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comparison quast.xml @ 18:c791615bcc55 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 5b2225491719b922003c69f0394bfc3eb238b360
author iuc
date Sat, 04 Oct 2025 15:48:40 +0000
parents 84032664991e
children
comparison
equal deleted inserted replaced
17:2f0ede3447fb 18:c791615bcc55
37 #end if 37 #end if
38 #end if 38 #end if
39 39
40 #if $assembly.type == 'metagenome' and $assembly.ref.origin == 'list' 40 #if $assembly.type == 'metagenome' and $assembly.ref.origin == 'list'
41 #set $temp_ref_list_fp = 'temp_ref_list' 41 #set $temp_ref_list_fp = 'temp_ref_list'
42 #for $i in $assembly.ref.references_list.split(',') 42 #for $i in str($assembly.ref.references_list).split(',')
43 echo $i >> $temp_ref_list_fp && 43 echo $i >> $temp_ref_list_fp &&
44 #end for 44 #end for
45 #end if 45 #end if
46 46
47 #if $mode.reads.reads_option == 'paired' 47 #if $mode.reads.reads_option == 'paired'
244 '$k.input' 244 '$k.input'
245 #end for 245 #end for
246 #end if 246 #end if
247 #end if 247 #end if
248 --threads \${GALAXY_SLOTS:-1} 248 --threads \${GALAXY_SLOTS:-1}
249
250 #if 'krona' not in $output_files or $assembly.ref.origin != 'silva'
251 --no-krona
252 #end if
249 253
250 #if $assembly.type == 'genome' 254 #if $assembly.type == 'genome'
251 && mkdir -p '$report_html.files_path' 255 && mkdir -p '$report_html.files_path'
252 && cp outputdir/*.html '$report_html.files_path' 256 && cp outputdir/*.html '$report_html.files_path'
253 #if $assembly.ref.use_ref 257 #if $assembly.ref.use_ref
443 <param argument="--upper-bound-assembly" type="boolean" truevalue="--upper-bound-assembly" falsevalue="" label="Simulate upper bound assembly" help="Simulate upper bound assembly based on the reference genome and a given set reads (mate-pairs or long reads, such as Pacbio SMRT/Oxford Nanopore, are REQUIRED). This assembly is added to the comparison and could be useful for estimating the upper bounds of completeness and contiguity that theoretically can be reached by assembly software from this particular set of reads. The concept is based on the fact that the reference genome cannot be completely reconstructed from raw reads due to long genomic repeats and low covered regions." /> 447 <param argument="--upper-bound-assembly" type="boolean" truevalue="--upper-bound-assembly" falsevalue="" label="Simulate upper bound assembly" help="Simulate upper bound assembly based on the reference genome and a given set reads (mate-pairs or long reads, such as Pacbio SMRT/Oxford Nanopore, are REQUIRED). This assembly is added to the comparison and could be useful for estimating the upper bounds of completeness and contiguity that theoretically can be reached by assembly software from this particular set of reads. The concept is based on the fact that the reference genome cannot be completely reconstructed from raw reads due to long genomic repeats and low covered regions." />
444 <param argument="--upper-bound-min-con" type="integer" value="" optional="true" label="Minimal number of 'connecting reads' needed for joining upper bound contigs into a scaffold" help="This is important for a realistic estimation of genome assembly fragmentation due to long repeats. The default values is 2 for mate-pairs and 1 for long reads (PacBio or Nanopore libraries)"/> 448 <param argument="--upper-bound-min-con" type="integer" value="" optional="true" label="Minimal number of 'connecting reads' needed for joining upper bound contigs into a scaffold" help="This is important for a realistic estimation of genome assembly fragmentation due to long repeats. The default values is 2 for mate-pairs and 1 for long reads (PacBio or Nanopore libraries)"/>
445 <param argument="--local-mis-size" type="integer" value="200" optional="true" label="Minimal local misassembly size" help="Lower threshold for the local misassembly size. Shorter inconsistencies are considered as (long) indels. The default value is 200 bp. Note that the threshold should be equal to or lower than minimal extensive misassembly size, which is 1000 bp by default"/> 449 <param argument="--local-mis-size" type="integer" value="200" optional="true" label="Minimal local misassembly size" help="Lower threshold for the local misassembly size. Shorter inconsistencies are considered as (long) indels. The default value is 200 bp. Note that the threshold should be equal to or lower than minimal extensive misassembly size, which is 1000 bp by default"/>
446 </section> 450 </section>
447 <section name="advanced" title="Advanced options"> 451 <section name="advanced" title="Advanced options">
