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comparison cat_contigs.xml @ 3:f41dbb0b9ff8 draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 47be73f0ca2b3a3bcb79a1fa7cf15a63c7facd19
author iuc
date Fri, 16 Feb 2024 10:45:07 +0000
parents 7aebc0137f20
children
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2:7aebc0137f20 3:f41dbb0b9ff8
1 <tool id="cat_contigs" name="CAT contigs" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> 1 <tool id="cat_contigs" name="CAT contigs" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description>annotate with taxonomic classification</description> 2 <description>annotate with taxonomic classification</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="version_command" /> 8 <expand macro="version_command" />
8 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
9 CAT contigs 10 CAT contigs
10 -c '$contigs_fasta' 11 -c '$contigs_fasta'
28 </inputs> 29 </inputs>
29 <outputs> 30 <outputs>
30 <expand macro="outputs" /> 31 <expand macro="outputs" />
31 </outputs> 32 </outputs>
32 <tests> 33 <tests>
33 <test> 34 <test expect_num_outputs="1">
34 <param name="contigs_fasta" ftype="fasta" value="contigs.fasta"/> 35 <param name="contigs_fasta" ftype="fasta" value="contigs.fasta"/>
35 <expand macro="test_catdb"/> 36 <expand macro="test_catdb"/>
36 <param name="select_outputs" value="contig2classification"/> 37 <param name="select_outputs" value="contig2classification"/>
37 <output name="contig2classification"> 38 <output name="contig2classification">
38 <assert_contents> 39 <assert_contents>
39 <has_text text="contig_38063" /> 40 <has_text text="contig_38063" />
40 </assert_contents> 41 </assert_contents>
41 </output> 42 </output>
42 </test> 43 </test>
43 <test> 44 <test expect_num_outputs="4">
44 <param name="contigs_fasta" ftype="fasta" value="contigs.fasta"/> 45 <param name="contigs_fasta" ftype="fasta" value="contigs.fasta"/>
45 <expand macro="test_catdb"/> 46 <expand macro="test_catdb"/>
46 <param name="select_outputs" value="predicted_proteins_faa"/> 47 <param name="select_outputs" value="predicted_proteins_faa"/>
47 <conditional name="names"> 48 <conditional name="names">
48 <param name="add_names" value="both"/> 49 <param name="add_names" value="both"/>