75" label="Minimum Breadth of Coverage" help="Minimum coverage (fraction) for a Viral Group to be reported."/>
308 </when>
309 <when value=""/>
310 </conditional>
314 </when> 311 </when>
315 <when value="history"> 312 <when value="history">
316 <param argument="--bowtie2db" type="data" format="fasta" label="Database with clade-specific marker genes from history"/> 313 <param argument="--db_dir" name="bowtie2db" type="data" format="fasta" label="Database with clade-specific marker genes from history"/>
317 <param argument="--mpa_pkl" type="data" format="json" label="Metadata associated to the database with clade-specific marker genes from history"/> 314 <param argument="--mpa_pkl" type="data" format="json" label="Metadata associated to the database with clade-specific marker genes from history"/>
318 </when> 315 </when>
319 </conditional> 316 </conditional>
320 </section> 317 </section>
321 <section name="analysis" title="Analysis" expanded="true"> 318 <section name="analysis" title="Analysis" expanded="true">
322 <conditional name="analysis_type"> 319 <conditional name="analysis_type">
323 <param argument="-t" type="select" label="Type of analysis to perform"> 320 <param argument="-t" type="select" label="Type of analysis to perform">
324 <option value="rel_ab" selected="true">rel_ab: Profiling a microbiota in terms of relative abundances</option> 321 <option value="rel_ab" selected="true">rel_ab: Profiling a microbiota in terms of relative abundances</option>
325 <option value="rel_ab_w_read_stats">rel_ab_w_read_stats: Profiling a microbiota in terms of relative abundances and estimate the number of reads comming from each clade</option> 322 <option value="rel_ab_w_read_stats">rel_ab_w_read_stats: Profiling a microbiota in terms of relative abundances and estimate the number of reads comming from each clade</option>
326 <option value="reads_map">reads_map: Mapping from reads to clades (only reads hitting a marker)</option>
327 <option value="clade_profiles">clade_profiles: Normalized marker counts for clades with at least a non-null marker</option> 323 <option value="clade_profiles">clade_profiles: Normalized marker counts for clades with at least a non-null marker</option>
328 <option value="clade_specific_strain_tracker">clade_specific_strain_tracker: List of markers present for a specific clade and all its subclades</option>
329 <option value="marker_ab_table">marker_ab_table: Normalized marker counts (only when &gt; 0.0 and normalized by microbiota size if number of reads is specified)</option> 324 <option value="marker_ab_table">marker_ab_table: Normalized marker counts (only when &gt; 0.0 and normalized by microbiota size if number of reads is specified)</option>
330 <option value="marker_counts">marker_counts: Non-normalized marker counts (use with extreme caution)</option>
331 <option value="marker_pres_table">marker_pres_table: List of markers present in the sample (threshold at 1.0 if not differently specified with --pres_th</option> 325 <option value="marker_pres_table">marker_pres_table: List of markers present in the sample (threshold at 1.0 if not differently specified with --pres_th</option>
332 </param> 326 </param>
333 <when value="rel_ab"> 327 <when value="rel_ab">
334 <expand macro="tax_lev"/> 328 <expand macro="tax_lev"/>
335 </when> 329 </when>
336 <when value="rel_ab_w_read_stats"> 330 <when value="rel_ab_w_read_stats">
337 <expand macro="tax_lev"/> 331 <expand macro="tax_lev"/>
338 </when> 332 </when>
339 <when value="reads_map"/>
340 <when value="clade_profiles"/> 333 <when value="clade_profiles"/>
341 <when value="clade_specific_strain_tracker">
342 <param argument="--clade" type="text" value="" label="Clade for which to extract list of markers present" help="Markers are also extracted for subclades"/>
343 <param argument="--min_ab" type="float" optional="true" label="The minimum percentage abundance for the clade"/>
344 </when>
345 <when value="marker_ab_table"> 334 <when value="marker_ab_table">
346 <param argument="--nreads" type="integer" optional="true" label="Total number of reads in the original microbiota" help="It is used for normalizing the length-normalized counts with the microbiota size as well. No normalization applied if the value is not specified"/> 335 <param argument="--nreads" type="integer" optional="true" label="Total number of reads in the original microbiota" help="It is used for normalizing the length-normalized counts with the microbiota size as well. No normalization applied if the value is not specified"/>
347 </when> 336 </when>
348 <when value="marker_counts"/>
349 <when value="marker_pres_table"> 337 <when value="marker_pres_table">
350 <param argument="--pres_th" type="integer" optional="true" label="Threshold for calling a marker present"/> 338 <param argument="--pres_th" type="integer" optional="true" label="Threshold for calling a marker present"/>
351 </when> 339 </when>
352 </conditional> 340 </conditional>
353 <param argument="--min_cu_len" type="integer" value="2000" label="Minimum total nucleotide length for the markers in a clade for estimating the abundance without considering sub-clade abundances"/>
354 <param argument="--min_alignment_len" type="integer" optional="true" label="Sam records for aligned reads with the longest subalignment length smaller than this threshold will be discarded."/> 341 <param argument="--min_alignment_len" type="integer" optional="true" label="Sam records for aligned reads with the longest subalignment length smaller than this threshold will be discarded."/>
355 <param name="organism_profiling" type="select" optional="true" label="Organisms to profile" multiple="true"> 342 <param name="organism_profiling" type="select" optional="true" label="Organisms to profile" multiple="true">
356 <option value="add_viruses" selected="true">Profile viral organisms (add_viruses)</option>
357 <option value="ignore_eukaryotes">Ignore eukaryotic organisms (ignore_eukaryotes)</option> 343 <option value="ignore_eukaryotes">Ignore eukaryotic organisms (ignore_eukaryotes)</option>
358 <option value="ignore_bacteria">Ignore bacteria organisms (ignore_bacteria)</option> 344 <option value="ignore_bacteria">Ignore bacteria organisms (ignore_bacteria)</option>
359 <option value="ignore_archaea">Ignore archea organisms (ignore_archaea)</option> 345 <option value="ignore_archaea">Ignore archea organisms (ignore_archaea)</option>
346 <option value="ignore_ksgbs">Do not profile known SGBs</option>
347 <option value="ignore_usgbs">Do not profile unknown SGBs</option>
360 </param> 348 </param>
361 <param argument="--stat" type="select" label="Statistical approach for converting marker abundances into clade abundances"> 349 <param argument="--stat" type="select" label="Statistical approach for converting marker abundances into clade abundances">
362 <option value="avg_g">avg_g: Clade global (i.e. normalizing all markers together) average (avg_g)</option> 350 <option value="avg_g">avg_g: Clade global (i.e. normalizing all markers together) average (avg_g)</option>
363 <option value="avg_l">avg_l: Average of length-normalized marker counts</option> 351 <option value="avg_l">avg_l: Average of length-normalized marker counts</option>
364 <option value="tavg_g" selected="true">tavg_g: Truncated clade global average at --stat_q quantile</option> 352 <option value="tavg_g" selected="true">tavg_g: Truncated clade global average at --stat_q quantile</option>
386 <when value="paired"> 374 <when value="paired">