448 <param argument="--contig-thresholds" type="text" value="0,1000" label="Comma-separated list of contig length thresholds (in bp)" help="Used in # contigs ≥ x and total length (≥ x) metrics"/> 452 <param argument="--contig-thresholds" type="text" value="0,1000,5000,10000,25000,50000" label="Comma-separated list of contig length thresholds (in bp)" help="Used in # contigs ≥ x and total length (≥ x) metrics"/>
449 <param argument="--strict-NA" type="boolean" truevalue="--strict-NA" falsevalue="" checked="false" label="Break contigs at every misassembly event (including local ones) to compute NAx and NGAx statistics?" help="By default, QUAST breaks contigs only at extensive misassemblies (not local ones)."/> 453 <param argument="--strict-NA" type="boolean" truevalue="--strict-NA" falsevalue="" checked="false" label="Break contigs at every misassembly event (including local ones) to compute NAx and NGAx statistics?" help="By default, QUAST breaks contigs only at extensive misassemblies (not local ones)."/>
450 <param argument="--extensive-mis-size" type="integer" value="1000" min="85" label="Lower threshold for the relocation size (gap or overlap size between left and right flanking sequence)" help="Shorter relocations are considered as local misassemblies. It does not affect other types of extensive misassemblies (inversions and translocations). The default value is 1000 bp. Note that the threshold should be greater than maximum indel length which is 85 bp."/> 454 <param argument="--extensive-mis-size" type="integer" value="1000" min="85" label="Lower threshold for the relocation size (gap or overlap size between left and right flanking sequence)" help="Shorter relocations are considered as local misassemblies. It does not affect other types of extensive misassemblies (inversions and translocations). The default value is 1000 bp. Note that the threshold should be greater than maximum indel length which is 85 bp."/>
451 <param argument="--scaffold-gap-max-size" type="integer" value="1000" label="Max allowed scaffold gap length difference for detecting corresponding type of misassemblies" help="Longer inconsistencies are considered as relocations and thus, counted as extensive misassemblies. The default value is 10000 bp. Note that the threshold make sense only if it is greater than extensive misassembly size"/> 455 <param argument="--scaffold-gap-max-size" type="integer" value="10000" label="Max allowed scaffold gap length difference for detecting corresponding type of misassemblies" help="Longer inconsistencies are considered as relocations and thus, counted as extensive misassemblies. The default value is 10000 bp. Note that the threshold make sense only if it is greater than extensive misassembly size"/>
452 <param argument="--unaligned-part-size" type="integer" value="500" label="Lower threshold for detecting partially unaligned contigs" help=""/> 456 <param argument="--unaligned-part-size" type="integer" value="500" label="Lower threshold for detecting partially unaligned contigs" help=""/>
453 <param argument="--skip-unaligned-mis-contigs" type="boolean" truevalue="" falsevalue="--skip-unaligned-mis-contigs" checked="true" label="Distinguish contigs with more than 50% unaligned bases as a separate group of contigs?" help="By default, QUAST breaks contigs only at extensive misassemblies (not local ones)."/> 457 <param argument="--skip-unaligned-mis-contigs" type="boolean" truevalue="" falsevalue="--skip-unaligned-mis-contigs" checked="true" label="Distinguish contigs with more than 50% unaligned bases as a separate group of contigs?" help="By default, QUAST breaks contigs only at extensive misassemblies (not local ones)."/>
454 <param argument="--fragmented-max-indent" type="integer" min="0" value="" optional="true" label="Fragment max indent" help="Mark translocation as fake if both alignments are located no further than N bases from the ends of the reference fragments. The value should be less than extensive misassembly size.Default value is 50. Note: requires --fragmented option" /> 458 <param argument="--fragmented-max-indent" type="integer" min="0" value="" optional="true" label="Fragment max indent" help="Mark translocation as fake if both alignments are located no further than N bases from the ends of the reference fragments. The value should be less than extensive misassembly size.Default value is 50. Note: requires --fragmented option" />
