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1 <tool id="filter_spades_output" name="Filter SPAdes output" version="0.1">
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2 <description>remove low coverage and short contigs/scaffolds</description>
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3 <command interpreter="perl">filter_spades_output.pl
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4 --coverage-cutoff $coverage_co
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5 --length-cutoff $length_co
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6 #if $keep_leftover
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7 --filtered-out $filtered_out
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8 #end if
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9 --tab $stats_in
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10 $fasta_in > $fasta_output
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11 </command>
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12
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13 <inputs>
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14 <param name="fasta_in" type="data" format="fasta" label="Sequences" help="Contigs or scaffolds. Make sure you input the corresponding stat file" />
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15 <param name="stats_in" type="data" format="tabular" label="Contig stats" />
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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" />
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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" />
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18 <param name="keep_leftover" type="boolean" checked="false" label="Save filtered-out sequences?" />
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19 </inputs>
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20 <outputs>
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21 <data format="fasta" name="fasta_output" label="Filtered sequences" />
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22 <data format="fasta" name="filtered_out" label="Discarded sequences">
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23 <filter>keep_leftover == "true"</filter>
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24 </data>
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25 </outputs>
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26 <help>
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27 **What it does**
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28
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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.
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30
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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.
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32 </help>
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33 </tool>
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