Mercurial > repos > devteam > fastq_paired_end_deinterlacer

annotate fastq_paired_end_deinterlacer.xml @ 2:b7ce72b00e62 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer commit 28c441e8aa66a55d276b0f6325d34086eb715872
author devteam
date Sat, 07 Oct 2017 10:00:52 -0400
parents 462abc5618ba
children 03d57fea6482
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
b7ce72b00e62 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer commit 28c441e8aa66a55d276b0f6325d34086eb715872
devteam
parents: 1
diff changeset
1 <tool id="fastq_paired_end_deinterlacer" name="FASTQ de-interlacer" version="1.1.2">
1
462abc5618ba planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 0
diff changeset
2 <description>on paired end reads</description>
462abc5618ba planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 0
diff changeset
3 <requirements>
2
b7ce72b00e62 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer commit 28c441e8aa66a55d276b0f6325d34086eb715872
devteam
parents: 1
diff changeset
4 <requirement type="package" version="1.1.2">galaxy_sequence_utils</requirement>
1
462abc5618ba planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 0
diff changeset
5 </requirements>
462abc5618ba planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 0
diff changeset
6 <command><![CDATA[
462abc5618ba planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 0
diff changeset
7 gx-fastq-paired-end-deinterlacer '$input_file' '${input_file.extension[len('fastq'):]}' '$output1_pairs_file' '$output2_pairs_file' '$output1_singles_file' '$output2_singles_file'
462abc5618ba planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 0
diff changeset
8 ]]></command>
462abc5618ba planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 0
diff changeset
9 <inputs>
462abc5618ba planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 0
diff changeset
10 <param name="input_file" type="data" format="fastqsanger,fastqcssanger,fastqsanger.gz,fastqcssanger.gz,fastqsanger.bz2,fastqcssanger.bz2" label="FASTQ reads" />
462abc5618ba planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 0
diff changeset
11 </inputs>
462abc5618ba planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 0
diff changeset
12 <outputs>
462abc5618ba planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 0
diff changeset
13 <data name="output1_pairs_file" format_source="input_file" label="FASTQ de-interlacer left mates from data ${input_file.hid}" />
462abc5618ba planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 0
diff changeset
14 <data name="output2_pairs_file" format_source="input_file" label="FASTQ de-interlacer right mates from data ${input_file.hid}"/>
462abc5618ba planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 0
diff changeset
15 <data name="output1_singles_file" format_source="input_file" label="FASTQ de-interlacer left singles from data ${input_file.hid}"/>
462abc5618ba planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 0
diff changeset
16 <data name="output2_singles_file" format_source="input_file" label="FASTQ de-interlacer right singles from data ${input_file.hid}"/>
462abc5618ba planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 0
diff changeset
17 </outputs>
462abc5618ba planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 0
diff changeset
18 <tests>
462abc5618ba planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 0
diff changeset
19 <test>
462abc5618ba planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 0
diff changeset
20 <param name="input_file" value="paired_end_merged.fastqsanger" ftype="fastqsanger" />
462abc5618ba planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 0
diff changeset
21 <output name="output1_pairs_file" file="paired_end_1.fastqsanger" ftype="fastqsanger" />
462abc5618ba planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 0
diff changeset
22 <output name="output2_pairs_file" file="paired_end_2.fastqsanger" ftype="fastqsanger" />
462abc5618ba planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 0
diff changeset
23 <output name="output1_singles_file" file="paired_end_1_singles.fastqsanger" ftype="fastqsanger" />
462abc5618ba planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 0
diff changeset
24 <output name="output2_singles_file" file="paired_end_2_singles.fastqsanger" ftype="fastqsanger" />
462abc5618ba planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 0
diff changeset
25 </test>
462abc5618ba planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 0
diff changeset
26 <test>
462abc5618ba planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 0
diff changeset
27 <param name="input_file" value="paired_end_merged_errors.fastqsanger" ftype="fastqsanger" />
462abc5618ba planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 0
diff changeset