387 <param argument="--subsampling_paired" type="integer" min="1" value="" label="Sumbsample reads" help="Specify the number of paired reads to be considered. For N there will be floor(N/2) reads selected from the forward and reverse reads each."/> 375 <param argument="--subsampling_paired" type="integer" min="1" value="" label="Sumbsample reads" help="Specify the number of paired reads to be considered. For N there will be floor(N/2) reads selected from the forward and reverse reads each."/>
388 <expand macro="subsample_common"/> 376 <expand macro="subsample_common"/>
389 </when> 377 </when>
390 </conditional> 378 </conditional>
391 <conditional name="viral_analysis">
392 <param argument="--profile_vsc" type="select" label="Profile Viruses with VSCs approach">
393 <option value="--profile_vsc">Yes (requires FASTQ input and reference data with VSG fasta)</option>
394 <option value="" selected="true">No</option>
395 </param>
396 <when value="--profile_vsc">
397 <param argument="--vsc_breadth" type="float" min="0" max="1" value="0.75" label="Minimum Breadth of Coverage" help="Minimum coverage (fraction) for a Viral Group to be reported."/>
398 </when>
399 <when value=""/>
400 </conditional>
401 <section name="out" title="Outputs" expanded="true"> 379 <section name="out" title="Outputs" expanded="true">
402 <param argument="--sample_id_key" type="text" value="SampleID" label="Sample ID key for this analysis"/> 380 <param argument="--sample_id_key" type="text" value="SampleID" label="Sample ID key for this analysis"/>
403 <param argument="--sample_id" type="text" value="Metaphlan_Analysis" label="Sample ID for this analysis"/> 381 <param argument="--sample_id" type="text" value="Metaphlan_Analysis" label="Sample ID for this analysis"/>
404 <param argument="--use_group_representative" type="boolean" truevalue="--use_group_representative" falsevalue="" checked="false" label="Use a species as representative for species groups?"/> 382 <param argument="--use_group_representative" type="boolean" truevalue="--use_group_representative" falsevalue="" checked="false" label="Use a species as representative for species groups?"/>
405 <param argument="--legacy-output" type="boolean" truevalue="--legacy-output" falsevalue="" checked="false" label="Old MetaPhlAn2 two columns output?"/>
406 <param argument="--CAMI_format_output" type="boolean" truevalue="--CAMI_format_output" falsevalue="" checked="false" label="Report the profiling using the CAMI output format?"/> 383 <param argument="--CAMI_format_output" type="boolean" truevalue="--CAMI_format_output" falsevalue="" checked="false" label="Report the profiling using the CAMI output format?"/>
407 <param argument="--unclassified_estimation" type="boolean" truevalue="--unclassified_estimation" falsevalue="" checked="false" label="Scale relative abundances to the number of reads mapping to known clades in order to estimate unknowness?"/> 384 <param argument="--skip_unclassified_estimation" type="boolean" truevalue="--skip_unclassified_estimation" falsevalue="" checked="false" label="Do not scale relative abundances to the estimate unclassified taxa"/>
385 <param argument="--biom_format_output" type="boolean" truevalue="--biom_format_output" falsevalue="" checked="false" label="Report the profiling using the biom output format"/>
408 <param name="krona_output" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Output for Krona?"/> 386 <param name="krona_output" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Output for Krona?"/>
409 </section> 387 </section>
410 <!-- enabling this in tests will allow metaphlan to download reference data (we do this only with the smallish TOY DB) --> 388 <!-- enabling this in tests will allow metaphlan to download reference data (we do this only with the smallish TOY DB) -->
411 <param name="test" type="hidden" value="false"/> 389 <param name="test" type="hidden" value="false"/>
412 </inputs> 390 </inputs>
413 <outputs> 391 <outputs>
414 <data name="output_file" format="tabular" label="${tool.name} on ${on_string}: Predicted taxon relative abundances"/> 392 <data name="output_file" format="tabular" label="${tool.name} on ${on_string}: Predicted taxon relative abundances">
415 <data name="bowtie2out" format="tabular" label="${tool.name} on ${on_string}: Bowtie2 output"> 393 <filter>not out['biom_format_output']</filter>
394 </data>
395 <data name="mapout" format="tabular" label="${tool.name} on ${on_string}: Bowtie2 output">
416 <filter>inputs['in']['selector'] == "raw"</filter> 396 <filter>inputs['in']['selector'] == "raw"</filter>
417 </data> 397 </data>
418 <data name="sam_output_file" format="sam" label="${tool.name} on ${on_string}: SAM file"> 398 <data name="sam_output_file" format="sam" label="${tool.name} on ${on_string}: SAM file">
419 <filter>inputs['in']['selector'] == "raw"</filter> 399 <filter>inputs['in']['selector'] == "raw"</filter>
420 </data> 400 </data>
421 <data name="biom_output_file" format="biom1" label="${tool.name} on ${on_string}: BIOM file"/> 401 <data name="biom_output_file" format="biom1" label="${tool.name} on ${on_string}: BIOM file">
402 <filter>out['biom_format_output']</filter>
403 </data>
422 <collection name="levels" type="list" label="${tool.name} on ${on_string}: Predicted taxon relative abundances at each taxonomic levels"> 404 <collection name="levels" type="list" label="${tool.name} on ${on_string}: Predicted taxon relative abundances at each taxonomic levels">
423 <discover_datasets pattern="(?P&lt;designation&gt;.+)" directory="split_levels/" format="tabular"/> 405 <discover_datasets pattern="(?P&lt;designation&gt;.+)" directory="split_levels/" format="tabular"/>
424 <filter>analysis['analysis_type']['t'] in ['rel_ab', 'rel_ab_w_read_stats'] and analysis['analysis_type']['tax_lev']['tax_lev'] == "a" and analysis['analysis_type']['tax_lev']['split_levels']</filter> 406 <filter>analysis['analysis_type']['t'] in ['rel_ab', 'rel_ab_w_read_stats'] and analysis['analysis_type']['tax_lev']['tax_lev'] == "a" and analysis['analysis_type']['tax_lev']['split_levels']</filter>
425 </collection> 407 </collection>
426 <data name="krona_output_file" format="tabular" label="${tool.name} on ${on_string}: Predicted taxon relative abundances for Krona"> 408 <data name="krona_output_file" format="tabular" label="${tool.name} on ${on_string}: Predicted taxon relative abundances for Krona">
427 <filter>out['krona_output']</filter> 409 <filter>out['krona_output']</filter>
428 </data> 410 </data>
429 <data name="vcs_breath_coverage" format="tabular" label="${tool.name} on ${on_string}: VSCs breadth-of-coverage"> 411 <data name="vcs_breath_coverage" format="tabular" label="${tool.name} on ${on_string}: VSCs breadth-of-coverage">
430 <filter>viral_analysis['profile_vsc']</filter> 412 <filter>inputs['db']['db_selector'] == "cached" and inputs['db']['viral_analysis']['profile_vsc'] != ""</filter>
431 </data> 413 </data>
432 <data name="subsample_single" format="fastqsanger" from_work_dir="subsampled.out" label="${tool.name} on ${on_string}: Subsampled reads"> 414 <data name="subsample_single" format="fastqsanger" from_work_dir="subsampled.out" label="${tool.name} on ${on_string}: Subsampled reads">
433 <filter>subsample['selector'] == 'single'</filter> 415 <filter>subsample['selector'] == 'single'</filter>
434 </data> 416 </data>
435 <collection name="subsample_paired" type="paired" label="${tool.name} on ${on_string}: Subsampled paired reads"> 417 <collection name="subsample_paired" type="paired" label="${tool.name} on ${on_string}: Subsampled paired reads">
438 <filter>subsample['selector'] == 'paired'</filter> 420 <filter>subsample['selector'] == 'paired'</filter>
