Mercurial > repos > lionelguy > spades
view tools/spades_3_1_1/filter_spades_output.xml @ 10:7d72faef9af0 draft
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author | takadonet |
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date | Fri, 10 Oct 2014 14:40:43 -0400 |
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<tool id="filter_spades_output" name="Filter SPAdes output" version="0.1"> <description>remove low coverage and short contigs/scaffolds</description> <command interpreter="perl">filter_spades_output.pl --coverage-cutoff $coverage_co --length-cutoff $length_co #if $keep_leftover --filtered-out $filtered_out #end if --tab $stats_in $fasta_in > $fasta_output </command> <inputs> <param name="fasta_in" type="data" format="fasta" label="Sequences" help="Contigs or scaffolds. Make sure you input the corresponding stat file" /> <param name="stats_in" type="data" format="tabular" label="Contig stats" /> <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" /> <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" /> <param name="keep_leftover" type="boolean" checked="false" label="Save filtered-out sequences?" /> </inputs> <outputs> <data format="fasta" name="fasta_output" label="Filtered sequences" /> <data format="fasta" name="filtered_out" label="Discarded sequences"> <filter>keep_leftover == "true"</filter> </data> </outputs> <help> **What it does** 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. 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. </help> </tool>