28 <output name="output1_pairs_file" file="paired_end_1_cleaned.fastqsanger" ftype="fastqsanger" />
462abc5618ba planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 0
diff changeset
29 <output name="output2_pairs_file" file="paired_end_2_cleaned.fastqsanger" ftype="fastqsanger" />
462abc5618ba planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 0
diff changeset
30 <output name="output1_singles_file" file="paired_end_1_cleaned_singles.fastqsanger" ftype="fastqsanger" />
462abc5618ba planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 0
diff changeset
31 <output name="output2_singles_file" file="paired_end_2_cleaned_singles.fastqsanger" ftype="fastqsanger" />
462abc5618ba planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 0
diff changeset
32 </test>
2
b7ce72b00e62 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer commit 28c441e8aa66a55d276b0f6325d34086eb715872
devteam
parents: 1
diff changeset
33 <test>
b7ce72b00e62 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer commit 28c441e8aa66a55d276b0f6325d34086eb715872
devteam
parents: 1
diff changeset
34 <param name="input_file" value="paired_end_merged_errors.fastqsanger.gz" ftype="fastqsanger.gz" />
b7ce72b00e62 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer commit 28c441e8aa66a55d276b0f6325d34086eb715872
devteam
parents: 1
diff changeset
35 <output name="output1_pairs_file" file="paired_end_1_cleaned.fastqsanger" ftype="fastqsanger.gz" decompress="true" />
b7ce72b00e62 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer commit 28c441e8aa66a55d276b0f6325d34086eb715872
devteam
parents: 1
diff changeset
36 <output name="output2_pairs_file" file="paired_end_2_cleaned.fastqsanger" ftype="fastqsanger.gz" decompress="true" />
b7ce72b00e62 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer commit 28c441e8aa66a55d276b0f6325d34086eb715872
devteam
parents: 1
diff changeset
37 <output name="output1_singles_file" file="paired_end_1_cleaned_singles.fastqsanger" ftype="fastqsanger.gz" decompress="true" />
b7ce72b00e62 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer commit 28c441e8aa66a55d276b0f6325d34086eb715872
devteam
parents: 1
diff changeset
38 <output name="output2_singles_file" file="paired_end_2_cleaned_singles.fastqsanger" ftype="fastqsanger.gz" decompress="true" />
b7ce72b00e62 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer commit 28c441e8aa66a55d276b0f6325d34086eb715872
devteam
parents: 1
diff changeset
39 </test>
b7ce72b00e62 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer commit 28c441e8aa66a55d276b0f6325d34086eb715872
devteam
parents: 1
diff changeset
40 <test>
b7ce72b00e62 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer commit 28c441e8aa66a55d276b0f6325d34086eb715872
devteam
parents: 1
diff changeset
41 <param name="input_file" value="paired_end_merged_errors.fastqsanger.bz2" ftype="fastqsanger.bz2" />
b7ce72b00e62 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer commit 28c441e8aa66a55d276b0f6325d34086eb715872
devteam
parents: 1
diff changeset
42 <output name="output1_pairs_file" file="paired_end_1_cleaned.fastqsanger" ftype="fastqsanger.bz2" decompress="true" />
b7ce72b00e62 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer commit 28c441e8aa66a55d276b0f6325d34086eb715872
devteam
parents: 1
diff changeset
43 <output name="output2_pairs_file" file="paired_end_2_cleaned.fastqsanger" ftype="fastqsanger.bz2" decompress="true" />
b7ce72b00e62 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer commit 28c441e8aa66a55d276b0f6325d34086eb715872
devteam
parents: 1
diff changeset
44 <output name="output1_singles_file" file="paired_end_1_cleaned_singles.fastqsanger" ftype="fastqsanger.bz2" decompress="true" />
b7ce72b00e62 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer commit 28c441e8aa66a55d276b0f6325d34086eb715872
devteam
parents: 1
diff changeset
45 <output name="output2_singles_file" file="paired_end_2_cleaned_singles.fastqsanger" ftype="fastqsanger.bz2" decompress="true" />
b7ce72b00e62 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer commit 28c441e8aa66a55d276b0f6325d34086eb715872
devteam
parents: 1
diff changeset
46 </test>
1
462abc5618ba planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 0
diff changeset
47 </tests>
462abc5618ba planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 0
diff changeset
48 <help><![CDATA[
0
f0949bc49926 Imported from capsule None
devteam
parents:
diff changeset
49 **What it does**
f0949bc49926 Imported from capsule None
devteam
parents:
diff changeset
50
f0949bc49926 Imported from capsule None
devteam
parents:
diff changeset
51 De-interlaces a single fastq dataset representing paired-end run into two fastq datasets containing only the first or second mate read. Reads without mate are saved in separate output files.
