Mercurial > repos > iuc > khmer_filter_abundance

comparison filter-abund.xml @ 11:4fc4b29ec2cd draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 238d0992c63de53623c4fc05eec8bd8d67001997
author iuc
date Thu, 03 Oct 2024 13:44:59 +0000
parents 7610ebc6e155
children
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10:7610ebc6e155 11:4fc4b29ec2cd
1 <tool id="khmer_filter_abundance" name="khmer: Filter reads" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> 1 <tool id="khmer_filter_abundance" name="khmer: Filter reads" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description> 2 <description>
3 by minimal k-mer abundance 3 by minimal k-mer abundance
4 </description> 4 </description>
5 <expand macro="bio_tools"/>
6 <macros> 5 <macros>
7 <token name="@BINARY@">filter-abund.py</token> 6 <token name="@BINARY@">filter-abund.py</token>
8 <import>macros.xml</import> 7 <import>macros.xml</import>
9 </macros> 8 </macros>
9 <expand macro="bio_tools"/>
10 <expand macro="requirements" /> 10 <expand macro="requirements" />
11 <expand macro="stdio" /> 11 <expand macro="stdio" />
12 <expand macro="version" /> 12 <expand macro="version" />
13 <command><![CDATA[ 13 <command><![CDATA[
14 set -u && 14 set -u &&
22 @USE_SEQUENCES@ 22 @USE_SEQUENCES@
23 ]]> 23 ]]>
24 </command> 24 </command>
25 <inputs> 25 <inputs>
26 <expand macro="input_sequences_filenames" /> 26 <expand macro="input_sequences_filenames" />
27 <param argument="--variable_coverage" name="variable_coverage" type="boolean" checked="false" truevalue="--variable-coverage" falsevalue="" 27 <param argument="--variable_coverage" type="boolean" checked="false" truevalue="--variable-coverage" falsevalue=""
28 label="Variable coverage" 28 label="Variable coverage"
29 help="Only trim when a sequence has high enough coverage; median abundance > 20" /> 29 help="Only trim when a sequence has high enough coverage; median abundance > 20" />
30 <param argument="--cutoff" name="cutoff" type="integer" value="2" label="Cutoff" 30 <param argument="--cutoff" type="integer" value="2" label="Cutoff"
31 help="Trim at k-mers below this abundance" /> 31 help="Trim at k-mers below this abundance" />
32 <expand macro="input_countgraph_filename" /> 32 <expand macro="input_countgraph_filename" />
33 </inputs> 33 </inputs>
34 <outputs> 34 <outputs>
35 <expand macro="output_sequences" extension="abundfilt"/> 35 <expand macro="output_sequences" extension="abundfilt"/>