PageRenderTime 98ms CodeModel.GetById 85ms app.highlight 3ms RepoModel.GetById 6ms app.codeStats 0ms

/tools/fastq/fastq_masker_by_quality.xml

https://bitbucket.org/h_morita_dbcls/galaxy-central
XML | 53 lines | 50 code | 3 blank | 0 comment | 0 complexity | 447e52a0843f35cf6fa505997f3cb391 MD5 | raw file
 1<tool id="fastq_masker_by_quality" name="FASTQ Masker" version="1.0.0">
 2  <description>by quality score</description>
 3  <command interpreter="python">fastq_masker_by_quality.py '$input_file' '$output_file' -f '${input_file.extension[len( 'fastq' ):]}' -s '${quality_score}' -c '${score_comparison}'
 4      #if $mask_type.value == 'lowercase'
 5      --lowercase
 6      #else
 7      -m '${mask_type}'
 8      #end if
 9  </command>
10  <inputs>
11    <param name="input_file" type="data" format="fastqsanger" label="File to mask" />
12    <param name="mask_type" type="select" label="Mask input with">
13      <option value="N">N's</option>
14      <option value="lowercase">Lowercase</option>
15    </param>
16    <param name="score_comparison" type="select" label="When score is">
17      <option value="le" selected="True">Less than or equal</option>
18      <option value="lt">Less than</option>
19      <option value="eq">Equal to</option>
20      <option value="ne">Not Equal to</option>
21      <option value="ge">Greater than</option>
22      <option value="gt">Greater than or equal</option>
23    </param>
24    <param name="quality_score" type="integer" value="0"/>
25  </inputs>
26  <outputs>
27    <data name="output_file" format="fastqsanger" />
28  </outputs>
29  <tests>
30    <test>
31      <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
32      <param name="mask_type" value="N" />
33      <param name="score_comparison" value="le" />
34      <param name="quality_score" value="20" />
35      <output name="output_file" file="sanger_full_range_masked_N.fastqsanger" />
36    </test>
37    <test>
38      <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
39      <param name="mask_type" value="lowercase" />
40      <param name="score_comparison" value="le" />
41      <param name="quality_score" value="20" />
42      <output name="output_file" file="sanger_full_range_masked_lowercase.fastqsanger" />
43    </test>
44  </tests>
45  <help>
46**What it does**
47
48This tool allows masking base characters in FASTQ format files dependent upon user specified quality score value and comparison method.
49
50This tool is not available for use on color space (csSanger) formats.
51
52  </help>
53</tool>