Mercurial > repos > devteam > fastq_paired_end_splitter
annotate fastq_paired_end_splitter.xml @ 4:249c8393f2d4 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
author | iuc |
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date | Wed, 19 Feb 2020 12:34:16 -0500 |
parents | 35e38452bb3f |
children | e39cc71d3ed6 |
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4
249c8393f2d4
"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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1 <tool id="fastq_paired_end_splitter" name="FASTQ splitter" version="@TOOL_VERSION@"> |
2
9bbe5b7ffa12
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> |
4
249c8393f2d4
"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> |
249c8393f2d4
"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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4 <import>macros.xml</import> |
249c8393f2d4
"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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5 </macros> |
249c8393f2d4
"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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6 <expand macro="requirements"/> |
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35e38452bb3f
"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> |
35e38452bb3f
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter commit 31edb920789fbd080260f853bc856be72fa7cfa8"
devteam
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8 <edam_topic>topic_0622</edam_topic> |
35e38452bb3f
"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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9 </edam_topics> |
35e38452bb3f
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter commit 31edb920789fbd080260f853bc856be72fa7cfa8"
devteam
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10 <edam_operations> |
35e38452bb3f
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter commit 31edb920789fbd080260f853bc856be72fa7cfa8"
devteam
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11 <edam_operation>operation_3359</edam_operation> |
35e38452bb3f
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter commit 31edb920789fbd080260f853bc856be72fa7cfa8"
devteam
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12 </edam_operations> |
2
9bbe5b7ffa12
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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13 <command><![CDATA[ |
9bbe5b7ffa12
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' |
9bbe5b7ffa12
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> |
9bbe5b7ffa12
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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16 <inputs> |
9bbe5b7ffa12
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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17 <param name="input1_file" type="data" format="fastqsanger,fastqcssanger,fastqsanger.gz,fastqcssanger.gz,fastqsanger.bz2,fastqcssanger.bz2" label="FASTQ reads" /> |
9bbe5b7ffa12
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
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changeset
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18 </inputs> |
9bbe5b7ffa12
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
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19 <outputs> |
9bbe5b7ffa12
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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changeset
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20 <data name="output1_file" format_source="input1_file" /> |
9bbe5b7ffa12
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
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changeset
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21 <data name="output2_file" format_source="input1_file" /> |
9bbe5b7ffa12
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
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changeset
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22 </outputs> |
9bbe5b7ffa12
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
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23 <tests> |
9bbe5b7ffa12
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
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changeset
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24 <test> |
9bbe5b7ffa12
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
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changeset
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25 <param name="input1_file" value="3.fastqsanger" ftype="fastqsanger" /> |
9bbe5b7ffa12
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents:
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changeset
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26 <output name="output1_file" file="split_pair_reads_1.fastqsanger" ftype="fastqsanger" /> |
9bbe5b7ffa12
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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changeset
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27 <output name="output2_file" file="split_pair_reads_2.fastqsanger" ftype="fastqsanger" /> |
9bbe5b7ffa12
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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28 </test> |
9bbe5b7ffa12
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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changeset
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29 </tests> |
9bbe5b7ffa12
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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30 <help><![CDATA[ |
0 | 31 **What it does** |
32 | |
2
9bbe5b7ffa12
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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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 | 34 |
35 Sequence identifiers will have /1 or /2 appended for the split left-hand and right-hand reads, respectively. | |
36 | |
37 ----- | |
38 | |
39 **Input format** | |
40 | |
41 A multiple-fastq file, for example:: | |
42 | |
43 @HWI-EAS91_1_30788AAXX:7:21:1542:1758 | |
44 GTCAATTGTACTGGTCAATACTAAAAGAATAGGATCGCTCCTAGCATCTGGAGTCTCTATCACCTGAGCCCA | |
45 +HWI-EAS91_1_30788AAXX:7:21:1542:1758 | |
46 hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh`hfhhVZSWehR | |
47 | |
48 ----- | |
49 | |
50 **Outputs** | |
51 | |
52 Left-hand Read:: | |
53 | |
54 @HWI-EAS91_1_30788AAXX:7:21:1542:1758/1 | |
55 GTCAATTGTACTGGTCAATACTAAAAGAATAGGATC | |
56 +HWI-EAS91_1_30788AAXX:7:21:1542:1758/1 | |
57 hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh | |
58 | |
59 Right-hand Read:: | |
60 | |
61 @HWI-EAS91_1_30788AAXX:7:21:1542:1758/2 | |
62 GCTCCTAGCATCTGGAGTCTCTATCACCTGAGCCCA | |
63 +HWI-EAS91_1_30788AAXX:7:21:1542:1758/2 | |
64 hhhhhhhhhhhhhhhhhhhhhhhh`hfhhVZSWehR | |
2
9bbe5b7ffa12
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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65 ]]></help> |
9bbe5b7ffa12
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> |
9bbe5b7ffa12
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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67 <citation type="doi">10.1093/bioinformatics/btq281</citation> |
9bbe5b7ffa12
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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68 </citations> |
0 | 69 </tool> |