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comparison tracy_align.xml @ 1:31599dc6380f 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 07:17:06 +0000
parents 726b73198fdc
children
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0:726b73198fdc 1:31599dc6380f
1 <tool id="tracy_align" name="tracy Align" version="@TOOL_VERSION@+galaxy0" profile="20.09"> 1 <tool id="tracy_align" name="tracy Align" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
2 <description>chromatogram to a FASTA reference</description> 2 <description>chromatogram to a FASTA reference</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" />
44 <data name="out_report" format="txt" from_work_dir="out.txt" label="tracy align report on ${on_string}" /> 44 <data name="out_report" format="txt" from_work_dir="out.txt" label="tracy align report on ${on_string}" />
45 <data name="out_alignment" format="fasta" from_work_dir="out.align.fa" label="tracy align aligned FASTA on ${on_string}" /> 45 <data name="out_alignment" format="fasta" from_work_dir="out.align.fa" label="tracy align aligned FASTA on ${on_string}" />
46 <expand macro="tabular_output" toolname="align" /> 46 <expand macro="tabular_output" toolname="align" />
47 </outputs> 47 </outputs>
48 <tests> 48 <tests>
49 <test expect_num_outputs="2"> 49 <test expect_num_outputs="2"> <!-- test 1 -->
50 <param name="reference" value="reference1.fasta" ftype="fasta" /> 50 <param name="reference" value="reference1.fasta" ftype="fasta" />
51 <param name="index_genome" value="false" /> 51 <param name="index_genome" value="false" />
52 <param name="tracefile" value="input1.ab1" ftype="ab1" /> 52 <param name="tracefile" value="input1_r.ab1" ftype="ab1" />
53 <output name="out_report" value="out1.txt" ftype="txt" /> 53 <output name="out_report" value="out1.txt" ftype="txt" />
54 <output name="out_alignment" value="out1.fasta" ftype="fasta" lines_diff="2" /> 54 <output name="out_alignment" value="out1.fasta" ftype="fasta" lines_diff="2" />
55 </test> 55 </test>
56 <test expect_num_outputs="2"> 56 <test expect_num_outputs="2"> <!-- test 2 -->
57 <param name="reference" value="reference1.fasta" ftype="fasta" /> 57 <param name="reference" value="reference1.fasta" ftype="fasta" />
58 <param name="index_genome" value="true" /> 58 <param name="index_genome" value="true" />
59 <param name="tracefile" value="input1.ab1" ftype="ab1" /> 59 <param name="tracefile" value="input1_r.ab1" ftype="ab1" />
60 <output name="out_report" value="out2.txt" ftype="txt" /> 60 <output name="out_report" value="out2.txt" ftype="txt" />
61 <output name="out_alignment" value="out2.fasta" ftype="fasta" lines_diff="2" /> 61 <output name="out_alignment" value="out2.fasta" ftype="fasta" lines_diff="2" />
62 </test> 62 </test>
63 <test expect_num_outputs="4"> 63 <test expect_num_outputs="4"> <!-- test 3 -->
64 <param name="reference" value="reference1.fasta" ftype="fasta" /> 64 <param name="reference" value="reference1.fasta" ftype="fasta" />
65 <param name="index_genome" value="false" /> 65 <param name="index_genome" value="false" />
66 <param name="tracefile" value="input1.ab1" ftype="ab1" /> 66 <param name="tracefile" value="input1_r.ab1" ftype="ab1" />
67 <param name="optional_outputs" value="json,tabular" /> 67 <param name="optional_outputs" value="json,tabular" />
68 <output name="out_report" value="out1.txt" ftype="txt" /> 68 <output name="out_report" value="out1.txt" ftype="txt" />
69 <output name="out_json" ftype="json"> 69 <output name="out_json" ftype="json">
70 <assert_contents> 70 <assert_contents>
71 <has_text text='"peakA": [5, 5, 5, 5, 5, 4' /> 71 <has_text text='"peakA": [20, 20, 20, 19, 19' />
72 </assert_contents> 72 </assert_contents>
73 </output> 73 </output>
74 <output name="out_stats" ftype="tabular"> 74 <output name="out_stats" ftype="tabular">
75 <assert_contents> 75 <assert_contents>
76 <has_text_matching expression="13\s1\s2\s2\s11\s2\sT\sG\sN\s5\sY" /> 76 <has_text_matching expression="8\s20\s4\s14\s37\s1\sT\sR\sN\s0\sY" />
77 </assert_contents> 77 </assert_contents>
78 </output> 78 </output>
79 <output name="out_alignment" value="out1.fasta" ftype="fasta" lines_diff="2" /> 79 <output name="out_alignment" value="out1.fasta" ftype="fasta" lines_diff="2" />
80 </test> 80 </test>
81
82 </tests> 81 </tests>
83 <help><![CDATA[ 82 <help><![CDATA[
84 **What it does**. 83 **What it does**.
85 84
86 Align a chromatogram trace to a reference nucleotide sequence (using tracy_). The reference can either be a FASTA file 85 Align a chromatogram trace to a reference nucleotide sequence (using tracy_). The reference can either be a FASTA file