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comparison cat_bins.xml @ 3:0e63d03c8790 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 10:45:27 +0000
parents 31853794ace2
children
comparison
equal deleted inserted replaced
2:31853794ace2 3:0e63d03c8790
1 <tool id="cat_bins" name="CAT bins" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> 1 <tool id="cat_bins" name="CAT bins" 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 #import re 10 #import re
10 #set $bin_dir = None 11 #set $bin_dir = None
49 </inputs> 50 </inputs>
50 <outputs> 51 <outputs>
51 <expand macro="outputs" /> 52 <expand macro="outputs" />
52 </outputs> 53 </outputs>
53 <tests> 54 <tests>
54 <test> 55 <test expect_num_outputs="1">
55 <param name="mags" ftype="fasta" value="genome2.fna"/> 56 <param name="mags" ftype="fasta" value="genome2.fna"/>
56 <expand macro="test_catdb"/> 57 <expand macro="test_catdb"/>
57 <param name="select_outputs" value="bin2classification"/> 58 <param name="select_outputs" value="bin2classification"/>
58 <output name="bin2classification"> 59 <output name="bin2classification">
59 <assert_contents> 60 <assert_contents>
60 <has_text text="666" /> 61 <has_text text="666" />
61 </assert_contents> 62 </assert_contents>
62 </output> 63 </output>
63 </test> 64 </test>
64 <test> 65 <test expect_num_outputs="1">
65 <param name="mags" ftype="fasta" value="genome3.fna"/> 66 <param name="mags" ftype="fasta" value="genome3.fna"/>
66 <expand macro="test_catdb"/> 67 <expand macro="test_catdb"/>
67 <param name="select_outputs" value="bin2classification"/> 68 <param name="select_outputs" value="bin2classification"/>
68 <output name="bin2classification"> 69 <output name="bin2classification">
69 <assert_contents> 70 <assert_contents>
70 <has_text text="1639" /> 71 <has_text text="1639" />
71 </assert_contents> 72 </assert_contents>
72 </output> 73 </output>
73 </test> 74 </test>
74 <test> 75 <test expect_num_outputs="1">
75 <param name="mags" ftype="fasta" value="genome2.fna,genome3.fna"/> 76 <param name="mags" ftype="fasta" value="genome2.fna,genome3.fna"/>
76 <expand macro="test_catdb"/> 77 <expand macro="test_catdb"/>
77 <param name="select_outputs" value="bin2classification"/> 78 <param name="select_outputs" value="bin2classification"/>
78 <output name="bin2classification"> 79 <output name="bin2classification">
79 <assert_contents> 80 <assert_contents>
80 <has_text text="666" /> 81 <has_text text="666" />
81 <has_text text="1639" /> 82 <has_text text="1639" />
82 </assert_contents> 83 </assert_contents>
83 </output> 84 </output>
84 </test> 85 </test>
85 <test> 86 <test expect_num_outputs="4">
86 <param name="mags" ftype="fasta" value="genome2.fna,genome3.fna"/> 87 <param name="mags" ftype="fasta" value="genome2.fna,genome3.fna"/>
87 <expand macro="test_catdb"/> 88 <expand macro="test_catdb"/>
88 <param name="select_outputs" value="bin2classification"/> 89 <param name="select_outputs" value="bin2classification"/>
89 <param name="select_outputs" value="predicted_proteins_faa"/> 90 <param name="select_outputs" value="predicted_proteins_faa"/>
90 <param name="fraction" value="0.6"/> 91 <param name="fraction" value="0.6"/>