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comparison metaphlan.xml @ 8:1a6cdf55390f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit d9038dd0880b963d36aea01eb4594bc30dc28b1c
author iuc
date Thu, 20 Apr 2023 11:26:53 +0000
parents 2131d7dca455
children 289b3807e80c
comparison
equal deleted inserted replaced
7:ec368db926f4 8:1a6cdf55390f
190 #if $inputs.in.selector == "raw" 190 #if $inputs.in.selector == "raw"
191 && 191 &&
192 mv 'bowtie2out' '$bowtie2out' 192 mv 'bowtie2out' '$bowtie2out'
193 #end if 193 #end if
194 194
195 #if $analysis.analysis_type.tax_lev.tax_lev == 'a' and $analysis.analysis_type.tax_lev.split_levels 195
196 && 196 #if $analysis.analysis_type.t in ['rel_ab', 'rel_ab_w_read_stats']
197 mkdir 'split_levels' 197 #if $analysis.analysis_type.tax_lev.tax_lev == 'a' and $analysis.analysis_type.tax_lev.split_levels
198 && 198 &&
199 python '$__tool_directory__/formatoutput.py' 199 mkdir 'split_levels'
200 split_levels 200 &&
201 --metaphlan_output '$output_file' 201 python '$__tool_directory__/formatoutput.py'
202 --outdir 'split_levels' 202 split_levels
203 $out.legacy_output 203 --metaphlan_output '$output_file'
204 204 --outdir 'split_levels'
205 $out.legacy_output
206 #end if
205 #end if 207 #end if
206 208
207 #if $out.krona_output 209 #if $out.krona_output
208 && 210 &&
209 python '$__tool_directory__/formatoutput.py' 211 python '$__tool_directory__/formatoutput.py'
359 <filter>inputs['in']['selector'] == "raw"</filter> 361 <filter>inputs['in']['selector'] == "raw"</filter>
360 </data> 362 </data>
361 <data name="biom_output_file" format="biom1" label="${tool.name} on ${on_string}: BIOM file" /> 363 <data name="biom_output_file" format="biom1" label="${tool.name} on ${on_string}: BIOM file" />
362 <collection name="levels" type="list" label="${tool.name} on ${on_string}: Predicted taxon relative abundances at each taxonomic levels" > 364 <collection name="levels" type="list" label="${tool.name} on ${on_string}: Predicted taxon relative abundances at each taxonomic levels" >
363 <discover_datasets pattern="(?P&lt;designation&gt;.+)" directory="split_levels/" format="tabular"/> 365 <discover_datasets pattern="(?P&lt;designation&gt;.+)" directory="split_levels/" format="tabular"/>
364 <filter>analysis['analysis_type']['tax_lev']['tax_lev'] == "a" and analysis['analysis_type']['tax_lev']['split_levels']</filter> 366 <filter>analysis['analysis_type']['t'] in ['rel_ab', 'rel_ab_w_read_stats'] and analysis['analysis_type']['tax_lev']['tax_lev'] == "a" and analysis['analysis_type']['tax_lev']['split_levels']</filter>
365 </collection> 367 </collection>
366 <data name="krona_output_file" format="tabular" label="${tool.name} on ${on_string}: Predicted taxon relative abundances for Krona"> 368 <data name="krona_output_file" format="tabular" label="${tool.name} on ${on_string}: Predicted taxon relative abundances for Krona">
367 <filter>out['krona_output']</filter> 369 <filter>out['krona_output']</filter>
368 </data> 370 </data>
369 </outputs> 371 </outputs>
433 <assert_contents> 435 <assert_contents>
434 <not_has_text text="k__Bacteria"/> 436 <not_has_text text="k__Bacteria"/>
435 <not_has_text text="p__Actinobacteria"/> 437 <not_has_text text="p__Actinobacteria"/>
436 </assert_contents> 438 </assert_contents>
437 </output> 439 </output>
438 <output_collection name="levels" type="list" > 440 <output_collection name="levels" type="list">
439
440 <element name="all" ftype="tabular"> 441 <element name="all" ftype="tabular">
441 <assert_contents> 442 <assert_contents>
442 <has_text text="class"/> 443 <has_text text="class"/>
443 <has_n_columns n="17"/> 444 <has_n_columns n="17"/>
444 <has_n_lines n="1"/> 445 <has_n_lines n="1"/>
1052 <has_text text="Corynebacterium accolens"/> 1053 <has_text text="Corynebacterium accolens"/>
1053 <has_n_columns n="9"/> 1054 <has_n_columns n="9"/>
1054 </assert_contents> 1055 </assert_contents>
1055 </output> 1056 </output>
1056 </test> 1057 </test>
1058 <!-- Check a non-default analysis mode -->
1059 <test expect_num_outputs="4">
1060 <section name="inputs">
1061 <conditional name="in">
1062 <param name="selector" value="raw"/>
1063 <conditional name="raw_in">
1064 <param name="selector" value="single"/>
1065 <param name="in" value="SRS014464-Anterior_nares.fasta"/>
1066 </conditional>
1067 </conditional>
1068 <conditional name="db">
1069 <param name="db_selector" value="cached"/>
1070 <param name="cached_db" value="test-db-20210409"/>
1071 </conditional>
1072 </section>
1073 <section name="analysis">
1074 <conditional name="analysis_type">
1075 <param name="t" value="marker_ab_table"/>
1076 </conditional>
1077 </section>
1078 <output name="output_file" ftype="tabular" file="SRS014464-Anterior_nares-legacy-abundances.tabular" compare="sim_size">
1079 <assert_contents>
1080 <has_text text="29394__H3NC06__B8A41_08715"/>
1081 <has_text text="SampleID"/>
1082 <has_text text="Metaphlan_Analysis"/>
1083 </assert_contents>
1084 </output>
1085 </test>
1057 </tests> 1086 </tests>
1058 <help><![CDATA[ 1087 <help><![CDATA[
1059 What it does 1088 What it does
1060 ============ 1089 ============
1061 1090