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comparison filtlong.xml @ 3:41b2ad601cf0 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong commit adf0341da7282c80c25336ae03130b2dc44c65bb"
author iuc
date Thu, 24 Feb 2022 21:22:16 +0000
parents a72af9de6bf5
children 1f296803dfa3
comparison
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2:a72af9de6bf5 3:41b2ad601cf0
1 <tool id="filtlong" name="filtlong" version="@WRAPPER_VERSION@+galaxy1" profile="@PROFILE@"> 1 <tool id="filtlong" name="filtlong" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>Filtering long reads by quality</description> 2 <description>Filtering long reads by quality</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
19 #if $output_thresholds.min_mean_q: 19 #if $output_thresholds.min_mean_q:
20 --min_mean_q '$output_thresholds.min_mean_q' 20 --min_mean_q '$output_thresholds.min_mean_q'
21 #end if 21 #end if
22 #if $output_thresholds.min_window_q: 22 #if $output_thresholds.min_window_q:
23 --min_window_q '$output_thresholds.min_window_q' 23 --min_window_q '$output_thresholds.min_window_q'
24 #end if
25 #if $output_thresholds.max_length:
26 --max_length '$output_thresholds.max_length'
24 #end if 27 #end if
25 #if $external_references.assembly: 28 #if $external_references.assembly:
26 --assembly '$external_references.assembly' 29 --assembly '$external_references.assembly'
27 #end if 30 #end if
28 #if $external_references.illumina_1: 31 #if $external_references.illumina_1:
46 <inputs> 49 <inputs>
47 <param name="input_file" type="data" format="fastqsanger,fastqsanger.gz" label="Input FASTQ" help="FASTQ of input reads"/> 50 <param name="input_file" type="data" format="fastqsanger,fastqsanger.gz" label="Input FASTQ" help="FASTQ of input reads"/>
48 <section name="output_thresholds" title="Output thresholds"> 51 <section name="output_thresholds" title="Output thresholds">
49 <param argument="--target_bases" type="integer" min="0" optional="True" label="Total bases" help="Keep only the best reads up to this many total bases"/> 52 <param argument="--target_bases" type="integer" min="0" optional="True" label="Total bases" help="Keep only the best reads up to this many total bases"/>
50 <param argument="--keep_percent" type="float" min="0" max="100" optional="True" label="Keep percentage" help="Keep only this percentage of the best reads (measured by bases)"/> 53 <param argument="--keep_percent" type="float" min="0" max="100" optional="True" label="Keep percentage" help="Keep only this percentage of the best reads (measured by bases)"/>
54 <param argument="--max_length" type="integer" min="0" optional="True" label="Max. length" help="Maximum length threshold"/>
51 <param argument="--min_length" type="integer" min="0" optional="True" label="Min. length" help="Minimum length threshold"/> 55 <param argument="--min_length" type="integer" min="0" optional="True" label="Min. length" help="Minimum length threshold"/>
52 <param argument="--min_mean_q" type="float" min="0" optional="True" label="Min. mean quality" help="Minimum mean quality threshold"/> 56 <param argument="--min_mean_q" type="float" min="0" optional="True" label="Min. mean quality" help="Minimum mean quality threshold"/>
53 <param argument="--min_window_q" type="float" min="0" optional="True" label="Min. window quality" help="Minimum window quality threshold"/> 57 <param argument="--min_window_q" type="float" min="0" optional="True" label="Min. window quality" help="Minimum window quality threshold"/>
54 </section> 58 </section>
55 <section name="external_references" title="External references"> 59 <section name="external_references" title="External references">
91 <param name="target_bases" value="500000000"/> 95 <param name="target_bases" value="500000000"/>
92 <param name="trim" value="True"/> 96 <param name="trim" value="True"/>
93 <param name="split" value="500"/> 97 <param name="split" value="500"/>
94 <output name="outfile" ftype="fastqsanger" file="output_reference.fastq"/> 98 <output name="outfile" ftype="fastqsanger" file="output_reference.fastq"/>
95 </test> 99 </test>
100 <test>
101 <param name="input_file" ftype="fastqsanger" value="test.fastq.gz"/>
102 <param name="max_length" value="5000"/>
103 <output name="outfile" ftype="fastqsanger" file="output_max_length.fastq"/>
104 </test>
96 </tests> 105 </tests>
97 <help><![CDATA[ 106 <help><![CDATA[
98 Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter. 107 Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter.
99 ]]></help> 108 ]]></help>
100 <citations> 109 <citations>