Mercurial > repos > devteam > fastq_trimmer
comparison fastq_trimmer.xml @ 2:430b9da91435 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer commit f2582539542b33240234e8ea6093e25d0aee9b6a
author | devteam |
---|---|
date | Sat, 30 Sep 2017 13:55:56 -0400 |
parents | e0cfb5a703ce |
children | 2d0d13b0b0f1 |
comparison
equal
deleted
inserted
replaced
1:e0cfb5a703ce | 2:430b9da91435 |
---|---|
1 <tool id="fastq_trimmer" name="FASTQ Trimmer" version="1.0.0"> | 1 <tool id="fastq_trimmer" name="FASTQ Trimmer" version="1.1.1"> |
2 <description>by column</description> | 2 <description>by column</description> |
3 <requirements> | 3 <requirements> |
4 <requirement type="package" version="1.0.0">galaxy_sequence_utils</requirement> | 4 <requirement type="package" version="1.1.1">galaxy_sequence_utils</requirement> |
5 </requirements> | 5 </requirements> |
6 <command interpreter="python">fastq_trimmer.py '$input_file' '$output_file' '${offset_type['left_column_offset']}' '${offset_type['right_column_offset']}' '${offset_type['base_offset_type']}' '${input_file.extension[len( 'fastq' ):]}' '$keep_zero_length'</command> | 6 <command><![CDATA[ |
7 <inputs> | 7 gx-fastq-trimmer '$input_file' '$output_file' ${offset_type['left_column_offset']} ${offset_type['right_column_offset']} ${offset_type['base_offset_type']} '${input_file.extension[len('fastq'):]}' $keep_zero_length |
8 <param name="input_file" type="data" format="fastqsanger,fastqcssanger" label="FASTQ File"/> | 8 ]]></command> |
9 <conditional name="offset_type"> | 9 <inputs> |
10 <param name="base_offset_type" type="select" label="Define Base Offsets as" help="Use Absolute for fixed length reads (Illumina, SOLiD)<br>Use Percentage for variable length reads (Roche/454)"> | 10 <param name="input_file" type="data" format="fastqsanger,fastqcssanger,fastqsanger.gz,fastqcssanger.gz,fastqsanger.bz2,fastqcssanger.bz" label="FASTQ file"/> |
11 <option value="offsets_absolute" selected="true">Absolute Values</option> | 11 <conditional name="offset_type"> |
12 <option value="offsets_percent">Percentage of Read Length</option> | 12 <param name="base_offset_type" type="select" label="Define Base Offsets as" help="Use Absolute for fixed length reads (Illumina, SOLiD)<br>Use Percentage for variable length reads (Roche/454)"> |
13 </param> | 13 <option value="offsets_absolute" selected="true">Absolute Values</option> |
14 <when value="offsets_absolute"> | 14 <option value="offsets_percent">Percentage of Read Length</option> |
15 <param name="left_column_offset" label="Offset from 5' end" value="0" type="integer" help="Values start at 0, increasing from the left"> | 15 </param> |
16 <validator type="in_range" message="Base Offsets must be positive" min="0" max="inf"/> | 16 <when value="offsets_absolute"> |
17 <validator type="expression" message="An integer is required.">int( float( value ) ) == float( value )</validator> | 17 <param name="left_column_offset" type="integer" min="0" value="0" label="Offset from 5' end" help="Values start at 0, increasing from the left" /> |
18 </param> | 18 <param name="right_column_offset" type="integer" value="0" label="Offset from 3' end" help="Values start at 0, increasing from the right; use a negative value to remove everything to the right of the absolute value of the position" /> |
19 <param name="right_column_offset" label="Offset from 3' end" value="0" type="integer" help="Values start at 0, increasing from the right"> | 19 </when> |
20 <validator type="in_range" message="Base Offsets must be positive" min="0" max="inf"/> | 20 <when value="offsets_percent"> |
21 <validator type="expression" message="An integer is required.">int( float( value ) ) == float( value )</validator> | 21 <param name="left_column_offset" type="float" min="0" max="100" value="0" label="Offset from 5' end" /> |