439 </collection> 421 </collection>
440 </outputs> 422 </outputs>
441 <tests> 423 <tests>
442 <!-- Single GZ file, Cached db --> 424 <!-- Single GZ file, Cached db -->
443 <test expect_num_outputs="6"> 425 <test expect_num_outputs="5">
444 <section name="inputs"> 426 <section name="inputs">
445 <conditional name="in"> 427 <conditional name="in">
446 <param name="selector" value="raw"/> 428 <param name="selector" value="raw"/>
447 <conditional name="raw_in"> 429 <conditional name="raw_in">
448 <param name="selector" value="single"/> 430 <param name="selector" value="single"/>
465 <conditional name="tax_lev"> 447 <conditional name="tax_lev">
466 <param name="tax_lev" value="a"/> 448 <param name="tax_lev" value="a"/>
467 <param name="split_levels" value="true"/> 449 <param name="split_levels" value="true"/>
468 </conditional> 450 </conditional>
469 </conditional> 451 </conditional>
470 <param name="min_cu_len" value="2000"/>
471 <param name="organism_profiling" value="add_viruses"/>
472 <param name="stat" value="avg_g"/> 452 <param name="stat" value="avg_g"/>
473 <param name="stat_q" value="0.2"/> 453 <param name="stat_q" value="0.2"/>
474 <param name="perc_nonzero" value="0.33"/> 454 <param name="perc_nonzero" value="0.33"/>
475 <param name="avoid_disqm" value="true"/> 455 <param name="avoid_disqm" value="true"/>
476 </section> 456 </section>
477 <section name="out"> 457 <section name="out">
478 <param name="sample_id_key" value="SampleID"/> 458 <param name="sample_id_key" value="SampleID"/>
479 <param name="sample_id" value="Metaphlan_Analysis"/> 459 <param name="sample_id" value="Metaphlan_Analysis"/>
480 <param name="use_group_representative" value="false"/> 460 <param name="use_group_representative" value="false"/>
481 <param name="legacy_output" value="false"/>
482 <param name="CAMI_format_output" value="false"/> 461 <param name="CAMI_format_output" value="false"/>
483 <param name="unclassified_estimation" value="false"/> 462 <param name="skip_unclassified_estimation" value="false"/>
484 <param name="krona_output" value="true"/> 463 <param name="krona_output" value="true"/>
485 </section> 464 </section>
486 <output name="output_file" ftype="tabular"> 465 <output name="output_file" ftype="tabular">
487 <assert_contents> 466 <assert_contents>
488 <has_text text="UNCLASSIFIED"/> 467 <has_text text="UNCLASSIFIED"/>
489 </assert_contents> 468 </assert_contents>
490 </output> 469 </output>
491 <output name="bowtie2out" ftype="tabular"> 470 <output name="mapout" ftype="tabular">
492 <assert_contents> 471 <assert_contents>
493 <not_has_text text="HWI-EAS109_102883399:3:104:7342:14360/1"/> 472 <not_has_text text="HWI-EAS109_102883399:3:104:7342:14360/1"/>
494 <has_n_lines n="2"/> 473 <has_n_lines n="2"/>
495 </assert_contents> 474 </assert_contents>
496 </output> 475 </output>
497 <output name="sam_output_file" ftype="sam"> 476 <output name="sam_output_file" ftype="sam">
498 <assert_contents> 477 <assert_contents>
499 <has_text text="SN:13076__A0A2I1PE66__CYJ72_10760"/> 478 <has_text text="SN:13076__A0A2I1PE66__CYJ72_10760"/>
500 </assert_contents>
501 </output>
502 <output name="biom_output_file" ftype="biom1">
503 <assert_contents>
504 <not_has_text text="k__Bacteria"/>
505 <not_has_text text="p__Actinobacteria"/>
506 </assert_contents> 479 </assert_contents>
507 </output> 480 </output>
508 <output_collection name="levels" type="list"> 481 <output_collection name="levels" type="list">
509 <element name="all" ftype="tabular"> 482 <element name="all" ftype="tabular">
510 <assert_contents> 483 <assert_contents>
587 <assert_stderr> 560 <assert_stderr>
588 <has_text text="Downloading" negate="true"/> 561 <has_text text="Downloading" negate="true"/>
589 </assert_stderr> 562 </assert_stderr>
590 </test> 563 </test>
591 <!-- Single GZ file, Cached db --> 564 <!-- Single GZ file, Cached db -->
592 <test expect_num_outputs="6"> 565 <test expect_num_outputs="5">
593 <section name="inputs"> 566 <section name="inputs">
594 <conditional name="in"> 567 <conditional name="in">
595 <param name="selector" value="raw"/> 568 <param name="selector" value="raw"/>
596 <conditional name="raw_in"> 569 <conditional name="raw_in">
597 <param name="selector" value="single"/> 570 <param name="selector" value="single"/>
614 <conditional name="tax_lev"> 587 <conditional name="tax_lev">
615 <param name="tax_lev" value="a"/> 588 <param name="tax_lev" value="a"/>
616 <param name="split_levels" value="true"/> 589 <param name="split_levels" value="true"/>
617 </conditional> 590 </conditional>
618 </conditional> 591 </conditional>
619 <param name="min_cu_len" value="2000"/>
620 <param name="organism_profiling" value="add_viruses"/>
621 <param name="stat" value="avg_g"/> 592 <param name="stat" value="avg_g"/>
622 <param name="stat_q" value="0.2"/> 593 <param name="stat_q" value="0.2"/>
623 <param name="perc_nonzero" value="0.33"/> 594 <param name="perc_nonzero" value="0.33"/>
624 <param name="avoid_disqm" value="true"/> 595 <param name="avoid_disqm" value="true"/>
625 </section> 596 </section>
626 <section name="out"> 597 <section name="out">
627 <param name="sample_id_key" value="SampleID"/> 598 <param name="sample_id_key" value="SampleID"/>
628 <param name="sample_id" value="Metaphlan_Analysis"/> 599 <param name="sample_id" value="Metaphlan_Analysis"/>
629 <param name="use_group_representative" value="false"/> 600 <param name="use_group_representative" value="false"/>
630 <param name="legacy_output" value="false"/>
631 <param name="CAMI_format_output" value="false"/> 601 <param name="CAMI_format_output" value="false"/>
632 <param name="unclassified_estimation" value="false"/> 602 <param name="skip_unclassified_estimation" value="false"/>
633 <param name="krona_output" value="true"/> 603 <param name="krona_output" value="true"/>
634 </section> 604 </section>
635 <output name="output_file" ftype="tabular" file="SRS014464-Anterior_nares-abundances.tabular" compare="sim_size"> 605 <output name="output_file" ftype="tabular">
636 <assert_contents> 606 <assert_contents>
607 <has_size size="12357"/>
637 <has_text text="k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens"/> 608 <has_text text="k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens"/>
638 </assert_contents> 609 </assert_contents>
639 </output> 610 </output>
640 <output name="bowtie2out" ftype="tabular" file="SRS014464-Anterior_nares-bowtie2out.tabular" compare="sim_size"> 611 <output name="mapout" ftype="tabular">
641 <assert_contents> 612 <assert_contents>
613 <has_size size="10504"/>
642 <has_text text="HWI-EAS109_102883399:3:104:7342:14360/1"/> 614 <has_text text="HWI-EAS109_102883399:3:104:7342:14360/1"/>
643 <has_text text="37637__U2I1U8__N579_01580"/> 615 <has_text text="37637__U2I1U8__N579_01580"/>
644 </assert_contents> 616 </assert_contents>
645 </output> 617 </output>
646 <output name="sam_output_file" ftype="sam" file="SRS014464-Anterior_nares.sam" compare="sim_size"> 618 <output name="sam_output_file" ftype="sam">
647 <assert_contents> 619 <assert_contents>
620 <has_size size="54554"/>
648 <has_text text="SN:13076__A0A2I1PE66__CYJ72_10760"/> 621 <has_text text="SN:13076__A0A2I1PE66__CYJ72_10760"/>
649 </assert_contents>
650 </output>
651 <output name="biom_output_file" ftype="biom1" file="SRS014464-Anterior_nares.biom" compare="sim_size">
652 <assert_contents>
653 <has_text text="k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_lacunata"/>
654 </assert_contents> 622 </assert_contents>
655 </output> 623 </output>
