Mercurial > repos > devteam > fastq_groomer
annotate fastq_groomer.xml @ 2:71e5fa25b8a2 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
author | devteam |
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date | Sat, 30 Sep 2017 14:58:07 -0400 |
parents | e4d28c94242d |
children | 8611b80a14d6 |
rev | line source |
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2
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
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changeset
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1 <tool id="fastq_groomer" name="FASTQ Groomer" version="1.1.1"> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
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changeset
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2 <description>convert between various FASTQ quality formats</description> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
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changeset
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3 <requirements> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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changeset
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4 <requirement type="package" version="1.1.1">galaxy_sequence_utils</requirement> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
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changeset
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5 </requirements> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
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changeset
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6 <command><![CDATA[ |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
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changeset
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7 gx-fastq-groomer '$input_file' |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
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changeset
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8 #if $input_file.extension.endswith(".gz"): |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
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diff
changeset
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9 #set $suffix = ".gz" |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
1
diff
changeset
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10 #elif $input_file.extension.endswith(".bz2"): |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
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diff
changeset
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11 #set $suffix = ".bz2" |
0 | 12 #else: |
2
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
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changeset
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13 #set $suffix = "" |
0 | 14 #end if |
2
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
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diff
changeset
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15 $input_type$suffix '$output_file' |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
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changeset
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16 #if $options_type['options_type_selector'] == 'basic': |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
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changeset
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17 #if str($input_type) == 'cssanger': |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
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changeset
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18 cssanger |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
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changeset
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19 #else: |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
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changeset
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20 sanger |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
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changeset
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21 #end if |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
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changeset
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22 ascii summarize_input |
0 | 23 #else: |
2
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
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changeset
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24 ${options_type.output_type} ${options_type.force_quality_encoding} ${options_type.summarize_input} |
0 | 25 #end if |
2
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
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changeset
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26 ]]></command> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
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changeset
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27 <inputs> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
1
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changeset
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28 <param name="input_file" type="data" format="fastq,fastq.gz,fastq.bz2" label="File to groom" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
1
diff
changeset
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29 <param name="input_type" type="select" label="Input FASTQ quality scores type"> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
1
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changeset
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30 <option value="solexa">Solexa</option> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
1
diff
changeset
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31 <option value="illumina">Illumina 1.3-1.7</option> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
1
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changeset
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32 <option value="sanger" selected="true">Sanger & Illumina 1.8+</option> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
1
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changeset
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33 <option value="cssanger">Color Space Sanger</option> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
1
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changeset
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34 </param> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
1
diff
changeset
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35 <conditional name="options_type"> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
1
diff
changeset
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36 <param name="options_type_selector" type="select" label="Advanced Options"> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
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diff
changeset
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37 <option value="basic" selected="true">Hide Advanced Options</option> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
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changeset
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38 <option value="advanced">Show Advanced Options</option> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
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changeset
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39 </param> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
1
diff
changeset
|
40 <when value="basic" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
1
diff
changeset
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41 <when value="advanced"> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
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changeset
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42 <param name="output_type" type="select" label="Output FASTQ quality scores type" help="Galaxy tools are designed to work with the Sanger Quality score format"> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
1
diff
changeset
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43 <option value="solexa">Solexa</option> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
1
diff
changeset
|
44 <option value="illumina">Illumina 1.3-1.7</option> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
1
diff
changeset
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45 <option value="sanger" selected="true">Sanger</option> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
1
diff
changeset
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46 <option value="cssanger">Color Space Sanger</option> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
1
diff
changeset
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47 <option value="solexa.gz">Solexa (gz compressed)</option> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
1
diff
changeset
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48 <option value="illumina.gz">Illumina 1.3-1.7 (gz compressed)</option> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
1
diff
changeset
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49 <option value="sanger.gz">Sanger (gz compressed - recommended)</option> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
1
diff
changeset
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50 <option value="cssanger.gz">Color Space Sanger (gz compressed)</option> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
1
diff
changeset
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51 <option value="solexa.bz2">Solexa (bz2 compressed)</option> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
1
diff
changeset
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52 <option value="illumina.bz2">Illumina 1.3-1.7 (bz2 compressed)</option> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
