Mercurial > repos > devteam > fastq_paired_end_interlacer
annotate fastq_paired_end_interlacer.xml @ 2:effda79f510c draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
author | devteam |
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date | Sat, 30 Sep 2017 14:59:00 -0400 |
parents | ec6ddf449651 |
children | ef49268ee579 |
rev | line source |
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effda79f510c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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1 <tool id="fastq_paired_end_interlacer" name="FASTQ interlacer" version="1.2.0"> |
effda79f510c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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2 <description>on paired end reads</description> |
effda79f510c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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3 <requirements> |
effda79f510c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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4 <requirement type="package" version="1.1.1">galaxy_sequence_utils</requirement> |
effda79f510c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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5 </requirements> |
effda79f510c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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6 <command><![CDATA[ |
effda79f510c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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7 gx-fastq-paired-end-interlacer |
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ec6ddf449651
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer commit a5821127c24ed3bf1e9d5ba4fb8b9f3eceb0f3f3
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8 #if $reads.reads_selector == 'paired' |
ec6ddf449651
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer commit a5821127c24ed3bf1e9d5ba4fb8b9f3eceb0f3f3
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9 '${reads.input1_file}' ${reads.input1_file.extension[len('fastq'):]} '${reads.input2_file}' ${reads.input2_file.extension[len('fastq'):]} |
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effda79f510c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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10 '$outfile_pairs' '$outfile_singles' |
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ec6ddf449651
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer commit a5821127c24ed3bf1e9d5ba4fb8b9f3eceb0f3f3
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11 #else |
ec6ddf449651
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer commit a5821127c24ed3bf1e9d5ba4fb8b9f3eceb0f3f3
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12 '${reads.reads_coll.forward}' ${reads.reads_coll.forward.extension[len('fastq'):]} '${reads.reads_coll.reverse}' ${reads.reads_coll.reverse.extension[len('fastq'):]} |
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effda79f510c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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13 '$outfile_pairs_from_coll' '$outfile_singles_from_coll' |
1
ec6ddf449651
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer commit a5821127c24ed3bf1e9d5ba4fb8b9f3eceb0f3f3
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14 #end if |
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effda79f510c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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15 ]]></command> |
effda79f510c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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16 <inputs> |
effda79f510c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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17 <conditional name="reads"> |
effda79f510c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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18 <param name="reads_selector" type="select" label="Type of paired-end datasets"> |
effda79f510c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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19 <option value="paired">2 separate datasets</option> |
effda79f510c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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20 <option value="paired_collection">1 paired dataset collection</option> |
effda79f510c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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21 </param> |
effda79f510c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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changeset
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22 <when value="paired"> |
effda79f510c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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23 <param name="input1_file" type="data" format="fastqsanger,fastqcssanger,fastqsanger.gz,fastqcssanger.gz,fastqsanger.bz2,fastqcssanger.bz2" label="Left-hand mates" /> |
effda79f510c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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24 <param name="input2_file" type="data" format="fastqsanger,fastqcssanger,fastqsanger.gz,fastqcssanger.gz,fastqsanger.bz2,fastqcssanger.bz2" label="Right-hand mates" /> |
effda79f510c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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25 </when> |
effda79f510c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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26 <when value="paired_collection"> |
effda79f510c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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27 <param name="reads_coll" type="data_collection" collection_type="paired" format="fastqsanger,fastqcssanger,fastqsanger.gz,fastqcssanger.gz,fastqsanger.bz2,fastqcssanger.bz2" label="Paired-end reads collection" /> |
effda79f510c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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28 </when> |
effda79f510c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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29 </conditional> |
effda79f510c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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30 </inputs> |
effda79f510c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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31 <outputs> |
effda79f510c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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32 <!-- $input1_file.name = filename , e.g. paired_end_2_errors.fastqsanger --> |
effda79f510c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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33 <!-- $input1_file.id = ID , e.g. 10 --> |
effda79f510c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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34 <!-- $input1_file.hid = history ID, e.g. 5 --> |
effda79f510c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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35 <data name="outfile_pairs" format_source="input1_file" label="FASTQ interlacer pairs from ${on_string}"> |
effda79f510c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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changeset
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36 <filter>reads['reads_selector'] == 'paired'</filter> |
effda79f510c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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37 </data> |
effda79f510c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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38 <data name="outfile_singles" format_source="input1_file" label="FASTQ interlacer singles from ${on_string}"> |
effda79f510c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