656 <output_collection name="levels" type="list"> 624 <output_collection name="levels" type="list">
657 <element name="all" ftype="tabular"> 625 <element name="all" ftype="tabular">
658 <assert_contents> 626 <assert_contents>
734 <assert_stderr> 702 <assert_stderr>
735 <has_text text="Downloading" negate="true"/> 703 <has_text text="Downloading" negate="true"/>
736 </assert_stderr> 704 </assert_stderr>
737 </test> 705 </test>
738 <!-- Multiple GZ file, Local db--> 706 <!-- Multiple GZ file, Local db-->
739 <test expect_num_outputs="4"> 707 <test expect_num_outputs="3">
740 <section name="inputs"> 708 <section name="inputs">
741 <conditional name="in"> 709 <conditional name="in">
742 <param name="selector" value="raw"/> 710 <param name="selector" value="raw"/>
743 <conditional name="raw_in"> 711 <conditional name="raw_in">
744 <param name="selector" value="multiple"/> 712 <param name="selector" value="multiple"/>
762 <conditional name="tax_lev"> 730 <conditional name="tax_lev">
763 <param name="tax_lev" value="a"/> 731 <param name="tax_lev" value="a"/>
764 <param name="split_levels" value="false"/> 732 <param name="split_levels" value="false"/>
765 </conditional> 733 </conditional>
766 </conditional> 734 </conditional>
767 <param name="min_cu_len" value="2000"/>
768 <param name="organism_profiling" value="add_viruses"/>
769 <param name="stat" value="avg_g"/> 735 <param name="stat" value="avg_g"/>
770 <param name="stat_q" value="0.2"/> 736 <param name="stat_q" value="0.2"/>
771 <param name="perc_nonzero" value="0.33"/> 737 <param name="perc_nonzero" value="0.33"/>
772 <param name="avoid_disqm" value="true"/> 738 <param name="avoid_disqm" value="true"/>
773 </section> 739 </section>
774 <section name="out"> 740 <section name="out">
775 <param name="sample_id_key" value="SampleID"/> 741 <param name="sample_id_key" value="SampleID"/>
776 <param name="sample_id" value="Metaphlan_Analysis"/> 742 <param name="sample_id" value="Metaphlan_Analysis"/>
777 <param name="use_group_representative" value="false"/> 743 <param name="use_group_representative" value="false"/>
778 <param name="legacy_output" value="false"/>
779 <param name="CAMI_format_output" value="false"/> 744 <param name="CAMI_format_output" value="false"/>
780 <param name="unclassified_estimation" value="false"/> 745 <param name="skip_unclassified_estimation" value="false"/>
781 <param name="krona_output" value="false"/> 746 <param name="krona_output" value="false"/>
782 </section> 747 </section>
783 <output name="output_file" ftype="tabular" file="SRS014464-Anterior_nares-abundances.tabular" compare="sim_size"> 748 <output name="output_file" ftype="tabular">
784 <assert_contents> 749 <assert_contents>
750 <has_size size="12298"/>
785 <has_text text="k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens"/> 751 <has_text text="k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens"/>
786 <has_text text="relative_abundance"/> 752 <has_text text="relative_abundance"/>
787 <has_text text="NCBI_tax_id"/> 753 <has_text text="NCBI_tax_id"/>
788 <has_text text="clade_name"/> 754 <has_text text="clade_name"/>
789 </assert_contents> 755 </assert_contents>
790 </output> 756 </output>
791 <output name="bowtie2out" ftype="tabular" file="SRS014464-Anterior_nares-two-inputs-bowtie2out.tabular" compare="sim_size"> 757 <output name="mapout" ftype="tabular">
792 <assert_contents> 758 <assert_contents>
759 <has_size size="20961"/>
793 <has_text text="HWI-EAS109_102883399:3:104:7342:14360/1"/> 760 <has_text text="HWI-EAS109_102883399:3:104:7342:14360/1"/>
794 <has_text text="37637__U2I1U8__N579_01580"/> 761 <has_text text="37637__U2I1U8__N579_01580"/>
795 </assert_contents> 762 </assert_contents>
796 </output> 763 </output>
797 <output name="sam_output_file" ftype="sam" file="SRS014464-Anterior_nares-two-inputs.sam" compare="sim_size"> 764 <output name="sam_output_file" ftype="sam">
798 <assert_contents> 765 <assert_contents>
766 <has_size size="104838"/>
799 <has_text text="SN:13076__A0A2I1PE66__CYJ72_10760"/> 767 <has_text text="SN:13076__A0A2I1PE66__CYJ72_10760"/>
800 </assert_contents>
801 </output>
802 <output name="biom_output_file" ftype="biom1" file="SRS014464-Anterior_nares.biom" compare="sim_size">
803 <assert_contents>
804 <has_text text="k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_lacunata"/>
805 </assert_contents> 768 </assert_contents>
806 </output> 769 </output>
807 <assert_stderr> 770 <assert_stderr>
808 <has_text text="Downloading" negate="true"/> 771 <has_text text="Downloading" negate="true"/>
809 </assert_stderr> 772 </assert_stderr>
810 </test> 773 </test>
811 <!-- Paired GZ file, Cached db (note sumsample_paired and the included forward and reverse reads are counted separatelym because they are all statically defined) --> 774 <!-- Paired GZ file, Cached db (note sumsample_paired and the included forward and reverse reads are counted separatelym because they are all statically defined) -->
812 <test expect_num_outputs="7"> 775 <test expect_num_outputs="6">
813 <section name="inputs"> 776 <section name="inputs">
814 <conditional name="in"> 777 <conditional name="in">
815 <param name="selector" value="raw"/> 778 <param name="selector" value="raw"/>
816 <conditional name="raw_in"> 779 <conditional name="raw_in">
817 <param name="selector" value="paired"/> 780 <param name="selector" value="paired"/>
835 <conditional name="tax_lev"> 798 <conditional name="tax_lev">
836 <param name="tax_lev" value="a"/> 799 <param name="tax_lev" value="a"/>
837 <param name="split_levels" value="false"/> 800 <param name="split_levels" value="false"/>
838 </conditional> 801 </conditional>
839 </conditional> 802 </conditional>
840 <param name="min_cu_len" value="2000"/>
841 <param name="organism_profiling" value="add_viruses"/>
842 <param name="stat" value="avg_g"/> 803 <param name="stat" value="avg_g"/>
843 <param name="stat_q" value="0.2"/> 804 <param name="stat_q" value="0.2"/>
844 <param name="perc_nonzero" value="0.33"/> 805 <param name="perc_nonzero" value="0.33"/>
845 <param name="avoid_disqm" value="true"/> 806 <param name="avoid_disqm" value="true"/>
846 </section> 807 </section>
851 </conditional> 812 </conditional>
852 <section name="out"> 813 <section name="out">
853 <param name="sample_id_key" value="SampleID"/> 814 <param name="sample_id_key" value="SampleID"/>
854 <param name="sample_id" value="Metaphlan_Analysis"/> 815 <param name="sample_id" value="Metaphlan_Analysis"/>
855 <param name="use_group_representative" value="false"/> 816 <param name="use_group_representative" value="false"/>
856 <param name="legacy_output" value="false"/>
857 <param name="CAMI_format_output" value="false"/> 817 <param name="CAMI_format_output" value="false"/>
858 <param name="unclassified_estimation" value="false"/> 818 <param name="skip_unclassified_estimation" value="false"/>
859 <param name="krona_output" value="false"/> 819 <param name="krona_output" value="false"/>
860 </section> 820 </section>
861 <output name="output_file" ftype="tabular" file="SRS014464-Anterior_nares-abundances.tabular" compare="sim_size"> 821 <output name="output_file" ftype="tabular">
862 <assert_contents> 822 <assert_contents>
823 <has_size size="9808"/>
863 <has_text text="k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens"/> 824 <has_text text="k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens"/>
864 <has_text text="relative_abundance"/> 825 <has_text text="relative_abundance"/>
865 <has_text text="NCBI_tax_id"/> 826 <has_text text="NCBI_tax_id"/>
866 <has_text text="clade_name"/> 827 <has_text text="clade_name"/>
867 </assert_contents> 828 </assert_contents>