1
diff
changeset
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53 <option value="sanger.bz2">Sanger (bz2 compressed)</option> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
1
diff
changeset
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54 <option value="cssanger.bz2">Color Space Sanger (bz2 compressed)</option> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
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changeset
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55 </param> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
1
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changeset
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56 <param name="force_quality_encoding" type="select" label="Force Quality Score encoding"> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
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changeset
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57 <option value="None">Use Source Encoding</option> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
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58 <option value="ascii" selected="true">ASCII</option> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
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59 <option value="decimal">Decimal</option> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
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60 </param> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
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61 <param name="summarize_input" type="select" label="Summarize input data"> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
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changeset
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62 <option value="summarize_input" selected="true">Summarize Input</option> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
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63 <option value="dont_summarize_input">Do not Summarize Input (faster)</option> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
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64 </param> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
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65 </when> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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66 </conditional> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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67 </inputs> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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68 <outputs> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
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69 <data name="output_file" format="fastqsanger"> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
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70 <change_format> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
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71 <when input="input_type" value="cssanger" format="fastqcssanger" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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changeset
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72 <when input="options_type.output_type" value="solexa" format="fastqsolexa" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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73 <when input="options_type.output_type" value="illumina" format="fastqillumina" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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74 <when input="options_type.output_type" value="sanger" format="fastqsanger" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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changeset
|
75 <when input="options_type.output_type" value="cssanger" format="fastqcssanger" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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76 <when input="options_type.output_type" value="solexa.gz" format="fastqsolexa.gz" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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77 <when input="options_type.output_type" value="illumina.gz" format="fastqillumina.gz" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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78 <when input="options_type.output_type" value="sanger.gz" format="fastqsanger.gz" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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79 <when input="options_type.output_type" value="cssanger.gz" format="fastqcssanger.gz" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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80 <when input="options_type.output_type" value="solexa.bz2" format="fastqsolexa.bz2" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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81 <when input="options_type.output_type" value="illumina.bz2" format="fastqillumina.bz2" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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82 <when input="options_type.output_type" value="sanger.bz2" format="fastqsanger.bz2" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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83 <when input="options_type.output_type" value="cssanger.bz2" format="fastqcssanger.bz2" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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84 </change_format> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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85 </data> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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86 </outputs> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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87 <tests> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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88 <!-- These tests include test files adapted from supplemental material in Cock PJ, Fields CJ, Goto N, Heuer ML, Rice PM. The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Res. 2009 Dec 16. --> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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89 <!-- Test basic options --> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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90 <test> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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91 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastq" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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92 <param name="input_type" value="sanger" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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93 <param name="options_type_selector" value="basic" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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94 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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95 </test> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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96 <test> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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97 <param name="input_file" value="sanger_full_range_as_cssanger.fastqcssanger" ftype="fastq" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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98 <param name="input_type" value="cssanger" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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99 <param name="options_type_selector" value="basic" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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100 <output name="output_file" file="sanger_full_range_as_cssanger.fastqcssanger" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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101 </test> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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102 <test> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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103 <param name="input_file" value="illumina_full_range_original_illumina.fastqillumina" ftype="fastq" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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104 <param name="input_type" value="illumina" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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105 <param name="options_type_selector" value="basic" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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106 <output name="output_file" file="illumina_full_range_as_sanger.fastqsanger" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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107 </test> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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108 <test> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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109 <param name="input_file" value="solexa_full_range_original_solexa.fastqsolexa" ftype="fastq" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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110 <param name="input_type" value="solexa" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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111 <param name="options_type_selector" value="basic" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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112 <output name="output_file" file="solexa_full_range_as_sanger.fastqsanger" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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113 </test> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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114 <test> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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115 <param name="input_file" value="sanger_full_range_as_illumina.fastqillumina" ftype="fastq" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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116 <param name="input_type" value="sanger" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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117 <param name="options_type_selector" value="basic" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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118 <output name="output_file" file="sanger_full_range_as_illumina.fastqillumina" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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119 </test> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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120 <!