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comparison metaphlan.xml @ 10:289b3807e80c draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit b8bc892a6d5eeae0b78c33058b532fcd52208179
author iuc
date Tue, 30 Apr 2024 09:09:32 +0000
parents 1a6cdf55390f
children
comparison
equal deleted inserted replaced
9:fd69c607b43f 10:289b3807e80c
178 --sample_id_key '$out.sample_id_key' 178 --sample_id_key '$out.sample_id_key'
179 --sample_id '$out.sample_id' 179 --sample_id '$out.sample_id'
180 $out.use_group_representative 180 $out.use_group_representative
181 $out.legacy_output 181 $out.legacy_output
182 $out.CAMI_format_output 182 $out.CAMI_format_output
183 $out.unknown_estimation 183 $out.unclassified_estimation
184 -o '$output_file' 184 -o '$output_file'
185 --bowtie2out 'bowtie2out' 185 --bowtie2out 'bowtie2out'
186 -s '$sam_output_file' 186 -s '$sam_output_file'
187 --biom '$biom_output_file' 187 --biom '$biom_output_file'
188 --nproc \${GALAXY_SLOTS:-4} 188 --nproc \${GALAXY_SLOTS:-4}
345 label="Use a species as representative for species groups?"/> 345 label="Use a species as representative for species groups?"/>
346 <param argument="--legacy-output" type='boolean' checked="false" truevalue='--legacy-output' falsevalue='' 346 <param argument="--legacy-output" type='boolean' checked="false" truevalue='--legacy-output' falsevalue=''
347 label="Old MetaPhlAn2 two columns output?"/> 347 label="Old MetaPhlAn2 two columns output?"/>
348 <param argument="--CAMI_format_output" type='boolean' checked="false" truevalue='--CAMI_format_output' falsevalue='' 348 <param argument="--CAMI_format_output" type='boolean' checked="false" truevalue='--CAMI_format_output' falsevalue=''
349 label="Report the profiling using the CAMI output format?"/> 349 label="Report the profiling using the CAMI output format?"/>
350 <param argument="--unknown_estimation" type='boolean' checked="false" truevalue='--unknown_estimation' falsevalue='' 350 <param argument="--unclassified_estimation" type='boolean' checked="false" truevalue='--unclassified_estimation' falsevalue=''
351 label="Scale relative abundances to the number of reads mapping to known clades in order to estimate unknowness?"/> 351 label="Scale relative abundances to the number of reads mapping to known clades in order to estimate unknowness?"/>
352 <param name="krona_output" type='boolean' checked="false" truevalue='true' falsevalue='false' label="Output for Krona?"/> 352 <param name="krona_output" type='boolean' checked="false" truevalue='true' falsevalue='false' label="Output for Krona?"/>
353 </section> 353 </section>
354 </inputs> 354 </inputs>
355 <outputs> 355 <outputs>
410 <param name="sample_id_key" value="SampleID"/> 410 <param name="sample_id_key" value="SampleID"/>
411 <param name="sample_id" value="Metaphlan_Analysis"/> 411 <param name="sample_id" value="Metaphlan_Analysis"/>
412 <param name="use_group_representative" value="false"/> 412 <param name="use_group_representative" value="false"/>
413 <param name="legacy_output" value="false"/> 413 <param name="legacy_output" value="false"/>
414 <param name="CAMI_format_output" value="false"/> 414 <param name="CAMI_format_output" value="false"/>
415 <param name="unknown_estimation" value="false"/> 415 <param name="unclassified_estimation" value="false"/>
416 <param name="krona_output" value="true"/> 416 <param name="krona_output" value="true"/>
417 </section> 417 </section>
418 <output name="output_file" ftype="tabular"> 418 <output name="output_file" ftype="tabular">
419 <assert_contents> 419 <assert_contents>
420 <has_text text="UNCLASSIFIED"/> 420 <has_text text="UNCLASSIFIED"/>
557 <param name="sample_id_key" value="SampleID"/> 557 <param name="sample_id_key" value="SampleID"/>
558 <param name="sample_id" value="Metaphlan_Analysis"/> 558 <param name="sample_id" value="Metaphlan_Analysis"/>
559 <param name="use_group_representative" value="false"/> 559 <param name="use_group_representative" value="false"/>
560 <param name="legacy_output" value="false"/> 560 <param name="legacy_output" value="false"/>
561 <param name="CAMI_format_output" value="false"/> 561 <param name="CAMI_format_output" value="false"/>
562 <param name="unknown_estimation" value="false"/> 562 <param name="unclassified_estimation" value="false"/>
563 <param name="krona_output" value="true"/> 563 <param name="krona_output" value="true"/>
564 </section> 564 </section>
565 <output name="output_file" ftype="tabular" file="SRS014464-Anterior_nares-abundances.tabular" compare="sim_size"> 565 <output name="output_file" ftype="tabular" file="SRS014464-Anterior_nares-abundances.tabular" compare="sim_size">
566 <assert_contents> 566 <assert_contents>
567 <has_text text="k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens"/> 567 <has_text text="k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens"/>
703 <param name="sample_id_key" value="SampleID"/> 703 <param name="sample_id_key" value="SampleID"/>
704 <param name="sample_id" value="Metaphlan_Analysis"/> 704 <param name="sample_id" value="Metaphlan_Analysis"/>
705 <param name="use_group_representative" value="false"/> 705 <param name="use_group_representative" value="false"/>
706 <param name="legacy_output" value="false"/> 706 <param name="legacy_output" value="false"/>
707 <param name="CAMI_format_output" value="false"/> 707 <param name="CAMI_format_output" value="false"/>
708 <param name="unknown_estimation" value="false"/> 708 <param name="unclassified_estimation" value="false"/>