868 </output> 829 </output>
869 <output name="bowtie2out" ftype="tabular" file="SRS014464-Anterior_nares-two-inputs-bowtie2out.tabular" compare="sim_size"> 830 <output name="mapout" ftype="tabular">
870 <assert_contents> 831 <assert_contents>
832 <has_size size="52535"/>
871 <has_text text="HWI-EAS109_102883399:3:107:9938:7093/1"/> 833 <has_text text="HWI-EAS109_102883399:3:107:9938:7093/1"/>
872 <has_text text="90240__A0A378QWM4__NCTC12877_00123"/> 834 <has_text text="90240__A0A378QWM4__NCTC12877_00123"/>
873 </assert_contents> 835 </assert_contents>
874 </output> 836 </output>
875 <output name="sam_output_file" ftype="sam"> 837 <output name="sam_output_file" ftype="sam">
876 <assert_contents> 838 <assert_contents>
877 <has_size min="52400" max="52600"/> 839 <has_size min="52400" max="52600"/>
878 <has_text text="SN:13076__A0A2I1PE66__CYJ72_10760"/> 840 <has_text text="SN:13076__A0A2I1PE66__CYJ72_10760"/>
879 </assert_contents>
880 </output>
881 <output name="biom_output_file" ftype="biom1" file="SRS014464-Anterior_nares.biom" compare="sim_size">
882 <assert_contents>
883 <has_text text="k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens"/>
884 </assert_contents> 841 </assert_contents>
885 </output> 842 </output>
886 <output_collection name="subsample_paired" type="paired"> 843 <output_collection name="subsample_paired" type="paired">
887 <element name="forward"> 844 <element name="forward">
888 <assert_contents> 845 <assert_contents>
898 <assert_stderr> 855 <assert_stderr>
899 <has_text text="Downloading" negate="true"/> 856 <has_text text="Downloading" negate="true"/>
900 </assert_stderr> 857 </assert_stderr>
901 </test> 858 </test>
902 <!-- Paired GZ file as collection, Cached db (note sumsample_paired and the included forward and reverse reads are counted separatelym because they are all statically defined) --> 859 <!-- Paired GZ file as collection, Cached db (note sumsample_paired and the included forward and reverse reads are counted separatelym because they are all statically defined) -->
903 <test expect_num_outputs="7"> 860 <test expect_num_outputs="6">
904 <section name="inputs"> 861 <section name="inputs">
905 <conditional name="in"> 862 <conditional name="in">
906 <param name="selector" value="raw"/> 863 <param name="selector" value="raw"/>
907 <conditional name="raw_in"> 864 <conditional name="raw_in">
908 <param name="selector" value="paired_collection"/> 865 <param name="selector" value="paired_collection"/>
930 <conditional name="tax_lev"> 887 <conditional name="tax_lev">
931 <param name="tax_lev" value="a"/> 888 <param name="tax_lev" value="a"/>
932 <param name="split_levels" value="false"/> 889 <param name="split_levels" value="false"/>
933 </conditional> 890 </conditional>
934 </conditional> 891 </conditional>
935 <param name="min_cu_len" value="2000"/>
936 <param name="organism_profiling" value="add_viruses"/>
937 <param name="stat" value="avg_g"/> 892 <param name="stat" value="avg_g"/>
938 <param name="stat_q" value="0.2"/> 893 <param name="stat_q" value="0.2"/>
939 <param name="perc_nonzero" value="0.33"/> 894 <param name="perc_nonzero" value="0.33"/>
940 <param name="avoid_disqm" value="true"/> 895 <param name="avoid_disqm" value="true"/>
941 </section> 896 </section>
946 </conditional> 901 </conditional>
947 <section name="out"> 902 <section name="out">
948 <param name="sample_id_key" value="SampleID"/> 903 <param name="sample_id_key" value="SampleID"/>
949 <param name="sample_id" value="Metaphlan_Analysis"/> 904 <param name="sample_id" value="Metaphlan_Analysis"/>
950 <param name="use_group_representative" value="false"/> 905 <param name="use_group_representative" value="false"/>
951 <param name="legacy_output" value="false"/>
952 <param name="CAMI_format_output" value="false"/> 906 <param name="CAMI_format_output" value="false"/>
953 <param name="unclassified_estimation" value="false"/> 907 <param name="skip_unclassified_estimation" value="false"/>
954 <param name="krona_output" value="false"/> 908 <param name="krona_output" value="false"/>
955 </section> 909 </section>
956 <output name="output_file" ftype="tabular" file="SRS014464-Anterior_nares-abundances.tabular" compare="sim_size"> 910 <output name="output_file" ftype="tabular">
957 <assert_contents> 911 <assert_contents>
912 <has_size size="9808"/>
958 <has_text text="k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens"/> 913 <has_text text="k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens"/>
959 <has_text text="relative_abundance"/> 914 <has_text text="relative_abundance"/>
960 <has_text text="NCBI_tax_id"/> 915 <has_text text="NCBI_tax_id"/>
961 <has_text text="clade_name"/> 916 <has_text text="clade_name"/>
962 </assert_contents> 917 </assert_contents>
963 </output> 918 </output>
964 <output name="bowtie2out" ftype="tabular" file="SRS014464-Anterior_nares-two-inputs-bowtie2out.tabular" compare="sim_size"> 919 <output name="mapout" ftype="tabular">
965 <assert_contents> 920 <assert_contents>
921 <has_size size="52535"/>
966 <has_text text="HWI-EAS109_102883399:3:107:9938:7093/1"/> 922 <has_text text="HWI-EAS109_102883399:3:107:9938:7093/1"/>
967 <has_text text="90240__A0A378QWM4__NCTC12877_00123"/> 923 <has_text text="90240__A0A378QWM4__NCTC12877_00123"/>
968 </assert_contents> 924 </assert_contents>
969 </output> 925 </output>
970 <output name="sam_output_file" ftype="sam"> 926 <output name="sam_output_file" ftype="sam">
971 <assert_contents> 927 <assert_contents>
972 <has_size min="52400" max="52600"/> 928 <has_size min="52400" max="52600"/>
973 <has_text text="SN:13076__A0A2I1PE66__CYJ72_10760"/> 929 <has_text text="SN:13076__A0A2I1PE66__CYJ72_10760"/>
974 </assert_contents>
975 </output>
976 <output name="biom_output_file" ftype="biom1" file="SRS014464-Anterior_nares.biom" compare="sim_size">
977 <assert_contents>
978 <has_text text="k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens"/>
979 </assert_contents> 930 </assert_contents>
980 </output> 931 </output>
981 <output_collection name="subsample_paired" type="paired"> 932 <output_collection name="subsample_paired" type="paired">
982 <element name="forward"> 933 <element name="forward">
983 <assert_contents> 934 <assert_contents>
993 <assert_stderr> 944 <assert_stderr>
994 <has_text text="Downloading" negate="true"/> 945 <has_text text="Downloading" negate="true"/>
995 </assert_stderr> 946 </assert_stderr>
996 </test> 947 </test>
997 <!-- Paired fastq file as collection, Cached db --> 948 <!-- Paired fastq file as collection, Cached db -->
998 <test expect_num_outputs="4"> 949 <test expect_num_outputs="3">
999 <section name="inputs"> 950 <section name="inputs">
1000 <conditional name="in"> 951 <conditional name="in">
1001 <param name="selector" value="raw"/> 952 <param name="selector" value="raw"/>
1002 <conditional name="raw_in"> 953 <conditional name="raw_in">
1003 <param name="selector" value="paired_collection"/> 954 <param name="selector" value="paired_collection"/>
1025 <conditional name="tax_lev"> 976 <conditional name="tax_lev">
1026 <param name="tax_lev" value="a"/> 977 <param name="tax_lev" value="a"/>
1027 <param name="split_levels" value="false"/> 978 <param name="split_levels" value="false"/>
1028 </conditional> 979 </conditional>
1029 </conditional> 980 </conditional>
1030 <param name="min_cu_len" value="2000"/>
1031 <param name="organism_profiling" value="add_viruses"/>
1032 <param name="stat" value="avg_g"/> 981 <param name="stat" value="avg_g"/>
1033 <param name="stat_q" value="0.2"/> 982 <param name="stat_q" value="0.2"/>