-- Test grooming from illumina --> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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121 <test> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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122 <param name="input_file" value="illumina_full_range_original_illumina.fastqillumina" ftype="fastq" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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123 <param name="input_type" value="illumina" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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124 <param name="options_type_selector" value="advanced" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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125 <param name="output_type" value="illumina" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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126 <param name="force_quality_encoding" value="None" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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127 <param name="summarize_input" value="summarize_input" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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128 <output name="output_file" file="illumina_full_range_original_illumina.fastqillumina" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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129 </test> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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130 <test> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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131 <param name="input_file" value="illumina_full_range_original_illumina.fastqillumina" ftype="fastq" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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132 <param name="input_type" value="illumina" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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133 <param name="options_type_selector" value="advanced" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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134 <param name="output_type" value="sanger" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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135 <param name="force_quality_encoding" value="None" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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136 <param name="summarize_input" value="summarize_input" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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137 <output name="output_file" file="illumina_full_range_as_sanger.fastqsanger" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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138 </test> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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139 <test> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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140 <param name="input_file" value="illumina_full_range_original_illumina.fastqillumina" ftype="fastq" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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141 <param name="input_type" value="illumina" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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142 <param name="options_type_selector" value="advanced" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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143 <param name="output_type" value="solexa" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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144 <param name="force_quality_encoding" value="None" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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145 <param name="summarize_input" value="summarize_input" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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146 <output name="output_file" file="illumina_full_range_as_solexa.fastqsolexa" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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147 </test> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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148 <test> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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149 <param name="input_file" value="illumina_full_range_original_illumina.fastqillumina" ftype="fastq" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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150 <param name="input_type" value="illumina" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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151 <param name="options_type_selector" value="advanced" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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152 <param name="output_type" value="cssanger" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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153 <param name="force_quality_encoding" value="None" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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154 <param name="summarize_input" value="summarize_input" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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155 <output name="output_file" file="illumina_full_range_as_cssanger.fastqcssanger" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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156 </test> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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157 <!-- Test grooming from sanger --> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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158 <test> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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159 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastq" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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160 <param name="input_type" value="sanger" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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161 <param name="options_type_selector" value="advanced" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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162 <param name="output_type" value="sanger" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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163 <param name="force_quality_encoding" value="None" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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164 <param name="summarize_input" value="summarize_input" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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165 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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166 </test> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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167 <test> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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168 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastq" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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169 <param name="input_type" value="sanger" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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170 <param name="options_type_selector" value="advanced" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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171 <param name="output_type" value="illumina" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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172 <param name="force_quality_encoding" value="None" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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173 <param name="summarize_input" value="summarize_input" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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174 <output name="output_file" file="sanger_full_range_as_illumina.fastqillumina" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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175 </test> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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176 <test> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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177 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastq" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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178 <param name="input_type" value="sanger" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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179 <param name="options_type_selector" value="advanced" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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180 <param name="output_type" value="solexa" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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181 <param name="force_quality_encoding" value="None" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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182 <param name="summarize_input" value="summarize_input" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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183 <output name="output_file" file="sanger_full_range_as_solexa.fastqsolexa" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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184 </test> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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185 <test> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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186 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastq" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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187 <param name="input_type" value="sanger" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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188 <param name="options_type_selector" value="advanced" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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189 <param name="output_type" value="cssanger" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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190 <param name="force_quality_encoding" value="None" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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191 <param name="summarize_input" value="summarize_input" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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192 <output name="output_file" file="sanger_full_range_as_cssanger.fastqcssanger" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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193 </test> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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194 <!-- Test grooming from solexa --> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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195 <test> |
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196 <param name="input_file" value="solexa_full_range_original_solexa.fastqsolexa" ftype="fastq" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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197 <param name="input_type" value="solexa" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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198 <param name="options_type_selector" value="advanced" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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199 <param name="output_type" value="solexa" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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200 <param name="force_quality_encoding" value="None" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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201 <param name="summarize_input" value="summarize_input" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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202 <output name="output_file" file="solexa_full_range_original_solexa.fastqsolexa" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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203 </test> |
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204 <test> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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205 <param name="input_file" value="solexa_full_range_original_solexa.fastqsolexa" ftype="fastq" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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206 <param name="input_type" value="solexa" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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207 <param name="options_type_selector" value="advanced" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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208 <param name="output_type" value="illumina" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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209 <param name="force_quality_encoding" value="None" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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210 <param name="summarize_input" value="summarize_input" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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211 <output name="output_file" file="solexa_full_range_as_illumina.fastqillumina" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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212 </test> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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213 <test> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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214 <param name="input_file" value="solexa_full_range_original_solexa.fastqsolexa" ftype="fastq" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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215 <param name="input_type" value="solexa" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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216 <param name="options_type_selector" value="advanced" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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217 <param name="output_type" value="sanger" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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218 <param name="force_quality_encoding" value="None" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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219 <param name="summarize_input" value="summarize_input" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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220 <output name="output_file" file="solexa_full_range_as_sanger.fastqsanger" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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221 </test> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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222 <test> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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223 <param name="input_file" value="solexa_full_range_original_solexa.fastqsolexa" ftype="fastq" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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224 <param name="input_type" value="solexa" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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225 <param name="options_type_selector" value="advanced" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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226 <param name="output_type" value="cssanger" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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227 <param name="force_quality_encoding" value="None" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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228 <param name="summarize_input" value="summarize_input" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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229 <output name="output_file" file="solexa_full_range_as_cssanger.fastqcssanger" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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230 </test> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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231 <!-- Test grooming from cssanger --> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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232 <test> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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233 <param name="input_file" value="sanger_full_range_as_cssanger.fastqcssanger" ftype="fastq" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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234 <param name="input_type" value="cssanger" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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235 <param name="options_type_selector" value="advanced" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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236 <param name="output_type" value="cssanger" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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237 <param name="force_quality_encoding" value="None" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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238 <param name="summarize_input" value="summarize_input" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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239 <output name="output_file" file="sanger_full_range_as_cssanger.fastqcssanger" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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240 </test> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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241 <test> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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242 <param name="input_file" value="sanger_full_range_as_cssanger.fastqcssanger" ftype="fastq" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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243 <param name="input_type" value="cssanger" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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244 <param name="options_type_selector" value="advanced" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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245 <param