Mercurial > repos > iuc > fastp

comparison fastp.xml @ 9:dbf9c561ef29 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit a64eb7904f80e90a5faff04ea3fb797ee1e07d36"
author iuc
date Tue, 21 Apr 2020 16:45:20 -0400
parents 1d8fe9bc4cb0
children c59d48774d03
comparison
equal deleted inserted replaced
8:1d8fe9bc4cb0 9:dbf9c561ef29
1 <tool id="fastp" name="fastp" version="@WRAPPER_VERSION@+galaxy1"> 1 <tool id="fastp" name="fastp" version="@WRAPPER_VERSION@+galaxy0">
2 <description>- fast all-in-one preprocessing for FASTQ files</description> 2 <description>- fast all-in-one preprocessing for FASTQ files</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
128 128
129 $filter_options.length_filtering_options.disable_length_filtering 129 $filter_options.length_filtering_options.disable_length_filtering
130 130
131 #if str($filter_options.length_filtering_options.length_required): 131 #if str($filter_options.length_filtering_options.length_required):
132 -l $filter_options.length_filtering_options.length_required 132 -l $filter_options.length_filtering_options.length_required
133 #end if
134
135 #if str($filter_options.length_filtering_options.length_limit):
136 --length_limit $filter_options.length_filtering_options.length_limit
133 #end if 137 #end if
134 138
135 ## Low complexity filtering options 139 ## Low complexity filtering options
136 140
137 $filter_options.low_complexity_filter.enable_low_complexity_filter 141 $filter_options.low_complexity_filter.enable_low_complexity_filter
249 </section> 253 </section>
250 254
251 <section name="length_filtering_options" title="Length filtering options" expanded="True"> 255 <section name="length_filtering_options" title="Length filtering options" expanded="True">
252 <param name="disable_length_filtering" argument="-L" type="boolean" truevalue="-L" falsevalue="" checked="false" label="Disable length filtering" help="Length filtering is enabled by default. If this option is specified, length filtering is disabled."/> 256 <param name="disable_length_filtering" argument="-L" type="boolean" truevalue="-L" falsevalue="" checked="false" label="Disable length filtering" help="Length filtering is enabled by default. If this option is specified, length filtering is disabled."/>
253 <param name="length_required" argument="-l" type="integer" optional="true" label="Length required" help="Reads shorter than this value will be discarded. Default is 15."/> 257 <param name="length_required" argument="-l" type="integer" optional="true" label="Length required" help="Reads shorter than this value will be discarded. Default is 15."/>
258 <param name="length_limit" argument="--length_limit" type="integer" optional="true" label="Maximum length" help="Reads longer than this value will be discarded. Default is 0 and means no limitation."/>
254 </section> 259 </section>
255 260
256 <section name="low_complexity_filter" title="Low complexity filtering options" expanded="True"> 261 <section name="low_complexity_filter" title="Low complexity filtering options" expanded="True">
257 <param name="enable_low_complexity_filter" argument="-y" type="boolean" truevalue="-y" falsevalue="" checked="false" label="Enable low complexity filter" help="The complexity is defined as the percentage of base that is different from its next base, default is No"/> 262 <param name="enable_low_complexity_filter" argument="-y" type="boolean" truevalue="-y" falsevalue="" checked="false" label="Enable low complexity filter" help="The complexity is defined as the percentage of base that is different from its next base, default is No"/>
258 <param name="complexity_threshold" argument="-Y" type="integer" optional="true" label="Complexity threshold" help="Threshold for low complexity filter (0~100). Default is 30, which means 30% complexity is required."/> 263 <param name="complexity_threshold" argument="-Y" type="integer" optional="true" label="Complexity threshold" help="Threshold for low complexity filter (0~100). Default is 30, which means 30% complexity is required."/>