1034 <param name="perc_nonzero" value="0.33"/> 983 <param name="perc_nonzero" value="0.33"/>
1035 <param name="avoid_disqm" value="true"/> 984 <param name="avoid_disqm" value="true"/>
1036 </section> 985 </section>
1039 </conditional> 988 </conditional>
1040 <section name="out"> 989 <section name="out">
1041 <param name="sample_id_key" value="SampleID"/> 990 <param name="sample_id_key" value="SampleID"/>
1042 <param name="sample_id" value="Metaphlan_Analysis"/> 991 <param name="sample_id" value="Metaphlan_Analysis"/>
1043 <param name="use_group_representative" value="false"/> 992 <param name="use_group_representative" value="false"/>
1044 <param name="legacy_output" value="false"/>
1045 <param name="CAMI_format_output" value="false"/> 993 <param name="CAMI_format_output" value="false"/>
1046 <param name="unclassified_estimation" value="false"/> 994 <param name="skip_unclassified_estimation" value="false"/>
1047 <param name="krona_output" value="false"/> 995 <param name="krona_output" value="false"/>
1048 </section> 996 </section>
1049 <output name="output_file" ftype="tabular" file="SRS014464-Anterior_nares-abundances.tabular" compare="sim_size"> 997 <output name="output_file" ftype="tabular">
1050 <assert_contents> 998 <assert_contents>
1051 <has_text text="k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens"/> 999 <has_size size="12356"/>
1052 <has_text text="relative_abundance"/> 1000 <has_text text="k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens"/>
1053 <has_text text="NCBI_tax_id"/> 1001 <has_text text="relative_abundance"/>
1054 <has_text text="clade_name"/> 1002 <has_text text="NCBI_tax_id"/>
1055 </assert_contents> 1003 <has_text text="clade_name"/>
1056 </output> 1004 </assert_contents>
1057 <output name="bowtie2out" ftype="tabular"> 1005 </output>
1058 <assert_contents> 1006 <output name="mapout" ftype="tabular">
1007 <assert_contents>
1008 <has_size size="20961"/>
1059 <has_text text="HWI-EAS109_102883399:3:107:9938:7093/1"/> 1009 <has_text text="HWI-EAS109_102883399:3:107:9938:7093/1"/>
1060 <has_text text="90240__A0A378QWM4__NCTC12877_00123"/> 1010 <has_text text="90240__A0A378QWM4__NCTC12877_00123"/>
1061 </assert_contents> 1011 </assert_contents>
1062 </output> 1012 </output>
1063 <output name="sam_output_file" ftype="sam"> 1013 <output name="sam_output_file" ftype="sam">
1064 <assert_contents> 1014 <assert_contents>
1065 <has_size min="8450" max="8550"/> 1015 <has_size min="8450" max="8550"/>
1066 <has_text text="SN:13076__A0A2I1PE66__CYJ72_10760"/> 1016 <has_text text="SN:13076__A0A2I1PE66__CYJ72_10760"/>
1067 </assert_contents>
1068 </output>
1069 <output name="biom_output_file" ftype="biom1" file="SRS014464-Anterior_nares.biom" compare="sim_size">
1070 <assert_contents>
1071 <has_text text="k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens"/>
1072 </assert_contents> 1017 </assert_contents>
1073 </output> 1018 </output>
1074 <assert_stderr> 1019 <assert_stderr>
1075 <has_text text="Downloading" negate="true"/> 1020 <has_text text="Downloading" negate="true"/>
1076 </assert_stderr> 1021 </assert_stderr>
1077 </test> 1022 </test>
1078 <!-- SAM, cached DB --> 1023 <!-- SAM, cached DB -->
1079 <test expect_num_outputs="2"> 1024 <test expect_num_outputs="1">
1080 <section name="inputs"> 1025 <section name="inputs">
1081 <conditional name="in"> 1026 <conditional name="in">
1082 <param name="selector" value="sam"/> 1027 <param name="selector" value="sam"/>
1083 <param name="in" value="SRS014464-Anterior_nares.sam"/> 1028 <param name="in" value="SRS014464-Anterior_nares.sam"/>
1084 </conditional> 1029 </conditional>
1093 <conditional name="tax_lev"> 1038 <conditional name="tax_lev">
1094 <param name="tax_lev" value="a"/> 1039 <param name="tax_lev" value="a"/>
1095 <param name="split_levels" value="false"/> 1040 <param name="split_levels" value="false"/>
1096 </conditional> 1041 </conditional>
1097 </conditional> 1042 </conditional>
1098 <param name="min_cu_len" value="2000"/>
1099 <param name="organism_profiling" value="add_viruses"/>
1100 <param name="stat" value="avg_g"/> 1043 <param name="stat" value="avg_g"/>
1101 <param name="stat_q" value="0.2"/> 1044 <param name="stat_q" value="0.2"/>
1102 <param name="perc_nonzero" value="0.33"/> 1045 <param name="perc_nonzero" value="0.33"/>
1103 <param name="avoid_disqm" value="true"/> 1046 <param name="avoid_disqm" value="true"/>
1104 </section> 1047 </section>
1105 <section name="out"> 1048 <section name="out">
1106 <param name="sample_id_key" value="SampleID"/> 1049 <param name="sample_id_key" value="SampleID"/>
1107 <param name="sample_id" value="Metaphlan_Analysis"/> 1050 <param name="sample_id" value="Metaphlan_Analysis"/>
1108 <param name="use_group_representative" value="false"/> 1051 <param name="use_group_representative" value="false"/>
1109 <param name="legacy_output" value="false"/>
1110 <param name="CAMI_format_output" value="false"/> 1052 <param name="CAMI_format_output" value="false"/>
1111 <param name="unclassified_estimation" value="false"/> 1053 <param name="skip_unclassified_estimation" value="false"/>
1112 <param name="krona_output" value="false"/> 1054 <param name="krona_output" value="false"/>
1113 </section> 1055 </section>
1114 <output name="output_file" ftype="tabular" file="SRS014464-Anterior_nares-abundances.tabular" compare="sim_size"> 1056 <output name="output_file" ftype="tabular">
1115 <assert_contents> 1057 <assert_contents>
1058 <has_size size="12281"/>
1116 <has_text text="k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens"/> 1059 <has_text text="k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens"/>
1117 <has_text text="relative_abundance"/> 1060 <has_text text="relative_abundance"/>
1118 <has_text text="NCBI_tax_id"/> 1061 <has_text text="NCBI_tax_id"/>
1119 <has_text text="clade_name"/> 1062 <has_text text="clade_name"/>
1120 </assert_contents> 1063 </assert_contents>
1121 </output> 1064 </output>
1122 <output name="biom_output_file" ftype="biom1" file="SRS014464-Anterior_nares.biom" compare="sim_size">
1123 <assert_contents>
1124 <has_text text="k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_lacunata"/>
1125 </assert_contents>
1126 </output>
1127 <assert_stderr> 1065 <assert_stderr>
1128 <has_text text="Downloading" negate="true"/> 1066 <has_text text="Downloading" negate="true"/>
1129 </assert_stderr> 1067 </assert_stderr>
1130 </test> 1068 </test>
1131 <!-- bowtie2out, cached DB --> 1069 <!-- mapout, cached DB -->
1132 <test expect_num_outputs="2"> 1070 <test expect_num_outputs="1">
1133 <section name="inputs"> 1071 <section name="inputs">
1134 <conditional name="in"> 1072 <conditional name="in">
1135 <param name="selector" value="bowtie2out"/> 1073 <param name="selector" value="mapout"/>
1136 <param name="in" value="SRS014464-Anterior_nares-bowtie2out.tabular"/> 1074 <param name="in" value="SRS014464-Anterior_nares-mapout.tabular"/>
1137 </conditional> 1075 </conditional>
1138 <conditional name="db"> 1076 <conditional name="db">
1139 <param name="db_selector" value="cached"/> 1077 <param name="db_selector" value="cached"/>
1140 <param name="cached_db" value="test-db-20210409"/> 1078 <param name="cached_db" value="test-db-20210409"/>
1141 </conditional> 1079 </conditional>
1146 <conditional name="tax_lev"> 1084 <conditional name="tax_lev">
1147 <param name="tax_lev" value="a"/> 1085 <param name="tax_lev" value="a"/>
1148 <param name="split_levels" value="false"/> 1086 <param name="split_levels" value="false"/>
1149 </conditional> 1087 </conditional>
1150 </conditional> 1088 </conditional>
1151 <param name="min_cu_len" value="2000"/>