f0949bc49926 Imported from capsule None
devteam
parents:
diff changeset
52
f0949bc49926 Imported from capsule None
devteam
parents:
diff changeset
53 Sequence identifiers for paired-end reads must follow the /1 and /2 convention.
f0949bc49926 Imported from capsule None
devteam
parents:
diff changeset
54
f0949bc49926 Imported from capsule None
devteam
parents:
diff changeset
55 -----
f0949bc49926 Imported from capsule None
devteam
parents:
diff changeset
56
f0949bc49926 Imported from capsule None
devteam
parents:
diff changeset
57 **Input**
f0949bc49926 Imported from capsule None
devteam
parents:
diff changeset
58
f0949bc49926 Imported from capsule None
devteam
parents:
diff changeset
59 A multiple-fastq file containing paired-end reads, for example::
f0949bc49926 Imported from capsule None
devteam
parents:
diff changeset
60
f0949bc49926 Imported from capsule None
devteam
parents:
diff changeset
61 @1539:931/1
f0949bc49926 Imported from capsule None
devteam
parents:
diff changeset
62 ACTTCCCGCGCGTGAAGGCGCCGGCAAACGAGGCTCGGGAAGGGGCTCCCG
f0949bc49926 Imported from capsule None
devteam
parents:
diff changeset
63 +1539:931/1
f0949bc49926 Imported from capsule None
devteam
parents:
diff changeset
64 BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
f0949bc49926 Imported from capsule None
devteam
parents:
diff changeset
65 @1539:931/2
f0949bc49926 Imported from capsule None
devteam
parents:
diff changeset
66 CGCCATTCCGAATCGTAGTTGTCGGCGTCTTCCAGTGCGGCAAGGCATCGT
f0949bc49926 Imported from capsule None
devteam
parents:
diff changeset
67 +1539:931/2
f0949bc49926 Imported from capsule None
devteam
parents:
diff changeset
68 WNUUZ\P^`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
f0949bc49926 Imported from capsule None
devteam
parents:
diff changeset
69
f0949bc49926 Imported from capsule None
devteam
parents:
diff changeset
70 -----
f0949bc49926 Imported from capsule None
devteam
parents:
diff changeset
71
f0949bc49926 Imported from capsule None
devteam
parents:
diff changeset
72 **Output**
f0949bc49926 Imported from capsule None
devteam
parents:
diff changeset
73
f0949bc49926 Imported from capsule None
devteam
parents:
diff changeset
74 Multi-fastq file with left-hand mate only::
f0949bc49926 Imported from capsule None
devteam
parents:
diff changeset
75
f0949bc49926 Imported from capsule None
devteam
parents:
diff changeset
76 @1539:931/1
f0949bc49926 Imported from capsule None
devteam
parents:
diff changeset
77 ACTTCCCGCGCGTGAAGGCGCCGGCAAACGAGGCTCGGGAAGGGGCTCCCG
f0949bc49926 Imported from capsule None
devteam
parents:
diff changeset
78 +1539:931/1
f0949bc49926 Imported from capsule None
devteam
parents:
diff changeset
79 BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
f0949bc49926 Imported from capsule None
devteam
parents:
diff changeset
80
f0949bc49926 Imported from capsule None
devteam
parents:
diff changeset
81 Multi-fastq file with right-hand mate only::
f0949bc49926 Imported from capsule None
devteam
parents:
diff changeset
82
f0949bc49926 Imported from capsule None
devteam
parents:
diff changeset
83 @1539:931/2
f0949bc49926 Imported from capsule None
devteam
parents:
diff changeset
84 CGCCATTCCGAATCGTAGTTGTCGGCGTCTTCCAGTGCGGCAAGGCATCGT
f0949bc49926 Imported from capsule None
devteam
parents:
diff changeset
85 +1539:931/2
f0949bc49926 Imported from capsule None
devteam
parents:
diff changeset
86 WNUUZ\P^`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
1
462abc5618ba planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 0
diff changeset
87 ]]></help>
462abc5618ba planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 0
diff changeset
88 <citations>
462abc5618ba planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 0
diff changeset
89 <citation type="doi">10.1093/bioinformatics/btq281</citation>
462abc5618ba planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 0
diff changeset
90 </citations>
0
f0949bc49926 Imported from capsule None
devteam
parents:
diff changeset
91 </tool>