name="output_type" value="sanger" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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246 <param name="force_quality_encoding" value="None" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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247 <param name="summarize_input" value="summarize_input" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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248 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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249 </test> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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250 <test> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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251 <param name="input_file" value="sanger_full_range_as_cssanger.fastqcssanger" ftype="fastq" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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252 <param name="input_type" value="cssanger" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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253 <param name="options_type_selector" value="advanced" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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254 <param name="output_type" value="illumina" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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255 <param name="force_quality_encoding" value="None" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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256 <param name="summarize_input" value="summarize_input" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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257 <output name="output_file" file="sanger_full_range_as_illumina.fastqillumina" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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258 </test> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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259 <test> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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260 <param name="input_file" value="sanger_full_range_as_cssanger.fastqcssanger" ftype="fastq" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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261 <param name="input_type" value="cssanger" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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262 <param name="options_type_selector" value="advanced" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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263 <param name="output_type" value="solexa" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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264 <param name="force_quality_encoding" value="None" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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265 <param name="summarize_input" value="summarize_input" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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266 <output name="output_file" file="sanger_full_range_as_solexa.fastqsolexa" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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267 </test> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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268 <test> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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269 <param name="input_file" value="sanger_full_range_as_cssanger_adapter_base_with_quality_score.fastqcssanger_fake_score" ftype="fastq" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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270 <param name="input_type" value="cssanger" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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271 <param name="options_type_selector" value="advanced" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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272 <param name="output_type" value="cssanger" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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273 <param name="force_quality_encoding" value="None" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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274 <param name="summarize_input" value="summarize_input" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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275 <output name="output_file" file="sanger_full_range_as_cssanger.fastqcssanger" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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276 </test> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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277 <!-- Test fastq with line wrapping --> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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278 <test> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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279 <param name="input_file" value="wrapping_original_sanger.fastqsanger" ftype="fastq" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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280 <param name="input_type" value="sanger" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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281 <param name="options_type_selector" value="advanced" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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282 <param name="output_type" value="sanger" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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283 <param name="force_quality_encoding" value="None" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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284 <param name="summarize_input" value="summarize_input" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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285 <output name="output_file" file="wrapping_as_sanger.fastqsanger" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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286 </test> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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287 <test> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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288 <param name="input_file" value="wrapping_original_sanger.fastqsanger" ftype="fastq" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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289 <param name="input_type" value="sanger" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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290 <param name="options_type_selector" value="advanced" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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291 <param name="output_type" value="illumina" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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292 <param name="force_quality_encoding" value="None" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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293 <param name="summarize_input" value="summarize_input" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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294 <output name="output_file" file="wrapping_as_illumina.fastqillumina" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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295 </test> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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296 <test> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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297 <param name="input_file" value="wrapping_original_sanger.fastqsanger" ftype="fastq" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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298 <param name="input_type" value="sanger" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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299 <param name="options_type_selector" value="advanced" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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300 <param name="output_type" value="solexa" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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301 <param name="force_quality_encoding" value="None" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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302 <param name="summarize_input" value="summarize_input" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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303 <output name="output_file" file="wrapping_as_solexa.fastqsolexa" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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304 </test> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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305 <!-- Test forcing quality score encoding --> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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306 <!