Mercurial > repos > devteam > fastq_masker_by_quality

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
author iuc
date Wed, 19 Feb 2020 16:56:17 +0000
parents bf7a192ad8e2
children
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fcf810725e6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
iuc
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1 <tool id="fastq_masker_by_quality" name="FASTQ Masker" version="@TOOL_VERSION@">
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2 <description>by quality score</description>
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fcf810725e6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
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3 <macros>
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4 <import>macros.xml</import>
fcf810725e6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
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5 </macros>
fcf810725e6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
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6 <expand macro="requirements"/>
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7 <edam_topics>
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8 <edam_topic>topic_0622</edam_topic>
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9 </edam_topics>
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10 <edam_operations>
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11 <edam_operation>operation_0368</edam_operation>
bf7a192ad8e2 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality commit 31edb920789fbd080260f853bc856be72fa7cfa8"
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12 </edam_operations>
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13 <command><![CDATA[
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fcf810725e6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
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14 gx-fastq-masker-by-quality '$input_file' '$output_file' -f '${input_file.extension[len('fastq'):]}' -s ${quality_score} -c ${score_comparison}
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15 #if $mask_type == 'lowercase'
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16 --lowercase
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17 #else
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18 -m ${mask_type}
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19 #end if
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20 ]]></command>
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21 <inputs>
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22 <param name="input_file" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="File to mask" />
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23 <param name="mask_type" type="select" label="Mask input with">
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24 <option value="N">N's</option>
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25 <option value="lowercase">Lowercase</option>
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26 </param>
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27 <param name="score_comparison" type="select" label="When score is">
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28 <option value="le" selected="true">Less than or equal</option>
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29 <option value="lt">Less than</option>
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30 <option value="eq">Equal to</option>
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31 <option value="ne">Not Equal to</option>
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32 <option value="ge">Greater than</option>
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33 <option value="gt">Greater than or equal</option>
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34 </param>
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35 <param name="quality_score" type="integer" value="0" label="Quality score"/>
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36 </inputs>
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37 <outputs>
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38 <data name="output_file" format_source="input_file" />
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39 </outputs>
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40 <tests>
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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="N" />
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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_N.fastqsanger" ftype="fastqsanger" />
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47 </test>
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48 <test>
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49 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
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50 <param name="mask_type" value="lowercase" />
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51 <param name="score_comparison" value="le" />
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52 <param name="quality_score" value="20" />
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53 <output name="output_file" file="sanger_full_range_masked_lowercase.fastqsanger" ftype="fastqsanger" />
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54 </test>
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55 </tests>
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56 <help><![CDATA[
0
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57 **What it does**
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58
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59 This tool allows masking base characters in FASTQ format files dependent upon user specified quality score value and comparison method.
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60
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61 This tool is not available for use on color space (csSanger) formats.
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62 ]]></help>
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63 <citations>
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64 <citation type="doi">10.1093/bioinformatics/btq281</citation>
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65 </citations>
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66 </tool>