Mercurial > repos > lionelguy > spades
comparison tools/spades_3_0/filter_spades_output.xml @ 8:ff058438080a draft
Version 0.8, supports SPAdes 3.0.0
| author | lionelguy |
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| date | Wed, 05 Feb 2014 05:19:03 -0500 |
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| 7:95ddc2380130 | 8:ff058438080a |
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| 1 <tool id="filter_spades_output" name="Filter SPAdes output" version="0.1"> | |
| 2 <description>remove low coverage and short contigs/scaffolds</description> | |
| 3 <command interpreter="perl">filter_spades_output.pl | |
| 4 --coverage-cutoff $coverage_co | |
| 5 --length-cutoff $length_co | |
| 6 #if $keep_leftover | |
| 7 --filtered-out $filtered_out | |
| 8 #end if | |
| 9 --tab $stats_in | |
| 10 $fasta_in > $fasta_output | |
| 11 </command> | |
| 12 | |
| 13 <inputs> | |
| 14 <param name="fasta_in" type="data" format="fasta" label="Sequences" help="Contigs or scaffolds. Make sure you input the corresponding stat file" /> | |
| 15 <param name="stats_in" type="data" format="tabular" label="Contig stats" /> | |
| 16 <param name="length_co" type="integer" value="1000" min="0" label="Length cut-off" help="Contigs with length under that value are shown in red" /> | |
| 17 <param name="coverage_co" type="integer" value="10" min="0" label="Coverage cut-off" help="Contigs with length under that value are shown in red" /> | |
| 18 <param name="keep_leftover" type="boolean" checked="false" label="Save filtered-out sequences?" /> | |
| 19 </inputs> | |
| 20 <outputs> | |
| 21 <data format="fasta" name="fasta_output" label="Filtered sequences" /> | |
| 22 <data format="fasta" name="filtered_out" label="Discarded sequences"> | |
| 23 <filter>keep_leftover == "true"</filter> | |
| 24 </data> | |
| 25 </outputs> | |
| 26 <help> | |
| 27 **What it does** | |
| 28 | |
| 29 Using the output of SPAdes (a fasta and a stats file, either from contigs or scaffolds), it filters the fasta files, discarding all sequences that are under a given length or under a given coverage. | |
| 30 | |
| 31 Typically, this is used to discard short contigs, or contaminations. To display a coverage vs. length plot, use the "SPAdes stats" tool in the same package. | |
| 32 </help> | |
| 33 </tool> |