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comparison bio_hansel.xml @ 2:1b88c1cf803d draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel commit 32833cd064153c009ff667f9526515d1aa15d48c
author iuc
date Sat, 05 Oct 2024 11:06:07 +0000
parents 4deefd708943
children
comparison
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1:4deefd708943 2:1b88c1cf803d
1 <tool id="bio_hansel" name="Salmonella Subtyping" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> 1 <tool id="bio_hansel" name="Salmonella Subtyping" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
2 <macros> 2 <macros>
3 <import>macros.xml</import> 3 <import>macros.xml</import>
4 </macros> 4 </macros>
5 <xrefs>
6 <xref type="bio.tools">Biohansel</xref>
7 </xrefs>
5 <expand macro="requirements" /> 8 <expand macro="requirements" />
6 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
7 #if $data_type.type == "paired": 10 #if $data_type.type == "paired":
8 #if $data_type.fastq_input1.ext.endswith('.gz'): 11 #if $data_type.fastq_input1.ext.endswith('.gz'):
9 gunzip -c '$data_type.fastq_input1' > fast_q_paired_1.fastq && 12 gunzip -c '$data_type.fastq_input1' > fast_q_paired_1.fastq &&
108 <data format="tabular" name="match_results" from_work_dir="match_results.tab" label="${tool.name} on ${on_string}: match_results.tab"/> 111 <data format="tabular" name="match_results" from_work_dir="match_results.tab" label="${tool.name} on ${on_string}: match_results.tab"/>
109 </outputs> 112 </outputs>
110 <tests> 113 <tests>
111 <test> 114 <test>
112 <param name="type" value="single"/> 115 <param name="type" value="single"/>
113 <param name="type_of_scheme" value="heidelberg"/> 116 <param name="type_of_scheme|scheme_type" value="heidelberg"/>
114 <param name="fastq_input1" ftype="fasta.gz" value="SRR1002850_SMALL.fasta.gz"/> 117 <param name="fastq_input1" ftype="fasta.gz" value="SRR1002850_SMALL.fasta.gz"/>
115 <output name="results" ftype="tabular" file="results1.tab" compare="contains"/> 118 <output name="results" ftype="tabular" file="results1.tab" compare="contains"/>
116 <output name="match_results" ftype="tabular" file="match_results1.tab" compare="contains"/> 119 <output name="match_results" ftype="tabular" file="match_results1.tab" compare="contains"/>
117 </test> 120 </test>
118 <test> 121 <test>
119 <param name="type" value="paired"/> 122 <param name="type" value="paired"/>
120 <param name="type_of_scheme" value="heidelberg"/> 123 <param name="type_of_scheme|scheme_type" value="heidelberg"/>
121 <param name="fastq_input1" ftype="fastq.gz" value="SRR5646583_SMALL_1.fastq.gz"/> 124 <param name="fastq_input1" ftype="fastq.gz" value="SRR5646583_SMALL_1.fastq.gz"/>
122 <param name="fastq_input2" value="SRR5646583_SMALL_2.fastq.gz"/> 125 <param name="fastq_input2" value="SRR5646583_SMALL_2.fastq.gz"/>
123 <output name="results" ftype="tabular" file="results2.tab" compare="contains"/> 126 <output name="results" ftype="tabular" file="results2.tab" compare="contains"/>
124 <output name="match_results" ftype="tabular" file="match_results2.tab" compare="contains"/> 127 <output name="match_results" ftype="tabular" file="match_results2.tab" compare="contains"/>
125 </test> 128 </test>