Mercurial > repos > devteam > fastq_trimmer

comparison fastq_trimmer.xml @ 3:b849e7c23b43 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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 13:54:04 -0400
parents fdff6f6a8763
children 70c29aef62cd
comparison
equal deleted inserted replaced
2:fdff6f6a8763 3:b849e7c23b43
1 <tool id="fastq_trimmer" name="FASTQ Trimmer" version="1.0.1"> 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)&lt;br&gt;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)&lt;br&gt;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; use a negative value to remove everything to the right of the absolute value of the position"> 19 </when>
20 <validator type="expression" message="An integer is required.">int( float( value ) ) == float( value )</validator> 20 <when value="offsets_percent">
21 </param> 21 <param name="left_column_offset" type="float" min="0" max="100" value="0" label="Offset from 5' end" />
22 </when> 22 <param name="right_column_offset" type="float" min="0" max="100" value="0" label="Offset from 3' end" />
23 <when value="offsets_percent"> 23 </when>
24 <param name="left_column_offset" label="Offset from 5' end" value="0" type="float"> 24 </conditional>
25 <validator type="in_range" message="Base Offsets must be between 0 and 100" min="0" max="100"/> 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 </param> 26 </inputs>
27 <param name="right_column_offset" label="Offset from 3' end" value="0" type="float"> 27 <outputs>
28 <validator type="in_range" message="Base Offsets must be between 0 and 100" min="0" max="100"/> 28 <data name="output_file" format_source="input_file" />
29 </param> 29 </outputs>
30 </when> 30 <tests>
31 </conditional> 31 <test>
32 <param name="keep_zero_length" label="Keep reads with zero length" type="boolean" truevalue="keep_zero_length" falsevalue="exclude_zero_length" selected="False"/> 32 <!-- Do nothing trim -->
33 </inputs> 33 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
34 <outputs> 34 <param name="base_offset_type" value="offsets_absolute"/>
35 <data name="output_file" format="input" /> 35 <param name="left_column_offset" value="0"/>
36 </outputs> 36 <param name="right_column_offset" value="0"/>
37 <tests> 37 <param name="keep_zero_length" value="keep_zero_length" />
38 <test> 38 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
39 <!-- Do nothing trim --> 39 </test>
40 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> 40 <!-- Trim to empty File -->
41 <param name="base_offset_type" value="offsets_absolute"/> 41 <test>
42 <param name="left_column_offset" value="0"/> 42 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
43 <param name="right_column_offset" value="0"/> 43 <param name="base_offset_type" value="offsets_absolute"/>
44 <param name="keep_zero_length" value="keep_zero_length" /> 44 <param name="left_column_offset" value="30"/>
45 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" /> 45 <param name="right_column_offset" value="64"/>
46 </test> 46 <param name="keep_zero_length" value="exclude_zero_length" />
47 <!-- Trim to empty File --> 47 <output name="output_file" file="empty_file.dat" ftype="fastqsanger" />
48 <test> 48 </test>
49 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> 49 <test>
50 <param name="base_offset_type" value="offsets_absolute"/> 50 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
51 <param name="left_column_offset" value="30"/> 51 <param name="base_offset_type" value="offsets_percent"/>
52 <param name="right_column_offset" value="64"/> 52 <param name="left_column_offset" value="50"/>
53 <param name="keep_zero_length" value="exclude_zero_length" /> 53 <param name="right_column_offset" value="50"/>