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39 <filter>reads['reads_selector'] == 'paired'</filter> |
effda79f510c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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40 </data> |
effda79f510c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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41 <data name="outfile_pairs_from_coll" format_source="reads_coll['forward']" label="FASTQ interlacer pairs from ${on_string}"> |
effda79f510c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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42 <filter>reads['reads_selector'] == 'paired_collection'</filter> |
effda79f510c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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43 </data> |
effda79f510c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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44 <data name="outfile_singles_from_coll" format_source="reads_coll['forward']" label="FASTQ interlacer singles from ${on_string}"> |
effda79f510c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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45 <filter>reads['reads_selector'] == 'paired_collection'</filter> |
effda79f510c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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46 </data> |
effda79f510c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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47 </outputs> |
effda79f510c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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48 <tests> |
effda79f510c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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49 <test> |
effda79f510c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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50 <param name="reads_selector" value="paired" /> |
effda79f510c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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51 <param name="input1_file" value="paired_end_1.fastqsanger" ftype="fastqsanger" /> |
effda79f510c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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52 <param name="input2_file" value="paired_end_2.fastqsanger" ftype="fastqsanger" /> |
effda79f510c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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53 <output name="outfile_pairs" file="paired_end_merged.fastqsanger" ftype="fastqsanger" /> |
effda79f510c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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54 <output name="outfile_singles" file="paired_end_merged_singles.fastqsanger" ftype="fastqsanger" /> |
effda79f510c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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55 </test> |
effda79f510c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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56 <test> |
effda79f510c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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57 <param name="reads_selector" value="paired" /> |
effda79f510c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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58 <param name="input1_file" value="paired_end_1_errors.fastqsanger" ftype="fastqsanger" /> |
effda79f510c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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59 <param name="input2_file" value="paired_end_2_errors.fastqsanger" ftype="fastqsanger" /> |
effda79f510c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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60 <output name="outfile_pairs" file="paired_end_merged_cleaned.fastqsanger" ftype="fastqsanger" /> |
effda79f510c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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61 <output name="outfile_singles" file="paired_end_merged_cleaned_singles.fastqsanger" ftype="fastqsanger" /> |
effda79f510c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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62 </test> |
effda79f510c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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63 <test> |
effda79f510c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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64 <param name="reads_selector" value="paired_collection" /> |
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65 <param name="reads_coll"> |
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66 <collection type="paired"> |
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67 <element name="forward" value="paired_end_1.fastqsanger" ftype="fastqsanger" /> |
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68 <element name="reverse" value="paired_end_2.fastqsanger" ftype="fastqsanger" /> |
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69 </collection> |
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70 </param> |
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71 <output name="outfile_pairs_from_coll" file="paired_end_merged.fastqsanger" ftype="fastqsanger" /> |
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72 <output name="outfile_singles_from_coll" file="paired_end_merged_singles.fastqsanger" ftype="fastqsanger" /> |
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73 </test> |
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74 </tests> |
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75 <help><![CDATA[ |
0 | 76 **What it does** |
77 | |
78 This tool joins paired end FASTQ reads from two separate files, one with the left mates and one with the right mates, into a single files where left mates alternate with their right mates. The join is performed using sequence identifiers, allowing the two files to contain differing ordering. If a sequence identifier does not appear in both files, it is included in a separate file. | |
79 | |
80 Sequence identifiers with /1 and /2 appended override the left-hand and right-hand designation; i.e. if the reads end with /1 and /2, the read containing /1 will be used as the left-hand read and the read containing /2 will be used as the right-hand read. Sequences without this designation will follow the left-hand and right-hand settings set by the user. | |
81 | |
82 ----- | |
83 | |
84 **Input** | |
85 | |
86 Left-hand mates, for example:: | |
87 | |
88 @1539:931/1 | |
89 ACTTCCCGCGCGTGAAGGCGCCGGCAAACGAGGCTCGGGAAGGGGCTCCCG | |
90 +1539:931/1 | |
91 BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB | |
92 | |
93 Right-hand mates, for example:: | |
94 | |
95 @1539:931/2 | |
96 CGCCATTCCGAATCGTAGTTGTCGGCGTCTTCCAGTGCGGCAAGGCATCGT | |
97 +1539:931/2 | |
98 WNUUZ\P^`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB | |
99 | |
100 ----- | |
101 | |
102 **Output** | |
103 | |
104 A multiple-fastq file containing interlaced left and right paired reads:: | |
105 | |
106 @1539:931/1 | |
107 ACTTCCCGCGCGTGAAGGCGCCGGCAAACGAGGCTCGGGAAGGGGCTCCCG | |
108 +1539:931/1 | |
109 BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB | |
110 @1539:931/2 | |
111 CGCCATTCCGAATCGTAGTTGTCGGCGTCTTCCAGTGCGGCAAGGCATCGT | |
112 +1539:931/2 | |
113 WNUUZ\P^`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB | |
114 | |
115 A multiple-fastq file containing reads that have no mate is also produced. | |
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116 ]]></help> |
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117 <citations> |
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118 <citation type="doi">10.1093/bioinformatics/btq281</citation> |
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119 </citations> |
0 | 120 </tool> |