-- Sanger, range 0 - 93 --> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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307 <test> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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308 <param name="input_file" value="sanger_full_range_as_decimal_sanger.fastqsanger" ftype="fastq" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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309 <param name="input_type" value="sanger" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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310 <param name="options_type_selector" value="advanced" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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311 <param name="output_type" value="sanger" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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312 <param name="force_quality_encoding" value="ascii" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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313 <param name="summarize_input" value="summarize_input" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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314 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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315 </test> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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316 <test> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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317 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastq" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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318 <param name="input_type" value="sanger" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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319 <param name="options_type_selector" value="advanced" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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320 <param name="output_type" value="sanger" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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321 <param name="force_quality_encoding" value="decimal" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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322 <param name="summarize_input" value="summarize_input" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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323 <output name="output_file" file="sanger_full_range_as_decimal_sanger.fastqsanger" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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324 </test> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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325 <test> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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326 <param name="input_file" value="sanger_full_range_as_tab_decimal_sanger.fastqsanger" ftype="fastq" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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327 <param name="input_type" value="sanger" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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328 <param name="options_type_selector" value="advanced" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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329 <param name="output_type" value="sanger" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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330 <param name="force_quality_encoding" value="ascii" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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331 <param name="summarize_input" value="summarize_input" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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332 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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333 </test> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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334 <!-- Solexa, range -5 - 62 --> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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335 <test> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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336 <param name="input_file" value="solexa_full_range_as_decimal_solexa.fastqsolexa" ftype="fastq" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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337 <param name="input_type" value="solexa" /> |
71e5fa25b8a2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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338 <param name="options_type_selector" value="advanced" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_groomer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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339 <param name="output_type" value="solexa" /> |
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340 <param name="force_quality_encoding" value="ascii" /> |
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341 <param name="summarize_input" value="summarize_input" /> |
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342 <output name="output_file" file="solexa_full_range_original_solexa.fastqsolexa" /> |
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343 </test> |
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344 <test> |
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345 <param name="input_file" value="solexa_full_range_original_solexa.fastqsolexa" ftype="fastq" /> |
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346 <param name="input_type" value="solexa" /> |
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347 <param name="options_type_selector" value="advanced" /> |
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348 <param name="output_type" value="solexa" /> |
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349 <param name="force_quality_encoding" value="decimal" /> |
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350 <param name="summarize_input" value="summarize_input" /> |
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351 <output name="output_file" file="solexa_full_range_as_decimal_solexa.fastqsolexa" /> |
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352 </test> |
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353 <!-- compressed formats --> |
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354 <test> |
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355 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger.gz" ftype="fastq.gz" /> |
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356 <param name="input_type" value="sanger" /> |
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357 <param name="options_type_selector" value="basic" /> |
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358 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" decompress="true" /> |
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359 </test> |
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360 <test> |
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361 <param name="input_file" value="sanger_full_range_as_cssanger.fastqcssanger.bz2" ftype="fastq.bz2" /> |
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362 <param name="input_type" value="cssanger" /> |
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363 <param name="options_type_selector" value="basic" /> |
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364 <output name="output_file" file="sanger_full_range_as_cssanger.fastqcssanger" decompress="true" /> |
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365 </test> |
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366 </tests> |
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367 <help><![CDATA[ |
0 | 368 **What it does** |
369 | |
370 This tool offers several conversions options relating to the FASTQ format. | |
371 | |
372 When using *Basic* options, the output will be *sanger* formatted or *cssanger* formatted (when the input is Color Space Sanger). | |
373 | |
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374 When converting, if a quality score falls outside of the target score range, it will be coerced to the closest available value (i.e. the minimum or maximum). |
0 | 375 |
376 When converting between Solexa and the other formats, quality scores are mapped between Solexa and PHRED scales using the equations found in `Cock PJ, Fields CJ, Goto N, Heuer ML, Rice PM. The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Res. 2009 Dec 16.`_ | |
377 | |
378 When converting between color space (csSanger) and base/sequence space (Sanger, Illumina, Solexa) formats, adapter bases are lost or gained; if gained, the base 'G' is used as the adapter. You cannot convert a color space read to base space if there is no adapter present in the color space sequence. Any masked or ambiguous nucleotides in base space will be converted to 'N's when determining color space encoding. | |
379 | |
380 ----- | |
381 | |
382 **Quality Score Comparison** | |
383 | |
384 :: | |
385 | |
386 SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS | |
387 ...............................IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII | |
388 ..........................XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX | |
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389 !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~ |
0 | 390 | | | | | | |
391 33 59 64 73 104 126 | |
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392 |
0 | 393 S - Sanger Phred+33, 93 values (0, 93) (0 to 60 expected in raw reads) |
394 I - Illumina 1.3 Phred+64, 62 values (0, 62) (0 to 40 expected in raw reads) | |
395 X - Solexa Solexa+64, 67 values (-5, 62) (-5 to 40 expected in raw reads) | |
396 | |
397 Diagram adapted from http://en.wikipedia.org/wiki/FASTQ_format | |
398 | |
399 .. class:: infomark | |
400 | |
401 Output from Illumina 1.8+ pipelines are Sanger encoded. | |
402 | |
403 ------ | |
404 | |
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405 .. _Cock PJ, Fields CJ, Goto N, Heuer ML, Rice PM. The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Res. 2009 Dec 16.: https://doi.org/10.1093/nar/gkp1137 |
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406 ]]></help> |
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407 <citations> |
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408 <citation type="doi">10.1093/bioinformatics/btq281</citation> |
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409 </citations> |
0 | 410 </tool> |