Mercurial > repos > devteam > fastq_trimmer
annotate fastq_trimmer.xml @ 4:33794bdb7fe0 draft
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer commit 31edb920789fbd080260f853bc856be72fa7cfa8"
author | devteam |
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date | Fri, 01 Nov 2019 13:26:50 -0400 |
parents | 2d0d13b0b0f1 |
children | b63b2bfb3ea3 |
rev | line source |
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430b9da91435
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
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changeset
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1 <tool id="fastq_trimmer" name="FASTQ Trimmer" version="1.1.1"> |
430b9da91435
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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2 <description>by column</description> |
430b9da91435
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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3 <requirements> |
430b9da91435
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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4 <requirement type="package" version="1.1.1">galaxy_sequence_utils</requirement> |
430b9da91435
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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5 </requirements> |
4
33794bdb7fe0
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer commit 31edb920789fbd080260f853bc856be72fa7cfa8"
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6 <edam_topics> |
33794bdb7fe0
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer commit 31edb920789fbd080260f853bc856be72fa7cfa8"
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7 <edam_topic>topic_0622</edam_topic> |
33794bdb7fe0
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer commit 31edb920789fbd080260f853bc856be72fa7cfa8"
devteam
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changeset
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8 </edam_topics> |
33794bdb7fe0
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer commit 31edb920789fbd080260f853bc856be72fa7cfa8"
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9 <edam_operations> |
33794bdb7fe0
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer commit 31edb920789fbd080260f853bc856be72fa7cfa8"
devteam
parents:
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10 <edam_operation>operation_3192</edam_operation> |
33794bdb7fe0
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer commit 31edb920789fbd080260f853bc856be72fa7cfa8"
devteam
parents:
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changeset
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11 </edam_operations> |
2
430b9da91435
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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changeset
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12 <command><![CDATA[ |
430b9da91435
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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13 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 |
430b9da91435
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
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changeset
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14 ]]></command> |
430b9da91435
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
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changeset
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15 <inputs> |
3
2d0d13b0b0f1
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer commit bb546ea5ff3b35ea76feb0c26470e7b422d2d493
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16 <param name="input_file" type="data" format="fastqsanger,fastqcssanger,fastqsanger.gz,fastqcssanger.gz,fastqsanger.bz2,fastqcssanger.bz2" label="FASTQ file"/> |
2
430b9da91435
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
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changeset
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17 <conditional name="offset_type"> |
430b9da91435
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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parents:
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changeset
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18 <param name="base_offset_type" type="select" label="Define Base Offsets as" help="Use Absolute for fixed length reads (Illumina, SOLiD)<br>Use Percentage for variable length reads (Roche/454)"> |
430b9da91435
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
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changeset
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19 <option value="offsets_absolute" selected="true">Absolute Values</option> |
430b9da91435
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
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changeset
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20 <option value="offsets_percent">Percentage of Read Length</option> |
430b9da91435
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
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changeset
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21 </param> |
430b9da91435
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
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diff
changeset
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22 <when value="offsets_absolute"> |
430b9da91435
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
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changeset
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23 <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" /> |
430b9da91435
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
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changeset
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24 <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" /> |
430b9da91435
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
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changeset
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25 </when> |
430b9da91435
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
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changeset
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26 <when value="offsets_percent"> |
430b9da91435
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
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changeset
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27 <param name="left_column_offset" type="float" min="0" max="100" value="0" label="Offset from 5' end" /> |
430b9da91435
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
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diff
changeset
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28 <param name="right_column_offset" type="float" min="0" max="100" value="0" label="Offset from 3' end" /> |
430b9da91435
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
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changeset
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29 </when> |
430b9da91435
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
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changeset
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30 </conditional> |
430b9da91435
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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31 <param name="keep_zero_length" type="boolean" truevalue="keep_zero_length" falsevalue="exclude_zero_length" checked="false" label="Keep reads with zero length" /> |
430b9da91435
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
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32 </inputs> |
430b9da91435
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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changeset
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33 <outputs> |
430b9da91435
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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34 <data name="output_file" format_source="input_file" /> |
430b9da91435
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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35 </outputs> |
430b9da91435
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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36 <tests> |
430b9da91435
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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37 <test> |