54 <output name="output_file" file="empty_file.dat" /> 54 <param name="keep_zero_length" value="exclude_zero_length" />
55 </test> 55 <output name="output_file" file="empty_file.dat" ftype="fastqsanger" />
56 <test> 56 </test>
57 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> 57 <!-- Trim to 4 inner-most bases -->
58 <param name="base_offset_type" value="offsets_percent"/> 58 <test>
59 <param name="left_column_offset" value="50"/> 59 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
60 <param name="right_column_offset" value="50"/> 60 <param name="base_offset_type" value="offsets_absolute"/>
61 <param name="keep_zero_length" value="exclude_zero_length" /> 61 <param name="left_column_offset" value="45"/>
62 <output name="output_file" file="empty_file.dat" /> 62 <param name="right_column_offset" value="45"/>
63 </test> 63 <param name="keep_zero_length" value="exclude_zero_length" />
64 <!-- Trim to 4 inner-most bases --> 64 <output name="output_file" file="fastq_trimmer_out1.fastqsanger" ftype="fastqsanger" />
65 <test> 65 </test>
66 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> 66 <test>
67 <param name="base_offset_type" value="offsets_absolute"/> 67 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
68 <param name="left_column_offset" value="45"/> 68 <param name="base_offset_type" value="offsets_percent"/>
69 <param name="right_column_offset" value="45"/> 69 <param name="left_column_offset" value="47.87"/>
70 <param name="keep_zero_length" value="exclude_zero_length" /> 70 <param name="right_column_offset" value="47.87"/>
71 <output name="output_file" file="fastq_trimmer_out1.fastqsanger" /> 71 <param name="keep_zero_length" value="exclude_zero_length" />
72 </test> 72 <output name="output_file" file="fastq_trimmer_out1.fastqsanger" ftype="fastqsanger" />
73 <test> 73 </test>
74 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> 74 </tests>
75 <param name="base_offset_type" value="offsets_percent"/> 75 <help><![CDATA[
76 <param name="left_column_offset" value="47.87"/>
77 <param name="right_column_offset" value="47.87"/>
78 <param name="keep_zero_length" value="exclude_zero_length" />
79 <output name="output_file" file="fastq_trimmer_out1.fastqsanger" />
80 </test>
81 </tests>
82 <help>
83 **What is does** 76 **What is does**
84 77
85 This tool allows you to trim the ends of reads. 78 This tool allows you to trim the ends of reads.
86 79
87 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.
88 81
89 For example, if you have a read of length 36:: 82 For example, if you have a read of length 36::
90 83
91 @Some FASTQ Sanger Read 84 @Some FASTQ Sanger Read
92 CAATATGTNCTCACTGATAAGTGGATATNAGCNCCA 85 CAATATGTNCTCACTGATAAGTGGATATNAGCNCCA
93 + 86 +
94 =@@.@;B-%?8&gt;CBA@&gt;7@7BBCA4-48%&lt;;;%&lt;B@ 87 =@@.@;B-%?8>CBA@>7@7BBCA4-48%<;;%<B@
95 88
96 And you set absolute offsets of 2 and 9:: 89 And you set absolute offsets of 2 and 9::
97 90
98 @Some FASTQ Sanger Read 91 @Some FASTQ Sanger Read
99 ATATGTNCTCACTGATAAGTGGATA 92 ATATGTNCTCACTGATAAGTGGATA
100 + 93 +
101 @.@;B-%?8&gt;CBA@&gt;7@7BBCA4-4 94 @.@;B-%?8>CBA@>7@7BBCA4-4
102 95
103 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)::
104 97
105 @Some FASTQ Sanger Read 98 @Some FASTQ Sanger Read
106 ATATGTNCTCACTGATAAGTGGATATN 99 ATATGTNCTCACTGATAAGTGGATATN
107 + 100 +
108 @.@;B-%?8&gt;CBA@&gt;7@7BBCA4-48% 101 @.@;B-%?8>CBA@>7@7BBCA4-48%
109 102
110 ----- 103 -----
111 104
112 .. class:: warningmark 105 .. class:: warningmark
113 106
114 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.
115 108 ]]></help>
116 ------ 109 <citations>
117 110 <citation type="doi">10.1093/bioinformatics/btq281</citation>
118 </help> 111 </citations>
119
120 <citations>
121 <citation type="doi">10.1093/bioinformatics/btq281</citation>
122 </citations>
123
124 </tool> 112 </tool>