22 </param> | 22 <param name="right_column_offset" type="float" min="0" max="100" value="0" label="Offset from 3' end" /> |
23 </when> | 23 </when> |
24 <when value="offsets_percent"> | 24 </conditional> |
25 <param name="left_column_offset" label="Offset from 5' end" value="0" type="float"> | 25 <param name="keep_zero_length" type="boolean" truevalue="keep_zero_length" falsevalue="exclude_zero_length" checked="false" label="Keep reads with zero length" /> |
26 <validator type="in_range" message="Base Offsets must be between 0 and 100" min="0" max="100"/> | 26 </inputs> |
27 </param> | 27 <outputs> |
28 <param name="right_column_offset" label="Offset from 3' end" value="0" type="float"> | 28 <data name="output_file" format_source="input_file" /> |
29 <validator type="in_range" message="Base Offsets must be between 0 and 100" min="0" max="100"/> | 29 </outputs> |
30 </param> | 30 <tests> |
31 </when> | 31 <test> |
32 </conditional> | 32 <!-- Do nothing trim --> |
33 <param name="keep_zero_length" label="Keep reads with zero length" type="boolean" truevalue="keep_zero_length" falsevalue="exclude_zero_length" selected="False"/> | 33 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> |
34 </inputs> | 34 <param name="base_offset_type" value="offsets_absolute"/> |
35 <outputs> | 35 <param name="left_column_offset" value="0"/> |
36 <data name="output_file" format="input" /> | 36 <param name="right_column_offset" value="0"/> |
37 </outputs> | 37 <param name="keep_zero_length" value="keep_zero_length" /> |
38 <tests> | 38 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> |
39 <test> | 39 </test> |
40 <!-- Do nothing trim --> | 40 <!-- Trim to empty File --> |
41 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> | 41 <test> |
42 <param name="base_offset_type" value="offsets_absolute"/> | 42 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> |
43 <param name="left_column_offset" value="0"/> | 43 <param name="base_offset_type" value="offsets_absolute"/> |
44 <param name="right_column_offset" value="0"/> | 44 <param name="left_column_offset" value="30"/> |
45 <param name="keep_zero_length" value="keep_zero_length" /> | 45 <param name="right_column_offset" value="64"/> |
46 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" /> | 46 <param name="keep_zero_length" value="exclude_zero_length" /> |
47 </test> | 47 <output name="output_file" file="empty_file.dat" ftype="fastqsanger" /> |
48 <!-- Trim to empty File --> | 48 </test> |
49 <test> | 49 <test> |
50 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> | 50 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> |
51 <param name="base_offset_type" value="offsets_absolute"/> | 51 <param name="base_offset_type" value="offsets_percent"/> |
52 <param name="left_column_offset" value="30"/> | 52 <param name="left_column_offset" value="50"/> |
53 <param name="right_column_offset" value="64"/> | 53 <param name="right_column_offset" value="50"/> |
54 <param name="keep_zero_length" value="exclude_zero_length" /> | 54 <param name="keep_zero_length" value="exclude_zero_length" /> |
55 <output name="output_file" file="empty_file.dat" /> | 55 <output name="output_file" file="empty_file.dat" ftype="fastqsanger" /> |
56 </test> | 56 </test> |
57 <test> | 57 <!-- Trim to 4 inner-most bases --> |
58 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> | 58 <test> |
59 <param name="base_offset_type" value="offsets_percent"/> | 59 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> |
60 <param name="left_column_offset" value="50"/> | 60 <param name="base_offset_type" value="offsets_absolute"/> |
61 <param name="right_column_offset" value="50"/> | 61 <param name="left_column_offset" value="45"/> |
62 <param name="keep_zero_length" value="exclude_zero_length" /> | 62 <param name="right_column_offset" value="45"/> |
