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