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comparison tracy_assemble.xml @ 1:d33fbee185ef 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 07:17:40 +0000
parents 99a9baef8c93
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0:99a9baef8c93 1:d33fbee185ef
1 <tool id="tracy_assemble" name="tracy Assemble" version="@TOOL_VERSION@+galaxy0" profile="20.09"> 1 <tool id="tracy_assemble" name="tracy Assemble" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
2 <description>genomic region from tiled, overlapping Sanger Chromatogram trace files</description> 2 <description>genomic region from tiled, overlapping Sanger Chromatogram trace files</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" />
68 </change_format> 68 </change_format>
69 </data> 69 </data>
70 <data name="out_alignment" format="fasta" from_work_dir="out.align.fa" label="tracy assemble alignment on ${on_string}" /> 70 <data name="out_alignment" format="fasta" from_work_dir="out.align.fa" label="tracy assemble alignment on ${on_string}" />
71 </outputs> 71 </outputs>
72 <tests> 72 <tests>
73 <test expect_num_outputs="2"> 73 <test expect_num_outputs="2"> <!-- test1 -->
74 <param name="tracefiles" value="input1.ab1,input1.ab1" ftype="ab1" /> 74 <param name="tracefiles" value="input1_f.ab1,input1_r.ab1" ftype="ab1" />
75 <output name="out_consensus" value="out1.consensus.fasta" ftype="fasta" /> 75 <output name="out_consensus" value="out1.consensus.fasta" ftype="fasta" />
76 <output name="out_alignment" value="out1.alignment.fasta" ftype="fasta" lines_diff="4" /> 76 <output name="out_alignment" value="out1.alignment.fasta" ftype="fasta" lines_diff="4" />
77 </test> 77 </test>
78 <test expect_num_outputs="2"> 78 <test expect_num_outputs="2"> <!-- test2 -->
79 <param name="tracefiles" value="input1.ab1,input1.ab1" ftype="ab1" /> 79 <param name="tracefiles" value="input1_f.ab1,input1_r.ab1" ftype="ab1" />
80 <conditional name="ref"> 80 <conditional name="ref">
81 <param name="useref" value="yes" /> 81 <param name="useref" value="yes" />
82 <param name="reference" value="reference1.fasta" /> 82 <param name="reference" value="reference1.fasta" />
83 </conditional> 83 </conditional>
84 <output name="out_consensus" value="out1.consensus.fasta" ftype="fasta" /> 84 <output name="out_consensus" value="out2.consensus.fasta" ftype="fasta" />
85 <output name="out_alignment" value="out2.alignment.fasta" ftype="fasta" lines_diff="4" /> 85 <output name="out_alignment" value="out2.alignment.fasta" ftype="fasta" lines_diff="4" />
86 </test> 86 </test>
87 <test expect_num_outputs="3"> 87 <test expect_num_outputs="3"> <!-- test3 -->
88 <param name="tracefiles" value="input1.ab1,input1.ab1" ftype="ab1" /> 88 <param name="tracefiles" value="input1_f.ab1,input1_r.ab1" ftype="ab1" />
89 <param name="json_output" value="true" /> 89 <param name="json_output" value="true" />
90 <output name="out_json" ftype="json"> 90 <output name="out_json" ftype="json">
91 <assert_contents> 91 <assert_contents>
92 <has_text text='"peakA": [5, 5, 5, 5, 5, 4' /> 92 <has_text text='"peakA": [283, 278, 264, 236, 194, 143' />
93 </assert_contents> 93 </assert_contents>
94 </output> 94 </output>
95 <output name="out_consensus" value="out1.consensus.fasta" ftype="fasta" /> 95 <output name="out_consensus" value="out1.consensus.fasta" ftype="fasta" />
96 <output name="out_alignment" value="out1.alignment.fasta" ftype="fasta" lines_diff="4" /> 96 <output name="out_alignment" value="out1.alignment.fasta" ftype="fasta" lines_diff="4" />
97 </test> 97 </test>