63 <output name="output_file" file="empty_file.dat" /> | 63 <param name="keep_zero_length" value="exclude_zero_length" /> |
64 </test> | 64 <output name="output_file" file="fastq_trimmer_out1.fastqsanger" ftype="fastqsanger" /> |
65 <!-- Trim to 4 inner-most bases --> | 65 </test> |
66 <test> | 66 <test> |
67 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> | 67 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> |
68 <param name="base_offset_type" value="offsets_absolute"/> | 68 <param name="base_offset_type" value="offsets_percent"/> |
69 <param name="left_column_offset" value="45"/> | 69 <param name="left_column_offset" value="47.87"/> |
70 <param name="right_column_offset" value="45"/> | 70 <param name="right_column_offset" value="47.87"/> |
71 <param name="keep_zero_length" value="exclude_zero_length" /> | 71 <param name="keep_zero_length" value="exclude_zero_length" /> |
72 <output name="output_file" file="fastq_trimmer_out1.fastqsanger" /> | 72 <output name="output_file" file="fastq_trimmer_out1.fastqsanger" ftype="fastqsanger" /> |
73 </test> | 73 </test> |
74 <test> | 74 </tests> |
75 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> | 75 <help><![CDATA[ |
76 <param name="base_offset_type" value="offsets_percent"/> | |
77 <param name="left_column_offset" value="47.87"/> | |
78 <param name="right_column_offset" value="47.87"/> | |
79 <param name="keep_zero_length" value="exclude_zero_length" /> | |
80 <output name="output_file" file="fastq_trimmer_out1.fastqsanger" /> | |
81 </test> | |
82 </tests> | |
83 <help> | |
84 **What is does** | 76 **What is does** |
85 | 77 |
86 This tool allows you to trim the ends of reads. | 78 This tool allows you to trim the ends of reads. |
87 | 79 |
88 You can specify either absolute or percent-based offsets. Offsets are calculated, starting at 0, from the respective end to be trimmed. When using the percent-based method, offsets are rounded to the nearest integer. | 80 You can specify either absolute or percent-based offsets. Offsets are calculated, starting at 0, from the respective end to be trimmed. When using the percent-based method, offsets are rounded to the nearest integer. |
89 | 81 |
90 For example, if you have a read of length 36:: | 82 For example, if you have a read of length 36:: |
91 | 83 |
92 @Some FASTQ Sanger Read | 84 @Some FASTQ Sanger Read |
93 CAATATGTNCTCACTGATAAGTGGATATNAGCNCCA | 85 CAATATGTNCTCACTGATAAGTGGATATNAGCNCCA |
94 + | 86 + |
95 =@@.@;B-%?8>CBA@>7@7BBCA4-48%<;;%<B@ | 87 =@@.@;B-%?8>CBA@>7@7BBCA4-48%<;;%<B@ |
96 | 88 |
97 And you set absolute offsets of 2 and 9:: | 89 And you set absolute offsets of 2 and 9:: |
98 | 90 |
99 @Some FASTQ Sanger Read | 91 @Some FASTQ Sanger Read |
100 ATATGTNCTCACTGATAAGTGGATA | 92 ATATGTNCTCACTGATAAGTGGATA |
101 + | 93 + |
102 @.@;B-%?8>CBA@>7@7BBCA4-4 | 94 @.@;B-%?8>CBA@>7@7BBCA4-4 |
103 | 95 |
104 Or you set percent offsets of 6% and 20% (corresponds to absolute offsets of 2,7 for a read length of 36):: | 96 Or you set percent offsets of 6% and 20% (corresponds to absolute offsets of 2,7 for a read length of 36):: |
105 | 97 |
106 @Some FASTQ Sanger Read | 98 @Some FASTQ Sanger Read |
107 ATATGTNCTCACTGATAAGTGGATATN | 99 ATATGTNCTCACTGATAAGTGGATATN |
108 + | 100 + |
109 @.@;B-%?8>CBA@>7@7BBCA4-48% | 101 @.@;B-%?8>CBA@>7@7BBCA4-48% |
110 | 102 |
111 ----- | 103 ----- |
112 | 104 |
113 .. class:: warningmark | 105 .. class:: warningmark |
114 | 106 |
115 Trimming a color space read will cause any adapter base to be lost. | 107 Trimming a color space read will cause any adapter base to be lost. |
116 | 108 ]]></help> |
117 ------ | 109 <citations> |
118 | 110 <citation type="doi">10.1093/bioinformatics/btq281</citation> |
119 </help> | 111 </citations> |
120 | |
121 <citations> | |
122 <citation type="doi">10.1093/bioinformatics/btq281</citation> | |
123 </citations> | |
124 | |
125 </tool> | 112 </tool> |