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annotate fastq_paired_end_splitter.xml @ 3:fec4c8314668 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter commit f2582539542b33240234e8ea6093e25d0aee9b6a
author devteam
date Sat, 30 Sep 2017 13:53:09 -0400
parents d2920111eeee
children eec33cc2e1a4
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fec4c8314668 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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1 <tool id="fastq_paired_end_splitter" name="FASTQ splitter" version="1.1.1">
fec4c8314668 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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2 <description>on joined paired end reads</description>
fec4c8314668 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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3 <requirements>
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4 <requirement type="package" version="1.1.1">galaxy_sequence_utils</requirement>
fec4c8314668 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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5 </requirements>
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6 <command><![CDATA[
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7 gx-fastq-paired-end-splitter '$input1_file' '${input1_file.extension[len('fastq'):]}' '$output1_file' '$output2_file'
fec4c8314668 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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8 ]]></command>
fec4c8314668 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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9 <inputs>
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10 <param name="input1_file" type="data" format="fastqsanger,fastqcssanger,fastqsanger.gz,fastqcssanger.gz,fastqsanger.bz2,fastqcssanger.bz2" label="FASTQ reads" />
fec4c8314668 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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11 </inputs>
fec4c8314668 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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12 <outputs>
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13 <data name="output1_file" format_source="input1_file" />
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14 <data name="output2_file" format_source="input1_file" />
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15 </outputs>
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16 <tests>
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17 <test>
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18 <param name="input1_file" value="3.fastqsanger" ftype="fastqsanger" />
fec4c8314668 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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19 <output name="output1_file" file="split_pair_reads_1.fastqsanger" ftype="fastqsanger" />
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20 <output name="output2_file" file="split_pair_reads_2.fastqsanger" ftype="fastqsanger" />
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21 </test>
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22 </tests>
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23 <help><![CDATA[
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24 **What it does**
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25
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fec4c8314668 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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26 Splits a single fastq dataset representing paired-end run into two datasets (one for each end). This tool works only for datasets where both ends have **the same** length.
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27
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28 Sequence identifiers will have /1 or /2 appended for the split left-hand and right-hand reads, respectively.
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29
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30 -----
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31
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32 **Input format**
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33
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34 A multiple-fastq file, for example::
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35
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36 @HWI-EAS91_1_30788AAXX:7:21:1542:1758
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37 GTCAATTGTACTGGTCAATACTAAAAGAATAGGATCGCTCCTAGCATCTGGAGTCTCTATCACCTGAGCCCA
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38 +HWI-EAS91_1_30788AAXX:7:21:1542:1758
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39 hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh`hfhhVZSWehR
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40
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41 -----
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42
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43 **Outputs**
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44
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45 Left-hand Read::
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46
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47 @HWI-EAS91_1_30788AAXX:7:21:1542:1758/1
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48 GTCAATTGTACTGGTCAATACTAAAAGAATAGGATC
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49 +HWI-EAS91_1_30788AAXX:7:21:1542:1758/1
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50 hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh
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51
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52 Right-hand Read::
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53
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54 @HWI-EAS91_1_30788AAXX:7:21:1542:1758/2
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55 GCTCCTAGCATCTGGAGTCTCTATCACCTGAGCCCA
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56 +HWI-EAS91_1_30788AAXX:7:21:1542:1758/2
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57 hhhhhhhhhhhhhhhhhhhhhhhh`hfhhVZSWehR
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58 ]]></help>
fec4c8314668 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter commit f2582539542b33240234e8ea6093e25d0aee9b6a
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59 <citations>
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60 <citation type="doi">10.1093/bioinformatics/btq281</citation>
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61 </citations>
0
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62 </tool>