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comparison obiclean.xml @ 4:08d873cdd5f6 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
author iuc
date Wed, 20 Mar 2024 13:17:36 +0000
parents 12baadec7809
children
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3:12baadec7809 4:08d873cdd5f6
1 <tool id="obi_clean" name="obiclean" version="@TOOL_VERSION@" profile="@PROFILE@"> 1 <tool id="obi_clean" name="obiclean" version="@TOOL_VERSION@" profile="@PROFILE@">
2 <description>tags a set of sequences for PCR/sequencing errors identification</description> 2 <description>tags a set of sequences for PCR/sequencing errors identification</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="bio_tools"/>
6 <expand macro="requirements"/> 7 <expand macro="requirements"/>
7 <expand macro="stdio"/> 8 <expand macro="stdio"/>
8 9
9 <command><![CDATA[ 10 <command><![CDATA[
10 @GUNZIP_INPUT@ 11 @GUNZIP_INPUT@
26 @GZIP_OUTPUT@ 27 @GZIP_OUTPUT@
27 >'$output' 28 >'$output'
28 @GENERATE_GALAXY_JSON@ 29 @GENERATE_GALAXY_JSON@
29 ]]></command> 30 ]]></command>
30 <inputs> 31 <inputs>
31 <param name="input" type="data" format="@INPUT_FORMATS@" label="Input sequences file" /> 32 <param name="input" type="data" format="@INPUT_FORMATS@" label="Input sequences file"/>
32 <param name="distance" type="integer" value="1" optional="true" label="Maximum numbers of differences between two variant sequences (default: 1)" /> 33 <param name="distance" type="integer" value="1" optional="true" label="Maximum numbers of differences between two variant sequences (default: 1)"/>
33 <param name="key" type="text" optional="true" label="Specify an attribute containing sample definition" /> 34 <param name="key" type="text" optional="true" label="Specify an attribute containing sample definition"/>
34 <param name="ratio" optional="true" type="float" value="1" label="Threshold ratio between counts (rare/abundant counts) of two sequence records so that the less abundant one is a variant of the more abundant (default: 1, i.e. all less abundant sequences are variants)" /> 35 <param name="ratio" optional="true" type="float" value="1" label="Threshold ratio between counts (rare/abundant counts) of two sequence records so that the less abundant one is a variant of the more abundant (default: 1, i.e. all less abundant sequences are variants)"/>
35 <param name="head" type="boolean" checked="false" truevalue="-H" falsevalue="" label="Do you want to select only sequences with the head status in a least one sample?" /> 36 <param name="head" type="boolean" checked="false" truevalue="-H" falsevalue="" label="Do you want to select only sequences with the head status in a least one sample?"/>
36 <expand macro="input_format_options_macro"/> 37 <expand macro="input_format_options_macro"/>
37 <expand macro="out_format_macro"/> 38 <expand macro="out_format_macro"/>
38 </inputs> 39 </inputs>
39 <outputs> 40 <outputs>
40 <data format="auto" name="output"/> 41 <data format="auto" name="output"/>
41 </outputs> 42 </outputs>
42 <tests> 43 <tests>
43 <test> 44 <test expect_num_outputs="1">
44 <param name="input" value="output_obiannotate.fasta" /> 45 <param name="input" value="output_obiannotate.fasta" />
45 <param name="head" value="True"/> 46 <param name="head" value="True"/>
46 <output name="output" file="output_obiclean_simple.fasta" ftype="fasta"/> 47 <output name="output" file="output_obiclean_simple.fasta" ftype="fasta"/>
47 </test> 48 </test>
48 <test> 49 <test expect_num_outputs="1">
49 <param name="input" value="output_obiannotate.fasta.gz" /> 50 <param name="input" value="output_obiannotate.fasta.gz" />
50 <param name="key" value="merged_sample"/> 51 <param name="key" value="merged_sample"/>
51 <param name="ratio" value="0.05"/> 52 <param name="ratio" value="0.05"/>
52 <param name="head" value="False"/> 53 <param name="head" value="False"/>
53 <output name="output" file="output_obiclean_advanced.fasta.gz" ftype="fasta.gz" decompress="true"/> 54 <output name="output" file="output_obiclean_advanced.fasta.gz" ftype="fasta.gz" decompress="true"/>
70 71
71 @OBITOOLS_LINK@ 72 @OBITOOLS_LINK@
72 73
73 ]]> 74 ]]>
74 </help> 75 </help>
75 <expand macro="citation" /> 76 <expand macro="citation"/>
76 </tool> 77 </tool>