430b9da91435
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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38 <!-- Do nothing trim --> |
430b9da91435
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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parents:
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39 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> |
430b9da91435
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
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40 <param name="base_offset_type" value="offsets_absolute"/> |
430b9da91435
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
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41 <param name="left_column_offset" value="0"/> |
430b9da91435
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
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42 <param name="right_column_offset" value="0"/> |
430b9da91435
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
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43 <param name="keep_zero_length" value="keep_zero_length" /> |
430b9da91435
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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parents:
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44 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> |
430b9da91435
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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45 </test> |
430b9da91435
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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46 <!-- Trim to empty File --> |
430b9da91435
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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47 <test> |
430b9da91435
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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48 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> |
430b9da91435
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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49 <param name="base_offset_type" value="offsets_absolute"/> |
430b9da91435
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
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50 <param name="left_column_offset" value="30"/> |
430b9da91435
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
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51 <param name="right_column_offset" value="64"/> |
430b9da91435
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
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52 <param name="keep_zero_length" value="exclude_zero_length" /> |
430b9da91435
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
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53 <output name="output_file" file="empty_file.dat" ftype="fastqsanger" /> |
430b9da91435
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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54 </test> |
430b9da91435
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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55 <test> |
430b9da91435
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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56 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> |
430b9da91435
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
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57 <param name="base_offset_type" value="offsets_percent"/> |
430b9da91435
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
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58 <param name="left_column_offset" value="50"/> |
430b9da91435
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
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59 <param name="right_column_offset" value="50"/> |
430b9da91435
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
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60 <param name="keep_zero_length" value="exclude_zero_length" /> |
430b9da91435
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
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61 <output name="output_file" file="empty_file.dat" ftype="fastqsanger" /> |
430b9da91435
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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62 </test> |
430b9da91435
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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63 <!-- Trim to 4 inner-most bases --> |
430b9da91435
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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64 <test> |
430b9da91435
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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65 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> |
430b9da91435
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
1
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changeset
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66 <param name="base_offset_type" value="offsets_absolute"/> |
430b9da91435
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
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67 <param name="left_column_offset" value="45"/> |
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68 <param name="right_column_offset" value="45"/> |
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69 <param name="keep_zero_length" value="exclude_zero_length" /> |
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70 <output name="output_file" file="fastq_trimmer_out1.fastqsanger" ftype="fastqsanger" /> |
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71 </test> |
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72 <test> |
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73 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> |
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74 <param name="base_offset_type" value="offsets_percent"/> |
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75 <param name="left_column_offset" value="47.87"/> |
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76 <param name="right_column_offset" value="47.87"/> |
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77 <param name="keep_zero_length" value="exclude_zero_length" /> |
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78 <output name="output_file" file="fastq_trimmer_out1.fastqsanger" ftype="fastqsanger" /> |
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79 </test> |
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80 </tests> |
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81 <help><![CDATA[ |
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82 **What is does** |
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83 |
0 | 84 This tool allows you to trim the ends of reads. |
85 | |
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86 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. |
0 | 87 |
88 For example, if you have a read of length 36:: | |
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89 |
0 | 90 @Some FASTQ Sanger Read |
91 CAATATGTNCTCACTGATAAGTGGATATNAGCNCCA | |
92 + | |
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93 =@@.@;B-%?8>CBA@>7@7BBCA4-48%<;;%<B@ |
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94 |
0 | 95 And you set absolute offsets of 2 and 9:: |
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96 |
0 | 97 @Some FASTQ Sanger Read |
98 ATATGTNCTCACTGATAAGTGGATA | |
99 + | |
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100 @.@;B-%?8>CBA@>7@7BBCA4-4 |
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101 |
0 | 102 Or you set percent offsets of 6% and 20% (corresponds to absolute offsets of 2,7 for a read length of 36):: |
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103 |
0 | 104 @Some FASTQ Sanger Read |
105 ATATGTNCTCACTGATAAGTGGATATN | |
106 + | |
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107 @.@;B-%?8>CBA@>7@7BBCA4-48% |
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108 |
0 | 109 ----- |
110 | |
111 .. class:: warningmark | |
112 | |
113 Trimming a color space read will cause any adapter base to be lost. | |
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114 ]]></help> |
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115 <citations> |
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116 <citation type="doi">10.1093/bioinformatics/btq281</citation> |
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117 </citations> |
0 | 118 </tool> |