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annotate fastq_paired_end_splitter.xml @ 6:b3a603b3fad1 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter commit a1525904286610e94e833a648d9b20aebb0967e7"
author iuc
date Wed, 09 Mar 2022 08:10:59 +0000
parents bac1702fd30b
children c47ce50a06e5
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b3a603b3fad1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter commit a1525904286610e94e833a648d9b20aebb0967e7"
iuc
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1 <tool id="fastq_paired_end_splitter" name="FASTQ splitter" version="@TOOL_VERSION@+galaxy1">
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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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2 <description>on joined paired end reads</description>
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bac1702fd30b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
iuc
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3 <macros>
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iuc
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4 <import>macros.xml</import>
bac1702fd30b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
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5 </macros>
bac1702fd30b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
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6 <expand macro="requirements"/>
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eec33cc2e1a4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter commit 31edb920789fbd080260f853bc856be72fa7cfa8"
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7 <edam_topics>
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8 <edam_topic>topic_0622</edam_topic>
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9 </edam_topics>
eec33cc2e1a4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter commit 31edb920789fbd080260f853bc856be72fa7cfa8"
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10 <edam_operations>
eec33cc2e1a4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter commit 31edb920789fbd080260f853bc856be72fa7cfa8"
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11 <edam_operation>operation_3359</edam_operation>
eec33cc2e1a4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter commit 31edb920789fbd080260f853bc856be72fa7cfa8"
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12 </edam_operations>
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13 <command><![CDATA[
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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14 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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15 ]]></command>
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16 <inputs>
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17 <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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18 </inputs>
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19 <outputs>
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b3a603b3fad1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter commit a1525904286610e94e833a648d9b20aebb0967e7"
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20 <data name="output1_file" format_source="input1_file" label="${tool.name} on ${on_string}: Forward"/>
b3a603b3fad1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter commit a1525904286610e94e833a648d9b20aebb0967e7"
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21 <data name="output2_file" format_source="input1_file" label="${tool.name} on ${on_string}: Reverse"/>
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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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22 </outputs>
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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23 <tests>
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24 <test>
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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25 <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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26 <output name="output1_file" file="split_pair_reads_1.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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27 <output name="output2_file" file="split_pair_reads_2.fastqsanger" ftype="fastqsanger" />
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28 </test>
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29 </tests>
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30 <help><![CDATA[
0
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31 **What it does**
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32
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33 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.
0
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34
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35 Sequence identifiers will have /1 or /2 appended for the split forward and reverse reads, respectively.
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36
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37 -----
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38
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39 **Input format**
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40
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41 A multiple-fastq file, for example::
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42
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43 @HWI-EAS91_1_30788AAXX:7:21:1542:1758
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44 GTCAATTGTACTGGTCAATACTAAAAGAATAGGATCGCTCCTAGCATCTGGAGTCTCTATCACCTGAGCCCA
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45 +HWI-EAS91_1_30788AAXX:7:21:1542:1758
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46 hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh`hfhhVZSWehR
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47
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48 -----
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49
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50 **Outputs**
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51
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52 Forward Read::
0
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53
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54 @HWI-EAS91_1_30788AAXX:7:21:1542:1758/1
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55 GTCAATTGTACTGGTCAATACTAAAAGAATAGGATC
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56 +HWI-EAS91_1_30788AAXX:7:21:1542:1758/1
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57 hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh
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58
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59 Reverse Read::
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60
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61 @HWI-EAS91_1_30788AAXX:7:21:1542:1758/2
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62 GCTCCTAGCATCTGGAGTCTCTATCACCTGAGCCCA
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63 +HWI-EAS91_1_30788AAXX:7:21:1542:1758/2
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64 hhhhhhhhhhhhhhhhhhhhhhhh`hfhhVZSWehR
3
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65 ]]></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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66 <citations>
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67 <citation type="doi">10.1093/bioinformatics/btq281</citation>
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68 </citations>
0
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69 </tool>