Mercurial > repos > iuc > tracy_decompose

comparison tracy_decompose.xml @ 1:c57264841d60 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8eb3532d394f6a44d1edbcbe5ef05fd0474cdab3
author iuc
date Thu, 20 Mar 2025 07:17:17 +0000
parents 6d4fa8880e60
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0:6d4fa8880e60 1:c57264841d60
1 <tool id="tracy_decompose" name="tracy Decompose" version="@TOOL_VERSION@+galaxy0" profile="20.09"> 1 <tool id="tracy_decompose" name="tracy Decompose" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
2 <description>heterozygous mutations (and call variants)</description> 2 <description>heterozygous mutations (and call variants)</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
51 <data name="out_bcf" format="bcf" from_work_dir="out.bcf" label="tracy decompose variants on ${on_string}"> 51 <data name="out_bcf" format="bcf" from_work_dir="out.bcf" label="tracy decompose variants on ${on_string}">
52 <filter>callVariants</filter> 52 <filter>callVariants</filter>
53 </data> 53 </data>
54 </outputs> 54 </outputs>
55 <tests> 55 <tests>
56 <test expect_num_outputs="3"> 56 <test expect_num_outputs="3"> <!-- test 1 -->
57 <param name="genome" value="reference1.fasta" ftype="fasta" /> 57 <param name="genome" value="reference1.fasta" ftype="fasta" />
58 <param name="tracefile" value="input1.ab1" ftype="ab1" /> 58 <param name="tracefile" value="input1_r.ab1" ftype="ab1" />
59 <output name="out_fasta1" value="out1.align1.fasta" ftype="fasta" /> 59 <output name="out_fasta1" value="out1.align1.fasta" ftype="fasta" />
60 <output name="out_fasta2" value="out1.align2.fasta" ftype="fasta" /> 60 <output name="out_fasta2" value="out1.align2.fasta" ftype="fasta" />
61 <output name="out_fasta3" value="out1.align3.fasta" ftype="fasta" /> 61 <output name="out_fasta3" value="out1.align3.fasta" ftype="fasta" />
62 </test> 62 </test>
63 <test expect_num_outputs="4"> 63 <test expect_num_outputs="4"> <!-- test 2 -->
64 <param name="genome" value="reference1.fasta" ftype="fasta" /> 64 <param name="genome" value="reference1.fasta" ftype="fasta" />
65 <param name="tracefile" value="input1.ab1" ftype="ab1" /> 65 <param name="tracefile" value="input1_r.ab1" ftype="ab1" />
66 <param name="callVariants" value="true" /> 66 <param name="callVariants" value="true" />
67 <output name="out_fasta1" value="out1.align1.fasta" ftype="fasta" /> 67 <output name="out_fasta1" value="out1.align1.fasta" ftype="fasta" />
68 <output name="out_fasta2" value="out1.align2.fasta" ftype="fasta" /> 68 <output name="out_fasta2" value="out1.align2.fasta" ftype="fasta" />
69 <output name="out_fasta3" value="out1.align3.fasta" ftype="fasta" /> 69 <output name="out_fasta3" value="out1.align3.fasta" ftype="fasta" />
70 <output name="out_bcf" compare="sim_size" value="out1.bcf" ftype="bcf" /> 70 <output name="out_bcf" compare="sim_size" value="out1.bcf" ftype="bcf" />
71 </test> 71 </test>
72 <test expect_num_outputs="5"> 72 <test expect_num_outputs="5"> <!-- test 3 -->
73 <param name="genome" value="reference1.fasta" ftype="fasta" /> 73 <param name="genome" value="reference1.fasta" ftype="fasta" />
74 <param name="tracefile" value="input1.ab1" ftype="ab1" /> 74 <param name="tracefile" value="input1_r.ab1" ftype="ab1" />
75 <param name="callVariants" value="true" /> 75 <param name="callVariants" value="true" />
76 <param name="optional_outputs" value="json" /> 76 <param name="optional_outputs" value="json" />
77 <output name="out_json" ftype="json"> 77 <output name="out_json" ftype="json">
78 <assert_contents> 78 <assert_contents>
79 <has_text text='"peakA": [5, 5, 5, 5, 5, 4' /> 79 <has_text text='"peakA": [20, 20, 20, 19, 19' />
80 </assert_contents> 80 </assert_contents>
81 </output> 81 </output>
82 <output name="out_fasta1" value="out1.align1.fasta" ftype="fasta" /> 82 <output name="out_fasta1" value="out1.align1.fasta" ftype="fasta" />
83 <output name="out_fasta2" value="out1.align2.fasta" ftype="fasta" /> 83 <output name="out_fasta2" value="out1.align2.fasta" ftype="fasta" />
84 <output name="out_fasta3" value="out1.align3.fasta" ftype="fasta" /> 84 <output name="out_fasta3" value="out1.align3.fasta" ftype="fasta" />
85 <output name="out_bcf" compare="sim_size" value="out1.bcf" ftype="bcf" /> 85 <output name="out_bcf" compare="sim_size" value="out1.bcf" ftype="bcf" />
86 </test> 86 </test>
87 <test expect_num_outputs="5"> 87 <test expect_num_outputs="5"> <!-- test 4 -->
88 <param name="genome" value="reference1.fasta" ftype="fasta" /> 88 <param name="genome" value="reference1.fasta" ftype="fasta" />
89 <param name="tracefile" value="input1.ab1" ftype="ab1" /> 89 <param name="tracefile" value="input1_r.ab1" ftype="ab1" />
90 <param name="callVariants" value="true" /> 90 <param name="callVariants" value="true" />
91 <param name="optional_outputs" value="tabular" /> 91 <param name="optional_outputs" value="tabular" />
92 <output name="out_stats" ftype="tabular"> 92 <output name="out_stats" ftype="tabular">
93 <assert_contents> 93 <assert_contents>
94 <has_text_matching expression="13\s1\s2\s2\s11\s2\sT\sG\sN\s5\sY" /> 94 <has_text_matching expression="8\s20\s4\s14\s37\s1\sT\sR\sN\s0\sY" />
95 </assert_contents> 95 </assert_contents>
96 </output> 96 </output>
97 <output name="out_fasta1" value="out1.align1.fasta" ftype="fasta" /> 97 <output name="out_fasta1" value="out1.align1.fasta" ftype="fasta" />
98 <output name="out_fasta2" value="out1.align2.fasta" ftype="fasta" /> 98 <output name="out_fasta2" value="out1.align2.fasta" ftype="fasta" />
99 <output name="out_fasta3" value="out1.align3.fasta" ftype="fasta" /> 99 <output name="out_fasta3" value="out1.align3.fasta" ftype="fasta" />