Mercurial > repos > devteam > fastq_to_tabular

annotate fastq_to_tabular.xml @ 6:45e810d28b63 draft default tip

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-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular commit bb5df9e62585e12f08dfc0a9f86eec8e205b4845
author iuc
date Fri, 04 Oct 2024 10:33:58 +0000
parents c9031442b526
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
6
45e810d28b63 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular commit bb5df9e62585e12f08dfc0a9f86eec8e205b4845
iuc
parents: 5
diff changeset
1 <tool id="fastq_to_tabular" name="FASTQ to Tabular" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
3
a63d1aa8e829 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
2 <description>converter</description>
5
c9031442b526 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
iuc
parents: 4
diff changeset
3 <macros>
c9031442b526 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
iuc
parents: 4
diff changeset
4 <import>macros.xml</import>
c9031442b526 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
iuc
parents: 4
diff changeset
5 </macros>
4
672ad99bbfe4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular commit 31edb920789fbd080260f853bc856be72fa7cfa8"
devteam
parents: 3
diff changeset
6 <edam_topics>
672ad99bbfe4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular commit 31edb920789fbd080260f853bc856be72fa7cfa8"
devteam
parents: 3
diff changeset
7 <edam_topic>topic_0622</edam_topic>
672ad99bbfe4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular commit 31edb920789fbd080260f853bc856be72fa7cfa8"
devteam
parents: 3
diff changeset
8 </edam_topics>
672ad99bbfe4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular commit 31edb920789fbd080260f853bc856be72fa7cfa8"
devteam
parents: 3
diff changeset
9 <edam_operations>
672ad99bbfe4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular commit 31edb920789fbd080260f853bc856be72fa7cfa8"
devteam
parents: 3
diff changeset
10 <edam_operation>operation_0233</edam_operation>
672ad99bbfe4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular commit 31edb920789fbd080260f853bc856be72fa7cfa8"
devteam
parents: 3
diff changeset
11 </edam_operations>
6
45e810d28b63 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular commit bb5df9e62585e12f08dfc0a9f86eec8e205b4845
iuc
parents: 5
diff changeset
12 <expand macro="requirements"/>
3
a63d1aa8e829 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
13 <command><![CDATA[
a63d1aa8e829 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
14 gx-fastq-to-tabular '$input_file' '$output_file' $descr_columns '${input_file.extension[len('fastq'):]}'
a63d1aa8e829 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
15 ]]></command>
a63d1aa8e829 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
16 <inputs>
a63d1aa8e829 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
17 <param name="input_file" type="data" format="fastqsanger,fastqcssanger,fastqillumina,fastqsolexa,fastqsanger.gz,fastqcssanger.gz,fastqillumina.gz,fastqsolexa.gz,fastqsanger.bz2,fastqcssanger.bz2,fastqillumina.bz2,fastqsolexa.bz2" label="FASTQ file to convert" />
a63d1aa8e829 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
18 <param name="descr_columns" type="integer" min="1" value="1" label="How many columns to divide title string into?" help="Typically 2 to take the ID (first word) and decription (rest) as two columns, or 1 to give a single column" />
a63d1aa8e829 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
19 </inputs>
a63d1aa8e829 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
20 <outputs>
a63d1aa8e829 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
21 <data name="output_file" format="tabular" />
a63d1aa8e829 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
22 </outputs>
a63d1aa8e829 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
23 <tests>
a63d1aa8e829 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
24 <!-- basic test -->
a63d1aa8e829 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
25 <test>
a63d1aa8e829 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
26 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
a63d1aa8e829 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
27 <param name="descr_columns" value="1"/>
a63d1aa8e829 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
28 <output name="output_file" file="fastq_to_tabular_out_1.tabular" />
a63d1aa8e829 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
29 </test>
a63d1aa8e829 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
30 <!-- compression test -->
a63d1aa8e829 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
31 <test>
a63d1aa8e829 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
32 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger.gz" ftype="fastqsanger.gz" />
a63d1aa8e829 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
33 <param name="descr_columns" value="1"/>
a63d1aa8e829 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
34 <output name="output_file" file="fastq_to_tabular_out_1.tabular" />
a63d1aa8e829 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
35 </test>
a63d1aa8e829 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
36 <!-- color space test -->
a63d1aa8e829 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
37 <test>
a63d1aa8e829 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
38 <param name="input_file" value="sanger_full_range_as_cssanger.fastqcssanger" ftype="fastqcssanger" />
a63d1aa8e829 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
39 <param name="descr_columns" value="1"/>
a63d1aa8e829 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
40 <output name="output_file" file="fastq_to_tabular_out_2.tabular" />
a63d1aa8e829 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
41 </test>
a63d1aa8e829 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
42 <!-- split title into columns -->
a63d1aa8e829 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
43 <test>
a63d1aa8e829 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
44 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
a63d1aa8e829 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
45 <param name="descr_columns" value="2"/>
a63d1aa8e829 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
46 <output name="output_file" file="fastq_to_tabular_out_3.tabular" />
a63d1aa8e829 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
47 </test>
a63d1aa8e829 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
48 </tests>
a63d1aa8e829 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
49 <help><![CDATA[
0
e018cfd2dc02 Imported from capsule None
devteam
parents:
diff changeset
50 **What it does**
e018cfd2dc02 Imported from capsule None
devteam
parents:
diff changeset
51
e018cfd2dc02 Imported from capsule None
devteam
parents:
