Mercurial > repos > devteam > fastq_paired_end_splitter
comparison fastq_paired_end_splitter.xml @ 3:fec4c8314668 draft
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 |
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date | Sat, 30 Sep 2017 13:53:09 -0400 |
parents | d2920111eeee |
children | eec33cc2e1a4 |
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2:eed0fe64987c | 3:fec4c8314668 |
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1 <tool id="fastq_paired_end_splitter" name="FASTQ splitter" version="1.0.0"> | 1 <tool id="fastq_paired_end_splitter" name="FASTQ splitter" version="1.1.1"> |
2 <description>on joined paired end reads</description> | 2 <description>on joined paired end reads</description> |
3 <requirements> | 3 <requirements> |
4 <requirement type="package" version="1.0.0">galaxy_sequence_utils</requirement> | 4 <requirement type="package" version="1.1.1">galaxy_sequence_utils</requirement> |
5 </requirements> | 5 </requirements> |
6 <command interpreter="python">fastq_paired_end_splitter.py '$input1_file' '${input1_file.extension[len( 'fastq' ):]}' '$output1_file' '$output2_file'</command> | 6 <command><![CDATA[ |
7 <inputs> | 7 gx-fastq-paired-end-splitter '$input1_file' '${input1_file.extension[len('fastq'):]}' '$output1_file' '$output2_file' |
8 <param name="input1_file" type="data" format="fastqsanger,fastqcssanger" label="FASTQ reads" /> | 8 ]]></command> |
9 </inputs> | 9 <inputs> |
10 <outputs> | 10 <param name="input1_file" type="data" format="fastqsanger,fastqcssanger,fastqsanger.gz,fastqcssanger.gz,fastqsanger.bz2,fastqcssanger.bz2" label="FASTQ reads" /> |
11 <data name="output1_file" format="input" /> | 11 </inputs> |
12 <data name="output2_file" format="input" /> | 12 <outputs> |
13 </outputs> | 13 <data name="output1_file" format_source="input1_file" /> |
14 <tests> | 14 <data name="output2_file" format_source="input1_file" /> |
15 <test> | 15 </outputs> |
16 <param name="input1_file" value="3.fastqsanger" ftype="fastqsanger" /> | 16 <tests> |
17 <output name="output1_file" file="split_pair_reads_1.fastqsanger" /> | 17 <test> |
18 <output name="output2_file" file="split_pair_reads_2.fastqsanger" /> | 18 <param name="input1_file" value="3.fastqsanger" ftype="fastqsanger" /> |
19 </test> | 19 <output name="output1_file" file="split_pair_reads_1.fastqsanger" ftype="fastqsanger" /> |
20 </tests> | 20 <output name="output2_file" file="split_pair_reads_2.fastqsanger" ftype="fastqsanger" /> |
21 <help> | 21 </test> |
22 </tests> | |
23 <help><![CDATA[ | |
22 **What it does** | 24 **What it does** |
23 | 25 |
24 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. | 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. |
25 | 27 |
26 Sequence identifiers will have /1 or /2 appended for the split left-hand and right-hand reads, respectively. | 28 Sequence identifiers will have /1 or /2 appended for the split left-hand and right-hand reads, respectively. |
27 | 29 |
28 ----- | 30 ----- |
29 | 31 |
33 | 35 |
34 @HWI-EAS91_1_30788AAXX:7:21:1542:1758 | 36 @HWI-EAS91_1_30788AAXX:7:21:1542:1758 |
35 GTCAATTGTACTGGTCAATACTAAAAGAATAGGATCGCTCCTAGCATCTGGAGTCTCTATCACCTGAGCCCA | 37 GTCAATTGTACTGGTCAATACTAAAAGAATAGGATCGCTCCTAGCATCTGGAGTCTCTATCACCTGAGCCCA |
36 +HWI-EAS91_1_30788AAXX:7:21:1542:1758 | 38 +HWI-EAS91_1_30788AAXX:7:21:1542:1758 |
37 hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh`hfhhVZSWehR | 39 hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh`hfhhVZSWehR |
38 | |
39 | 40 |
40 ----- | 41 ----- |
41 | 42 |
42 **Outputs** | 43 **Outputs** |
43 | 44 |
52 | 53 |
53 @HWI-EAS91_1_30788AAXX:7:21:1542:1758/2 | 54 @HWI-EAS91_1_30788AAXX:7:21:1542:1758/2 |
54 GCTCCTAGCATCTGGAGTCTCTATCACCTGAGCCCA | 55 GCTCCTAGCATCTGGAGTCTCTATCACCTGAGCCCA |
55 +HWI-EAS91_1_30788AAXX:7:21:1542:1758/2 | 56 +HWI-EAS91_1_30788AAXX:7:21:1542:1758/2 |
56 hhhhhhhhhhhhhhhhhhhhhhhh`hfhhVZSWehR | 57 hhhhhhhhhhhhhhhhhhhhhhhh`hfhhVZSWehR |
57 | 58 ]]></help> |
58 ------ | 59 <citations> |
59 | 60 <citation type="doi">10.1093/bioinformatics/btq281</citation> |
60 | 61 </citations> |
61 </help> | |
62 | |
63 <citations> | |
64 <citation type="doi">10.1093/bioinformatics/btq281</citation> | |
65 </citations> | |
66 | |
67 </tool> | 62 </tool> |