1152 <param name="organism_profiling" value="add_viruses"/>
1153 <param name="stat" value="avg_g"/> 1089 <param name="stat" value="avg_g"/>
1154 <param name="stat_q" value="0.2"/> 1090 <param name="stat_q" value="0.2"/>
1155 <param name="perc_nonzero" value="0.33"/> 1091 <param name="perc_nonzero" value="0.33"/>
1156 <param name="avoid_disqm" value="true"/> 1092 <param name="avoid_disqm" value="true"/>
1157 </section> 1093 </section>
1158 <section name="out"> 1094 <section name="out">
1159 <param name="sample_id_key" value="SampleID"/> 1095 <param name="sample_id_key" value="SampleID"/>
1160 <param name="sample_id" value="Metaphlan_Analysis"/> 1096 <param name="sample_id" value="Metaphlan_Analysis"/>
1161 <param name="use_group_representative" value="false"/> 1097 <param name="use_group_representative" value="false"/>
1162 <param name="legacy_output" value="false"/>
1163 <param name="CAMI_format_output" value="false"/> 1098 <param name="CAMI_format_output" value="false"/>
1164 <param name="unclassified_estimation" value="false"/> 1099 <param name="skip_unclassified_estimation" value="false"/>
1165 <param name="krona_output" value="false"/> 1100 <param name="krona_output" value="false"/>
1166 </section> 1101 </section>
1167 <output name="output_file" ftype="tabular" file="SRS014464-Anterior_nares-abundances.tabular" compare="sim_size"> 1102 <output name="output_file" ftype="tabular">
1168 <assert_contents> 1103 <assert_contents>
1104 <has_size size="12273"/>
1169 <has_text text="k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens"/> 1105 <has_text text="k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens"/>
1170 <has_text text="relative_abundance"/> 1106 <has_text text="relative_abundance"/>
1171 <has_text text="NCBI_tax_id"/> 1107 <has_text text="NCBI_tax_id"/>
1172 <has_text text="clade_name"/> 1108 <has_text text="clade_name"/>
1173 </assert_contents>
1174 </output>
1175 <output name="biom_output_file" ftype="biom1" file="SRS014464-Anterior_nares.biom" compare="sim_size">
1176 <assert_contents>
1177 <has_text text="k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_lacunata"/>
1178 </assert_contents> 1109 </assert_contents>
1179 </output> 1110 </output>
1180 <assert_stderr> 1111 <assert_stderr>
1181 <has_text text="Downloading" negate="true"/> 1112 <has_text text="Downloading" negate="true"/>
1182 </assert_stderr> 1113 </assert_stderr>
1183 </test> 1114 </test>
1184 <!-- Single FASTA file, Cached db --> 1115 <!-- Single FASTA file, Cached db -->
1185 <test expect_num_outputs="6"> 1116 <test expect_num_outputs="5">
1186 <section name="inputs"> 1117 <section name="inputs">
1187 <conditional name="in"> 1118 <conditional name="in">
1188 <param name="selector" value="raw"/> 1119 <param name="selector" value="raw"/>
1189 <conditional name="raw_in"> 1120 <conditional name="raw_in">
1190 <param name="selector" value="single"/> 1121 <param name="selector" value="single"/>
1207 <conditional name="tax_lev"> 1138 <conditional name="tax_lev">
1208 <param name="tax_lev" value="a"/> 1139 <param name="tax_lev" value="a"/>
1209 <param name="split_levels" value="true"/> 1140 <param name="split_levels" value="true"/>
1210 </conditional> 1141 </conditional>
1211 </conditional> 1142 </conditional>
1212 <param name="min_cu_len" value="2000"/>
1213 <param name="organism_profiling" value="add_viruses"/>
1214 <param name="stat" value="avg_g"/> 1143 <param name="stat" value="avg_g"/>
1215 <param name="stat_q" value="0.2"/> 1144 <param name="stat_q" value="0.2"/>
1216 <param name="perc_nonzero" value="0.33"/> 1145 <param name="perc_nonzero" value="0.33"/>
1217 <param name="ignore_markers" value="marker.txt"/> 1146 <param name="ignore_markers" value="marker.txt"/>
1218 <param name="avoid_disqm" value="true"/> 1147 <param name="avoid_disqm" value="true"/>
1219 </section> 1148 </section>
1220 <section name="out"> 1149 <section name="out">
1221 <param name="sample_id_key" value="SampleID"/> 1150 <param name="sample_id_key" value="SampleID"/>
1222 <param name="sample_id" value="Metaphlan_Analysis"/> 1151 <param name="sample_id" value="Metaphlan_Analysis"/>
1223 <param name="use_group_representative" value="false"/> 1152 <param name="use_group_representative" value="false"/>
1224 <param name="legacy_output" value="true"/>
1225 <param name="CAMI_format_output" value="false"/> 1153 <param name="CAMI_format_output" value="false"/>
1226 <param name="unclassified_estimation" value="false"/> 1154 <param name="skip_unclassified_estimation" value="false"/>
1227 <param name="krona_output" value="true"/> 1155 <param name="krona_output" value="true"/>
1228 </section> 1156 </section>
1229 <output name="output_file" ftype="tabular" file="SRS014464-Anterior_nares-legacy-abundances.tabular" compare="sim_size"> 1157 <output name="output_file" ftype="tabular">
1230 <assert_contents> 1158 <assert_contents>
1159 <has_size size="11869"/>
1231 <has_text text="k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens"/> 1160 <has_text text="k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens"/>
1232 <has_text text="SampleID"/> 1161 <has_text text="SampleID"/>
1233 <has_text text="Metaphlan_Analysis"/> 1162 <has_text text="Metaphlan_Analysis"/>
1234 </assert_contents> 1163 </assert_contents>
1235 </output> 1164 </output>
1236 <output name="bowtie2out" ftype="tabular" file="SRS014464-Anterior_nares-bowtie2out.tabular" compare="sim_size"> 1165 <output name="mapout" ftype="tabular">
1237 <assert_contents> 1166 <assert_contents>
1167 <has_size size="10504"/>
1238 <has_text text="HWI-EAS109_102883399:3:104:7342:14360/1"/> 1168 <has_text text="HWI-EAS109_102883399:3:104:7342:14360/1"/>
1239 <has_text text="37637__U2I1U8__N579_01580"/> 1169 <has_text text="37637__U2I1U8__N579_01580"/>
1240 </assert_contents> 1170 </assert_contents>
1241 </output> 1171 </output>
1242 <output name="sam_output_file" ftype="sam" file="SRS014464-Anterior_nares.sam" compare="sim_size"> 1172 <output name="sam_output_file" ftype="sam">
1243 <assert_contents> 1173 <assert_contents>
1174 <has_size size="54554"/>
1244 <has_text text="SN:13076__A0A2I1PE66__CYJ72_10760"/> 1175 <has_text text="SN:13076__A0A2I1PE66__CYJ72_10760"/>
1245 </assert_contents>
1246 </output>
1247 <output name="biom_output_file" ftype="biom1" file="SRS014464-Anterior_nares.biom" compare="sim_size">
1248 <assert_contents>
1249 <has_text text="k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_lacunata"/>
1250 </assert_contents> 1176 </assert_contents>
1251 </output> 1177 </output>
1252 <output_collection name="levels" type="list"> 1178 <output_collection name="levels" type="list">
1253 <element name="all" ftype="tabular"> 1179 <element name="all" ftype="tabular">
1254 <assert_contents> 1180 <assert_contents>
1255 <has_text text="Gammaproteobacteria"/> 1181 <has_text text="Gammaproteobacteria"/>
1256 <has_text text="Corynebacterium accolens"/> 1182 <has_text text="Corynebacterium accolens"/>
1257 <has_n_columns n="9"/> 1183 <has_n_columns n="17"/>
1258 </assert_contents> 1184 </assert_contents>
1259 </element> 1185 </element>
1260 <element name="class" ftype="tabular"> 1186 <element name="class" ftype="tabular">
1261 <assert_contents> 1187 <assert_contents>
1262 <has_text text="class"/> 1188 <has_text text="class"/>
1263 <has_text text="Actinobacteria"/> 1189 <has_text text="Actinobacteria"/>
1264 <has_n_columns n="2"/> 1190 <has_n_columns n="3"/>
1265 </assert_contents> 1191 </assert_contents>
1266 </element> 1192 </element>
1267 <element name="family" ftype="tabular"> 1193 <element name="family" ftype="tabular">
