Mercurial > repos > lionelguy > spades
diff tools/spades_2_5/filter_spades_output.xml @ 2:b5ce24f34dd7 draft
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author | lionelguy |
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date | Thu, 05 Sep 2013 07:43:48 -0400 |
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children | 95ddc2380130 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/spades_2_5/filter_spades_output.xml Thu Sep 05 07:43:48 2013 -0400 @@ -0,0 +1,33 @@ +<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 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 dispaly a coverage vs. length plot, use the "SPAdes stats" tool in the same package. + </help> +</tool> \ No newline at end of file