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comparison stacks_procrad.xml @ 12:eded025438db draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 74ee33c6e30744a6da8deb7116d431d80ee80edb
author iuc
date Fri, 07 Apr 2023 22:00:56 +0000
parents be78e39d56b3
children
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11:be78e39d56b3 12:eded025438db
1 <tool id="stacks_procrad" name="Stacks: process radtags" version="@WRAPPER_VERSION@.0"> 1 <tool id="stacks_procrad" name="Stacks: process radtags" version="@WRAPPER_VERSION@.0">
2 <description>the Stacks demultiplexing script</description> 2 <description>the Stacks demultiplexing script</description>
3 <expand macro="bio_tools"/>
4 <macros> 3 <macros>
5 <import>macros.xml</import> 4 <import>macros.xml</import>
6 </macros> 5 </macros>
6 <expand macro="bio_tools"/>
7 <expand macro="requirements"/> 7 <expand macro="requirements"/>
8 <expand macro="stdio"/> 8 <expand macro="stdio"/>
9 <command><![CDATA[ 9 <command><![CDATA[
10 10
11 #if $input_type.options_type_selector == "single" 11 #if $input_type.options_type_selector == "single"
133 <param name="remove" type="boolean" checked="false" truevalue="-c" falsevalue="" argument="-c" label="Clean data, remove any read with an uncalled base" /> 133 <param name="remove" type="boolean" checked="false" truevalue="-c" falsevalue="" argument="-c" label="Clean data, remove any read with an uncalled base" />
134 <param name="discard" type="boolean" checked="false" truevalue="-q" falsevalue="" argument="-q" label="Discard reads with low quality scores"/> 134 <param name="discard" type="boolean" checked="false" truevalue="-q" falsevalue="" argument="-q" label="Discard reads with low quality scores"/>
135 <param name="score" type="integer" value="10" argument="-s" label="Set the score limit. If the average score within the sliding window drops below this value, the read is discarded (default 10)" /> 135 <param name="score" type="integer" value="10" argument="-s" label="Set the score limit. If the average score within the sliding window drops below this value, the read is discarded (default 10)" />
136 <param name="rescue" type="boolean" checked="false" truevalue="-r" falsevalue="" argument="-r" label="Rescue barcodes and RAD-Tags?"/> 136 <param name="rescue" type="boolean" checked="false" truevalue="-r" falsevalue="" argument="-r" label="Rescue barcodes and RAD-Tags?"/>
137 <param name="truncate" type="integer" value="" optional="True" argument="-t" label="Truncate final read length to this value" /> 137 <param name="truncate" type="integer" value="" optional="True" argument="-t" label="Truncate final read length to this value" />
138 <param name="retain_header" type="boolean" checked="false" truevalue="--retain_header" falsevalue="" argument="--retain_header" label="Retain unmodified FASTQ headers in the output" /> 138 <param type="boolean" checked="false" truevalue="--retain_header" falsevalue="" argument="--retain_header" label="Retain unmodified FASTQ headers in the output" />
139 </section> 139 </section>
140 140
141 <param name="outype" argument="-y" type="select" label="Output format" > 141 <param name="outype" argument="-y" type="select" label="Output format" >
142 <option value="auto" selected="True">Same as input</option> 142 <option value="auto" selected="True">Same as input</option>
143 <option value="fastq">fastq</option> 143 <option value="fastq">fastq</option>