1268 <assert_contents> 1194 <assert_contents>
1269 <has_text text="family"/> 1195 <has_text text="family"/>
1270 <has_text text="Propionibacteriaceae"/> 1196 <has_text text="Propionibacteriaceae"/>
1271 <has_n_columns n="2"/> 1197 <has_n_columns n="3"/>
1272 </assert_contents> 1198 </assert_contents>
1273 </element> 1199 </element>
1274 <element name="genus" ftype="tabular"> 1200 <element name="genus" ftype="tabular">
1275 <assert_contents> 1201 <assert_contents>
1276 <has_text text="genus"/> 1202 <has_text text="genus"/>
1277 <has_text text="Cutibacterium"/> 1203 <has_text text="Cutibacterium"/>
1278 <has_n_columns n="2"/> 1204 <has_n_columns n="3"/>
1279 </assert_contents> 1205 </assert_contents>
1280 </element> 1206 </element>
1281 <element name="kingdom" ftype="tabular"> 1207 <element name="kingdom" ftype="tabular">
1282 <assert_contents> 1208 <assert_contents>
1283 <has_text text="kingdom"/> 1209 <has_text text="kingdom"/>
1284 <has_text text="Bacteria"/> 1210 <has_text text="Bacteria"/>
1285 <has_n_columns n="2"/> 1211 <has_n_columns n="3"/>
1286 </assert_contents> 1212 </assert_contents>
1287 </element> 1213 </element>
1288 <element name="order" ftype="tabular"> 1214 <element name="order" ftype="tabular">
1289 <assert_contents> 1215 <assert_contents>
1290 <has_text text="order"/> 1216 <has_text text="order"/>
1291 <has_text text="Propionibacteriales"/> 1217 <has_text text="Propionibacteriales"/>
1292 <has_n_columns n="2"/> 1218 <has_n_columns n="3"/>
1293 </assert_contents> 1219 </assert_contents>
1294 </element> 1220 </element>
1295 <element name="phylum" ftype="tabular"> 1221 <element name="phylum" ftype="tabular">
1296 <assert_contents> 1222 <assert_contents>
1297 <has_text text="phylum"/> 1223 <has_text text="phylum"/>
1298 <has_text text="Firmicutes"/> 1224 <has_text text="Firmicutes"/>
1299 <has_n_columns n="2"/> 1225 <has_n_columns n="3"/>
1300 </assert_contents> 1226 </assert_contents>
1301 </element> 1227 </element>
1302 <element name="species" ftype="tabular"> 1228 <element name="species" ftype="tabular">
1303 <assert_contents> 1229 <assert_contents>
1304 <has_text text="species"/> 1230 <has_text text="species"/>
1305 <has_text text="Corynebacterium accolens"/> 1231 <has_text text="Corynebacterium accolens"/>
1306 <has_n_columns n="2"/> 1232 <has_n_columns n="3"/>
1307 </assert_contents> 1233 </assert_contents>
1308 </element> 1234 </element>
1309 <element name="strains" ftype="tabular"> 1235 <element name="strains" ftype="tabular">
1310 <assert_contents> 1236 <assert_contents>
1311 <has_text text="strains"/> 1237 <has_text text="strains"/>
1312 <has_n_columns n="2"/> 1238 <has_n_columns n="3"/>
1313 </assert_contents> 1239 </assert_contents>
1314 </element> 1240 </element>
1315 </output_collection> 1241 </output_collection>
1316 <output name="krona_output_file" ftype="tabular"> 1242 <output name="krona_output_file" ftype="tabular">
1317 <assert_contents> 1243 <assert_contents>
1324 <has_text text="Downloading" negate="true"/> 1250 <has_text text="Downloading" negate="true"/>
1325 </assert_stderr> 1251 </assert_stderr>
1326 </test> 1252 </test>
1327 <!-- Check a non-default analysis mode 1253 <!-- Check a non-default analysis mode
1328 and viral analysis --> 1254 and viral analysis -->
1329 <test expect_num_outputs="6"> 1255 <test expect_num_outputs="5">
1330 <section name="inputs"> 1256 <section name="inputs">
1331 <conditional name="in"> 1257 <conditional name="in">
1332 <param name="selector" value="raw"/> 1258 <param name="selector" value="raw"/>
1333 <conditional name="raw_in"> 1259 <conditional name="raw_in">
1334 <param name="selector" value="single"/> 1260 <param name="selector" value="single"/>
1336 </conditional> 1262 </conditional>
1337 </conditional> 1263 </conditional>
1338 <conditional name="db"> 1264 <conditional name="db">
1339 <param name="db_selector" value="cached"/> 1265 <param name="db_selector" value="cached"/>
1340 <param name="cached_db" value="mpa_vJan21_TOY_CHOCOPhlAnSGB"/> 1266 <param name="cached_db" value="mpa_vJan21_TOY_CHOCOPhlAnSGB"/>
1267 <conditional name="viral_analysis">
1268 <param name="profile_vsc" value="--profile_vsc"/>
1269 </conditional>
1341 </conditional> 1270 </conditional>
1342 </section> 1271 </section>
1343 <section name="analysis"> 1272 <section name="analysis">
1344 <conditional name="analysis_type"> 1273 <conditional name="analysis_type">
1345 <param name="t" value="marker_ab_table"/> 1274 <param name="t" value="marker_ab_table"/>
1346 </conditional> 1275 </conditional>
1347 </section> 1276 </section>
1348 <conditional name="viral_analysis">
1349 <param name="profile_vsc" value="--profile_vsc"/>
1350 </conditional>
1351 <conditional name="subsample"> 1277 <conditional name="subsample">
1352 <param name="selector" value="single"/> 1278 <param name="selector" value="single"/>
1353 <param name="subsampling" value="10000"/> 1279 <param name="subsampling" value="10000"/>
1354 <param name="subsampling_seed" value="42"/> 1280 <param name="subsampling_seed" value="42"/>
1355 </conditional> 1281 </conditional>
1356 <param name="test" value="true"/> 1282 <param name="test" value="true"/>
1357 <output name="output_file" ftype="tabular" file="SRS014464-Anterior_nares-legacy-abundances.tabular" compare="sim_size"> 1283 <output name="output_file" ftype="tabular">
1358 <assert_contents> 1284 <assert_contents>
1285 <has_size size="7690"/>
1359 <has_text text="SGB7017__MKDPKOFL_00679"/> 1286 <has_text text="SGB7017__MKDPKOFL_00679"/>
1360 <has_text text="SampleID"/> 1287 <has_text text="SampleID"/>
1361 <has_text text="Metaphlan_Analysis"/> 1288 <has_text text="Metaphlan_Analysis"/>
1362 </assert_contents> 1289 </assert_contents>
1363 </output> 1290 </output>
1415 aggregated marker information. Such capability comes with several slightly different flavours and 1342 aggregated marker information. Such capability comes with several slightly different flavours and
1416 are a way to perform strain tracking and comparison across multiple samples. 1343 are a way to perform strain tracking and comparison across multiple samples.
1417 1344
1418 Usually, MetaPhlAn is first ran with default parameters for the type of analysis to profile the 1345 Usually, MetaPhlAn is first ran with default parameters for the type of analysis to profile the
1419 species present in the community, and then a strain-level profiling can be performed to zoom-in on 1346 species present in the community, and then a strain-level profiling can be performed to zoom-in on
1420 specific species of interest. This operation can be performed quickly as it exploits the bowtie2out 1347 specific species of interest. This operation can be performed quickly as it exploits the mapout
1421 intermediate file saved during the execution of the default analysis type. 1348 intermediate file saved during the execution of the default analysis type.
1422 1349
1423 Inputs 1350 Inputs
1424 ====== 1351 ======
1425 1352
1434 Outputs 1361 Outputs
1435 ======= 1362 =======
1436 1363
1437 The main output is a tab-separated file with the predicted taxon relative abundances. 1364 The main output is a tab-separated file with the predicted taxon relative abundances.
1438 1365
1439 It also generates a BIOM file and some intermediate files (SAM and BowTie2out) if sequence files are given as inputs. 1366 It also generates a BIOM file and some intermediate files (SAM and mapout) if sequence files are given as inputs.
1440 1367
1441 1368
1442 More help and use cases 1369 More help and use cases
1443 ======================= 1370 =======================
1444 1371