Mercurial > repos > greg > filter_contigs
changeset 2:1442e77ee8e9 draft default tip
Uploaded
| author | greg |
|---|---|
| date | Tue, 25 Apr 2023 12:59:47 +0000 |
| parents | 2c61adbbdbdb |
| children | |
| files | filter_contigs.xml |
| diffstat | 1 files changed, 19 insertions(+), 3 deletions(-) [+] |
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--- a/filter_contigs.xml Thu Jan 26 16:17:43 2023 +0000 +++ b/filter_contigs.xml Tue Apr 25 12:59:47 2023 +0000 @@ -1,4 +1,4 @@ -<tool id="filter_contigs" name="PIMA: filter contigs" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> +<tool id="filter_contigs" name="Filter contigs" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description>from an assembled FASTA file</description> <macros> <import>macros.xml</import> @@ -10,11 +10,27 @@ #else: ln -s '$input' 'input.fasta' && #end if -faidx -i chromsizes 'input.fasta' | awk '($2 <= $max_len) {print $1}' | parallel -n1 -n1 \$(which faidx) 'input.fasta' > '$output' +#if str($max_min_cond.max_min) == 'max': + faidx -i chromsizes 'input.fasta' | awk '($2 <= $max_min_cond.max_len) {print $1}' | parallel -n1 -n1 \$(which faidx) 'input.fasta' > '$output' +#else: + faidx -i chromsizes 'input.fasta' | awk '($2 > $max_min_cond.min_len) {print $1}' | parallel -n1 -n1 \$(which faidx) 'input.fasta' > '$output' +#end if + ]]></command> <inputs> <param name="input" type="data" format="fasta,fasta.gz" label="Assembled FASTA file"/> - <param name="max_len" type="integer" value="1500000" min="0" label="Maximum contig length"/> + <conditional name="max_min_cond"> + <param name="max_min" type="select" label="Use minimum or maximum contig length when filtering?"> + <option value="max" selected="true">Maximum - contigs shorter than or equal to this length will be filtered</option> + <option value="min">Minimum - contigs longer than this length will be filtered</option> + </param> + <when value="max"> + <param name="max_len" type="integer" value="1500000" min="0" label="Maximum contig length"/> + </when> + <when value="min"> + <param name="min_len" type="integer" value="1000" min="0" label="Maximum contig length"/> + </when> + </conditional> </inputs> <outputs> <data name="output" format="fasta"/>