709 <param name="krona_output" value="false"/> 709 <param name="krona_output" value="false"/>
710 </section> 710 </section>
711 <output name="output_file" ftype="tabular" file="SRS014464-Anterior_nares-abundances.tabular" compare="sim_size"> 711 <output name="output_file" ftype="tabular" file="SRS014464-Anterior_nares-abundances.tabular" compare="sim_size">
712 <assert_contents> 712 <assert_contents>
713 <has_text text="k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens"/> 713 <has_text text="k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens"/>
774 <param name="sample_id_key" value="SampleID"/> 774 <param name="sample_id_key" value="SampleID"/>
775 <param name="sample_id" value="Metaphlan_Analysis"/> 775 <param name="sample_id" value="Metaphlan_Analysis"/>
776 <param name="use_group_representative" value="false"/> 776 <param name="use_group_representative" value="false"/>
777 <param name="legacy_output" value="false"/> 777 <param name="legacy_output" value="false"/>
778 <param name="CAMI_format_output" value="false"/> 778 <param name="CAMI_format_output" value="false"/>
779 <param name="unknown_estimation" value="false"/> 779 <param name="unclassified_estimation" value="false"/>
780 <param name="krona_output" value="false"/> 780 <param name="krona_output" value="false"/>
781 </section> 781 </section>
782 <output name="output_file" ftype="tabular" file="SRS014464-Anterior_nares-abundances.tabular" compare="sim_size"> 782 <output name="output_file" ftype="tabular" file="SRS014464-Anterior_nares-abundances.tabular" compare="sim_size">
783 <assert_contents> 783 <assert_contents>
784 <has_text text="k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens"/> 784 <has_text text="k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens"/>
836 <param name="sample_id_key" value="SampleID"/> 836 <param name="sample_id_key" value="SampleID"/>
837 <param name="sample_id" value="Metaphlan_Analysis"/> 837 <param name="sample_id" value="Metaphlan_Analysis"/>
838 <param name="use_group_representative" value="false"/> 838 <param name="use_group_representative" value="false"/>
839 <param name="legacy_output" value="false"/> 839 <param name="legacy_output" value="false"/>
840 <param name="CAMI_format_output" value="false"/> 840 <param name="CAMI_format_output" value="false"/>
841 <param name="unknown_estimation" value="false"/> 841 <param name="unclassified_estimation" value="false"/>
842 <param name="krona_output" value="false"/> 842 <param name="krona_output" value="false"/>
843 </section> 843 </section>
844 <output name="output_file" ftype="tabular" file="SRS014464-Anterior_nares-abundances.tabular" compare="sim_size"> 844 <output name="output_file" ftype="tabular" file="SRS014464-Anterior_nares-abundances.tabular" compare="sim_size">
845 <assert_contents> 845 <assert_contents>
846 <has_text text="k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens"/> 846 <has_text text="k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens"/>
895 <param name="sample_id_key" value="SampleID"/> 895 <param name="sample_id_key" value="SampleID"/>
896 <param name="sample_id" value="Metaphlan_Analysis"/> 896 <param name="sample_id" value="Metaphlan_Analysis"/>
897 <param name="use_group_representative" value="false"/> 897 <param name="use_group_representative" value="false"/>
898 <param name="legacy_output" value="false"/> 898 <param name="legacy_output" value="false"/>
899 <param name="CAMI_format_output" value="false"/> 899 <param name="CAMI_format_output" value="false"/>
900 <param name="unknown_estimation" value="false"/> 900 <param name="unclassified_estimation" value="false"/>
901 <param name="krona_output" value="false"/> 901 <param name="krona_output" value="false"/>
902 </section> 902 </section>
903 <output name="output_file" ftype="tabular" file="SRS014464-Anterior_nares-abundances.tabular" compare="sim_size"> 903 <output name="output_file" ftype="tabular" file="SRS014464-Anterior_nares-abundances.tabular" compare="sim_size">
904 <assert_contents> 904 <assert_contents>
905 <has_text text="k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens"/> 905 <has_text text="k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens"/>
955 <param name="sample_id_key" value="SampleID"/> 955 <param name="sample_id_key" value="SampleID"/>
956 <param name="sample_id" value="Metaphlan_Analysis"/> 956 <param name="sample_id" value="Metaphlan_Analysis"/>
957 <param name="use_group_representative" value="false"/> 957 <param name="use_group_representative" value="false"/>
958 <param name="legacy_output" value="true"/> 958 <param name="legacy_output" value="true"/>
959 <param name="CAMI_format_output" value="false"/> 959 <param name="CAMI_format_output" value="false"/>
960 <param name="unknown_estimation" value="false"/> 960 <param name="unclassified_estimation" value="false"/>
961 <param name="krona_output" value="true"/> 961 <param name="krona_output" value="true"/>
962 </section> 962 </section>
963 <output name="output_file" ftype="tabular" file="SRS014464-Anterior_nares-legacy-abundances.tabular" compare="sim_size"> 963 <output name="output_file" ftype="tabular" file="SRS014464-Anterior_nares-legacy-abundances.tabular" compare="sim_size">
964 <assert_contents> 964 <assert_contents>
965 <has_text text="k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens"/> 965 <has_text text="k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens"/>