455 <param argument="--report-all-metrics" type="boolean" truevalue="--report-all-metrics" falsevalue="" checked="false" label="Report all metrics" help="Keep all quality metrics in the main report. Usually, all not-relevant metrics are not included in the report, e.g., reference-based metrics in the no-reference mode. Also, if metric values are undefined for all input assemblies, the metric is removed from the report" /> 459 <param argument="--report-all-metrics" type="boolean" truevalue="--report-all-metrics" falsevalue="" checked="false" label="Report all metrics" help="Keep all quality metrics in the main report. Usually, all not-relevant metrics are not included in the report, e.g., reference-based metrics in the no-reference mode. Also, if metric values are undefined for all input assemblies, the metric is removed from the report" />
456 <param argument="--x-for-Nx" type="integer" min="0" max="100" value="90" label="Report Nx, Lx, etc metrics for specific value of 'x'" help="Value of 'x' for Nx, Lx, NGx, NGAx, etc metrics reported in addition to N50, L50, NG50, NGA50, etc" /> 460 <param argument="--x-for-Nx" type="integer" min="0" max="100" value="90" label="Report Nx, Lx, etc metrics for specific value of 'x'" help="Value of 'x' for Nx, Lx, NGx, NGAx, etc metrics reported in addition to N50, L50, NG50, NGA50, etc" />
508 <collection name="metrics_pdf" type="list" label="${tool.name} on ${on_string}: PDF reports for key metrics" > 512 <collection name="metrics_pdf" type="list" label="${tool.name} on ${on_string}: PDF reports for key metrics" >
509 <discover_datasets pattern="(?P&lt;designation&gt;.+).pdf" directory="outputdir/summary/PDF/" format="pdf"/> 513 <discover_datasets pattern="(?P&lt;designation&gt;.+).pdf" directory="outputdir/summary/PDF/" format="pdf"/>
510 <filter>assembly['type'] == 'metagenome' and 'summary' in output_files</filter> 514 <filter>assembly['type'] == 'metagenome' and 'summary' in output_files</filter>
511 </collection> 515 </collection>
512 <data name="krona" format="html" label="${tool.name} on ${on_string}: Krona chart" from_work_dir="outputdir/krona_charts/*.html"> 516 <data name="krona" format="html" label="${tool.name} on ${on_string}: Krona chart" from_work_dir="outputdir/krona_charts/*.html">
513 <filter>assembly['type'] == 'metagenome' and assembly['ref']['origin'] == 'none' and 'krona' in output_files</filter> 517 <filter>assembly['type'] == 'metagenome' and assembly['ref']['origin'] == 'silva' and 'krona' in output_files</filter>
514 </data> 518 </data>
515 </outputs> 519 </outputs>
516 <tests> 520 <tests>
517 <!-- Test 01: reference, genes annotations and operon coordinates --> 521 <!-- Test 01: reference, genes annotations and operon coordinates -->
518 <test expect_num_outputs="2"> 522 <test expect_num_outputs="2">
999 <output name="report_tabular" ftype="tabular"> 1003 <output name="report_tabular" ftype="tabular">
1000 <assert_contents> 1004 <assert_contents>
1001 <has_text text="# contigs (>= 0 bp)"/> 1005 <has_text text="# contigs (>= 0 bp)"/>
1002 <has_text text="contig1"/> 1006 <has_text text="contig1"/>
1003 <has_text text="# N's per 100 kbp"/> 1007 <has_text text="# N's per 100 kbp"/>
1004 <has_n_lines n="22"/> 1008 <has_n_lines n="30"/>
1005 </assert_contents> 1009 </assert_contents>
1006 </output> 1010 </output>
1007 </test> 1011 </test>
1008 <!-- Test 12: Test paired-collection fastq.gz inputs --> 1012 <!-- Test 12: Test paired-collection fastq.gz inputs -->
1009 <test expect_num_outputs="1"> 1013 <test expect_num_outputs="1">
1034 <output name="report_tabular" ftype="tabular"> 1038 <output name="report_tabular" ftype="tabular">
1035 <assert_contents> 1039 <assert_contents>
1036 <has_text text="# contigs (>= 0 bp)"/> 1040 <has_text text="# contigs (>= 0 bp)"/>
1037 <has_text text="contig1"/> 1041 <has_text text="contig1"/>
1038 <has_text text="# N's per 100 kbp"/> 1042 <has_text text="# N's per 100 kbp"/>
1039 <has_n_lines n="15"/> 1043 <has_n_lines n="23"/>
1040 </assert_contents> 1044 </assert_contents>
1041 </output> 1045 </output>
1042 </test> 1046 </test>
1043 <!-- Test 13: Test co-assembly with paired-collection fastq.gz inputs --> 1047 <!-- Test 13: Test co-assembly with paired-collection fastq.gz inputs -->
1044 <test expect_num_outputs="1"> 1048 <test expect_num_outputs="1">
1078 <output name="report_tabular" ftype="tabular"> 1082 <output name="report_tabular" ftype="tabular">
1079 <assert_contents> 1083 <assert_contents>
1080 <has_text text="# contigs (>= 0 bp)"/> 1084 <has_text text="# contigs (>= 0 bp)"/>
1081 <has_text text="contigs1"/> 1085 <has_text text="contigs1"/>
1082 <has_text text="# N's per 100 kbp"/> 1086 <has_text text="# N's per 100 kbp"/>
1083 <has_n_lines n="22"/> 1087 <has_n_lines n="30"/>
1084 </assert_contents> 1088 </assert_contents>
1085 </output> 1089 </output>
1086 </test> 1090 </test>
1087 </tests> 1091 </tests>
1088 <help> 1092 <help>