Mercurial > repos > iuc > obi_ngsfilter

comparison ngsfilter.xml @ 4:91a1ed0b486f 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 13:16:28 +0000
parents 3bf57dadf7cd
children
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3:3bf57dadf7cd 4:91a1ed0b486f
1 <tool id="obi_ngsfilter" name="NGSfilter" version="@TOOL_VERSION@" profile="@PROFILE@"> 1 <tool id="obi_ngsfilter" name="NGSfilter" version="@TOOL_VERSION@" profile="@PROFILE@">
2 <description>Assigns sequence records to the corresponding experiment/sample based on DNA tags and primers</description> 2 <description>Assigns sequence records to the corresponding experiment/sample based on DNA tags and primers</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 <command><![CDATA[ 9 <command><![CDATA[
9 @GUNZIP_INPUT@ 10 @GUNZIP_INPUT@
10 11
31 #set outputs = [("output", $output), ("unident", $unident)] 32 #set outputs = [("output", $output), ("unident", $unident)]
32 #end if 33 #end if
33 @GENERATE_GALAXY_JSON@ 34 @GENERATE_GALAXY_JSON@
34 ]]></command> 35 ]]></command>
35 <inputs> 36 <inputs>
36 <param name="inputextrafile" type="data" format="tabular" label="Parameter file" help="extrafile describing the DNA tags and primers sequences used for each sample" /> 37 <param name="inputextrafile" type="data" format="tabular" label="Parameter file" help="extrafile describing the DNA tags and primers sequences used for each sample"/>
37 <param name="input" type="data" format="@INPUT_FORMATS@" label="Read from file" help="file of Illumina pair-end reads assembled by illuminapairedend" /> 38 <param name="input" type="data" format="@INPUT_FORMATS@" label="Read from file" help="file of Illumina pair-end reads assembled by illuminapairedend"/>
38 <param name="mismatch" type="integer" value="2" label="Number of errors allowed for matching primers (default = 2)" /> 39 <param name="mismatch" type="integer" value="2" label="Number of errors allowed for matching primers (default = 2)"/>
39 <param name="bool" type="boolean" checked="true" label="Do you want to generate a file with unidentified sequences?" /> 40 <param name="bool" type="boolean" checked="true" label="Do you want to generate a file with unidentified sequences?"/>
40 <expand macro="input_format_options_macro"/> 41 <expand macro="input_format_options_macro"/>
41 <expand macro="out_format_macro"/> 42 <expand macro="out_format_macro"/>
42 </inputs> 43 </inputs>
43 <outputs> 44 <outputs>
44 <data name="unident" format="auto" label="${tool.name} on ${on_string}: Unassigned sequences"> 45 <data name="unident" format="auto" label="${tool.name} on ${on_string}: Unassigned sequences">
45 <filter>bool is True</filter> 46 <filter>bool is True</filter>
46 </data> 47 </data>
47 <data name="output" format="auto" label="${tool.name} on ${on_string}: Trimmed and annotated" /> 48 <data name="output" format="auto" label="${tool.name} on ${on_string}: Trimmed and annotated"/>
48 </outputs> 49 </outputs>
49 <tests> 50 <tests>
50 <test> 51 <test expect_num_outputs="1">
51 <param name="inputextrafile" value="input_ngsfilter_extrafile.txt" /> 52 <param name="inputextrafile" value="input_ngsfilter_extrafile.txt" />
52 <param name="input" value="illuminapairedend.output.fastq" ftype="fastqsanger" /> 53 <param name="input" value="illuminapairedend.output.fastq" ftype="fastqsanger"/>
53 <param name="mismatch" value="2" /> 54 <param name="mismatch" value="2" />
54 <param name="bool" value="False" /> 55 <param name="bool" value="False" />
55 <output name="output" file="output_ngsfilter.fastq" ftype="fastqsanger"/> 56 <output name="output" file="output_ngsfilter.fastq" ftype="fastqsanger"/>
56 </test> 57 </test>
57 <test> 58 <test expect_num_outputs="2">
58 <param name="inputextrafile" value="input_ngsfilter_extrafile.txt" /> 59 <param name="inputextrafile" value="input_ngsfilter_extrafile.txt"/>
59 <param name="input" value="illuminapairedend.output.fastq.gz" ftype="fastqsanger.gz" /> 60 <param name="input" value="illuminapairedend.output.fastq.gz" ftype="fastqsanger.gz"/>
60 <param name="mismatch" value="3" /> 61 <param name="mismatch" value="3"/>
61 <param name="bool" value="True" /> 62 <param name="bool" value="True"/>
62 <output name="output" file="output_ngsfilter_error_3.fastq" ftype="fastqsanger.gz" decompress="true"/> 63 <output name="output" file="output_ngsfilter_error_3.fastq" ftype="fastqsanger.gz" decompress="true"/>
63 <output name="unident" file="output_ngsfilter_unidentified.fastq" ftype="fastqsanger.gz" decompress="true"/> 64 <output name="unident" file="output_ngsfilter_unidentified.fastq" ftype="fastqsanger.gz" decompress="true"/>
64 </test> 65 </test>
65 </tests> 66 </tests>
66 <help><![CDATA[ 67 <help><![CDATA[