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comparison fastq_trimmer.xml @ 8:744add24f472 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_trimmer commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
author iuc
date Sun, 23 Nov 2025 17:49:44 +0000
parents 9e095a36386c
children
comparison
equal deleted inserted replaced
7:9e095a36386c 8:744add24f472
36 </outputs> 36 </outputs>
37 <tests> 37 <tests>
38 <test> 38 <test>
39 <!-- Do nothing trim --> 39 <!-- Do nothing trim -->
40 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> 40 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
41 <param name="base_offset_type" value="offsets_absolute"/> 41 <conditional name="offset_type">
42 <param name="left_column_offset" value="0"/> 42 <param name="base_offset_type" value="offsets_absolute"/>
43 <param name="right_column_offset" value="0"/> 43 <param name="left_column_offset" value="0"/>
44 <param name="keep_zero_length" value="keep_zero_length" /> 44 <param name="right_column_offset" value="0"/>
45 </conditional>
46 <param name="keep_zero_length" value="true" />
45 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> 47 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
46 </test> 48 </test>
47 <!-- Trim to empty File --> 49 <!-- Trim to empty File -->
48 <test> 50 <test>
49 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> 51 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
50 <param name="base_offset_type" value="offsets_absolute"/> 52 <conditional name="offset_type">
51 <param name="left_column_offset" value="30"/> 53 <param name="base_offset_type" value="offsets_absolute"/>
52 <param name="right_column_offset" value="64"/> 54 <param name="left_column_offset" value="30"/>
53 <param name="keep_zero_length" value="exclude_zero_length" /> 55 <param name="right_column_offset" value="64"/>
56 </conditional>
57 <param name="keep_zero_length" value="false" />
54 <output name="output_file" file="empty_file.dat" ftype="fastqsanger" /> 58 <output name="output_file" file="empty_file.dat" ftype="fastqsanger" />
55 </test> 59 </test>
56 <test> 60 <test>
57 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> 61 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
58 <param name="base_offset_type" value="offsets_percent"/> 62 <conditional name="offset_type">
59 <param name="left_column_offset" value="50"/> 63 <param name="base_offset_type" value="offsets_percent"/>
60 <param name="right_column_offset" value="50"/> 64 <param name="left_column_offset" value="50"/>
61 <param name="keep_zero_length" value="exclude_zero_length" /> 65 <param name="right_column_offset" value="50"/>
66 </conditional>
67 <param name="keep_zero_length" value="false" />
62 <output name="output_file" file="empty_file.dat" ftype="fastqsanger" /> 68 <output name="output_file" file="empty_file.dat" ftype="fastqsanger" />
63 </test> 69 </test>
64 <!-- Trim to 4 inner-most bases --> 70 <!-- Trim to 4 inner-most bases -->
65 <test> 71 <test>
66 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> 72 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
67 <param name="base_offset_type" value="offsets_absolute"/> 73 <conditional name="offset_type">
68 <param name="left_column_offset" value="45"/> 74 <param name="base_offset_type" value="offsets_absolute"/>
69 <param name="right_column_offset" value="45"/> 75 <param name="left_column_offset" value="45"/>
70 <param name="keep_zero_length" value="exclude_zero_length" /> 76 <param name="right_column_offset" value="45"/>
77 </conditional>
78 <param name="keep_zero_length" value="false" />
71 <output name="output_file" file="fastq_trimmer_out1.fastqsanger" ftype="fastqsanger" /> 79 <output name="output_file" file="fastq_trimmer_out1.fastqsanger" ftype="fastqsanger" />
72 </test> 80 </test>
73 <test> 81 <test>
74 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> 82 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
75 <param name="base_offset_type" value="offsets_percent"/> 83 <conditional name="offset_type">
76 <param name="left_column_offset" value="47.87"/> 84 <param name="base_offset_type" value="offsets_percent"/>
77 <param name="right_column_offset" value="47.87"/> 85 <param name="left_column_offset" value="47.87"/>
78 <param name="keep_zero_length" value="exclude_zero_length" /> 86 <param name="right_column_offset" value="47.87"/>
87 </conditional>
88 <param name="keep_zero_length" value="false" />
79 <output name="output_file" file="fastq_trimmer_out1.fastqsanger" ftype="fastqsanger" /> 89 <output name="output_file" file="fastq_trimmer_out1.fastqsanger" ftype="fastqsanger" />
80 </test> 90 </test>
81 </tests> 91 </tests>
82 <help><![CDATA[ 92 <help><![CDATA[
83 **What is does** 93 **What is does**