Mercurial > repos > iuc > quast
comparison quast.xml @ 2:2f581f956e1c draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 930a43568ac0d4d32dde38a56fbb0b826f8f591b
| author | iuc |
|---|---|
| date | Fri, 04 Nov 2016 05:06:15 -0400 |
| parents | 0edbf19cf5eb |
| children | 6fcbee531de6 |
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| 1:0edbf19cf5eb | 2:2f581f956e1c |
|---|---|
| 9 level="fatal" | 9 level="fatal" |
| 10 description="Something went wrong. Check the following errors : No labels..." /> | 10 description="Something went wrong. Check the following errors : No labels..." /> |
| 11 </stdio> | 11 </stdio> |
| 12 <command> | 12 <command> |
| 13 <![CDATA[ | 13 <![CDATA[ |
| 14 #import re | |
| 14 quast | 15 quast |
| 15 -o outputdir | 16 -o outputdir |
| 16 #if $gene_selection == "eukaryote": | 17 #if $gene_selection == "eukaryote": |
| 17 --eukaryote | 18 --eukaryote |
| 18 #else if $gene_selection == "metagenes": | 19 #else if $gene_selection == "metagenes": |
| 30 #if $input_size: | 31 #if $input_size: |
| 31 --est-ref-size $input_size | 32 --est-ref-size $input_size |
| 32 #end if | 33 #end if |
| 33 --min-contig $min_contig | 34 --min-contig $min_contig |
| 34 -l | 35 -l |
| 35 #set names = ','.join( ['"'+str( $x.input.element_identifier)+'"' for $x in $files ]) | 36 #set names = ','.join( ['"'+ re.sub('[^\w\-_]', '_', str( $x.input.element_identifier))+'"' for $x in $files ]) |
| 37 | |
| 36 $names | 38 $names |
| 37 --contig-thresholds $threshold_contig | 39 --contig-thresholds $threshold_contig |
| 38 #for $k in $files: | 40 #for $k in $files: |
| 39 #if $k.type_file == "scaffold": | 41 #if $k.type_file == "scaffold": |
| 40 -s | 42 -s |