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comparison fastq_masker_by_quality.xml @ 2:eb592e9ec47a draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality commit f2582539542b33240234e8ea6093e25d0aee9b6a
author devteam
date Sat, 30 Sep 2017 14:58:34 -0400
parents 9d234265981e
children 9282652e7234
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1:9d234265981e 2:eb592e9ec47a
1 <tool id="fastq_masker_by_quality" name="FASTQ Masker" version="1.0.0"> 1 <tool id="fastq_masker_by_quality" name="FASTQ Masker" version="1.1.1">
2 <description>by quality score</description> 2 <description>by quality score</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_masker_by_quality.py '$input_file' '$output_file' -f '${input_file.extension[len( 'fastq' ):]}' -s '${quality_score}' -c '${score_comparison}' 6 <command><![CDATA[
7 #if $mask_type.value == 'lowercase' 7 gx-fastq-masker-by-quality '$input_file' '$output_file' -f '${input_file.extension[len( 'fastq' ):]}' -s ${quality_score} -c ${score_comparison}
8 --lowercase 8 #if $mask_type.value == 'lowercase'
9 #else 9 --lowercase
10 -m '${mask_type}' 10 #else
11 #end if 11 -m ${mask_type}
12 </command> 12 #end if
13 <inputs> 13 ]]></command>
14 <param name="input_file" type="data" format="fastqsanger" label="File to mask" /> 14 <inputs>
15 <param name="mask_type" type="select" label="Mask input with"> 15 <param name="input_file" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="File to mask" />
16 <option value="N">N's</option> 16 <param name="mask_type" type="select" label="Mask input with">
17 <option value="lowercase">Lowercase</option> 17 <option value="N">N's</option>
18 </param> 18 <option value="lowercase">Lowercase</option>
19 <param name="score_comparison" type="select" label="When score is"> 19 </param>
20 <option value="le" selected="True">Less than or equal</option> 20 <param name="score_comparison" type="select" label="When score is">
21 <option value="lt">Less than</option> 21 <option value="le" selected="true">Less than or equal</option>
22 <option value="eq">Equal to</option> 22 <option value="lt">Less than</option>
23 <option value="ne">Not Equal to</option> 23 <option value="eq">Equal to</option>
24 <option value="ge">Greater than</option> 24 <option value="ne">Not Equal to</option>
25 <option value="gt">Greater than or equal</option> 25 <option value="ge">Greater than</option>
26 </param> 26 <option value="gt">Greater than or equal</option>
27 <param name="quality_score" type="integer" value="0" label="Quality score"/> 27 </param>
28 </inputs> 28 <param name="quality_score" type="integer" value="0" label="Quality score"/>
29 <outputs> 29 </inputs>
30 <data name="output_file" format="fastqsanger" /> 30 <outputs>
31 </outputs> 31 <data name="output_file" format_source="input_file" />
32 <tests> 32 </outputs>
33 <test> 33 <tests>
34 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> 34 <test>
35 <param name="mask_type" value="N" /> 35 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
36 <param name="score_comparison" value="le" /> 36 <param name="mask_type" value="N" />
37 <param name="quality_score" value="20" /> 37 <param name="score_comparison" value="le" />
38 <output name="output_file" file="sanger_full_range_masked_N.fastqsanger" /> 38 <param name="quality_score" value="20" />
39 </test> 39 <output name="output_file" file="sanger_full_range_masked_N.fastqsanger" ftype="fastqsanger" />
40 <test> 40 </test>
41 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> 41 <test>
42 <param name="mask_type" value="lowercase" /> 42 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
43 <param name="score_comparison" value="le" /> 43 <param name="mask_type" value="lowercase" />
44 <param name="quality_score" value="20" /> 44 <param name="score_comparison" value="le" />
45 <output name="output_file" file="sanger_full_range_masked_lowercase.fastqsanger" /> 45 <param name="quality_score" value="20" />
46 </test> 46 <output name="output_file" file="sanger_full_range_masked_lowercase.fastqsanger" ftype="fastqsanger" />
47 </tests> 47 </test>
48 <help> 48 </tests>
49 <help><![CDATA[
49 **What it does** 50 **What it does**
50 51
51 This tool allows masking base characters in FASTQ format files dependent upon user specified quality score value and comparison method. 52 This tool allows masking base characters in FASTQ format files dependent upon user specified quality score value and comparison method.
52 53
53 This tool is not available for use on color space (csSanger) formats. 54 This tool is not available for use on color space (csSanger) formats.
54 55 ]]></help>
55 </help> 56 <citations>
56 57 <citation type="doi">10.1093/bioinformatics/btq281</citation>
57 <citations> 58 </citations>
58 <citation type="doi">10.1093/bioinformatics/btq281</citation>
59 </citations>
60
61 </tool> 59 </tool>