diff changeset
52 This tool converts FASTQ sequencing reads to a Tabular file.
e018cfd2dc02 Imported from capsule None
devteam
parents:
diff changeset
53
e018cfd2dc02 Imported from capsule None
devteam
parents:
diff changeset
54 It is conventional to take the first word of the FASTQ "@" title line as the identifier, and any remaining text to be a free form description.
e018cfd2dc02 Imported from capsule None
devteam
parents:
diff changeset
55 It is therefore often useful to split this text into two columns in Galaxy (identifier and any description) by setting **How many columns to divide title string into?** to **2**.
e018cfd2dc02 Imported from capsule None
devteam
parents:
diff changeset
56 In some cases the description can be usefully broken up into more columns -- see the examples .
e018cfd2dc02 Imported from capsule None
devteam
parents:
diff changeset
57
e018cfd2dc02 Imported from capsule None
devteam
parents:
diff changeset
58 Tab characters, if present in the source FASTQ title, will be converted to spaces.
e018cfd2dc02 Imported from capsule None
devteam
parents:
diff changeset
59
3
a63d1aa8e829 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
60 -----
0
e018cfd2dc02 Imported from capsule None
devteam
parents:
diff changeset
61
e018cfd2dc02 Imported from capsule None
devteam
parents:
diff changeset
62 **Example**
e018cfd2dc02 Imported from capsule None
devteam
parents:
diff changeset
63
e018cfd2dc02 Imported from capsule None
devteam
parents:
diff changeset
64 Consider the following two 454 reads in Sanger FASTQ format (using line wrapping for display, but do note not all tools will accept line wrapped FASTQ files)::
e018cfd2dc02 Imported from capsule None
devteam
parents:
diff changeset
65
e018cfd2dc02 Imported from capsule None
devteam
parents:
diff changeset
66 @FSRRS4401BE7HA [length=395] [gc=36.46] [flows=800] [phred_min=0] [phred_max=40] [trimmed_length=95]
e018cfd2dc02 Imported from capsule None
devteam
parents:
diff changeset
67 tcagTTAAGATGGGATAATATCCTCAGATTGCGTGATGAACTTTGTTCTGGTGGAGGAGAAGGAAGTGCATTCGACGTAT
e018cfd2dc02 Imported from capsule None
devteam
parents:
diff changeset
68 GCCCGTTTGTCGATATTTGtatttaaagtaatccgtcacaaatcagtgacataaatattatttagatttcgggagcaact
e018cfd2dc02 Imported from capsule None
devteam
parents:
diff changeset
69 ttatttattccacaagcaggtttaaattttaaatttaaattattgcagaagactttaaattaacctcgttgtcggagtca
e018cfd2dc02 Imported from capsule None
devteam
parents:
diff changeset
70 tttgttcggttattggtcgaaagtaaccncgggaagtgccgaaaactaacaaacaaaagaagatagtgaaattttaatta
e018cfd2dc02 Imported from capsule None
devteam
parents:
diff changeset
71 aaanaaatagccaaacgtaactaactaaaacggacccgtcgaggaactgccaacggacgacacagggagtagnnn
4
672ad99bbfe4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular commit 31edb920789fbd080260f853bc856be72fa7cfa8"
devteam
parents: 3
diff changeset
72 +FSRRS4401BE7HA [length=395] [gc=36.46] [flows=800] [phred_min=0] [phred_max=40] [trimmed_length=95]
0
e018cfd2dc02 Imported from capsule None
devteam
parents:
diff changeset
73 FFFDDDDDDDA666?688FFHGGIIIIIIIIIIIIIIIIIIHHHIIIIIIIIIGHGFFFFF====DFFFFFFFFFFFFFF
3
a63d1aa8e829 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
74 D???:3104/76=:5...4.3,,,366////4<ABBAAA=CCFDDDDDDDD:666CDFFFF=<ABA=;:333111<===9
4
672ad99bbfe4 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular commit 31edb920789fbd080260f853bc856be72fa7cfa8"
devteam
parents: 3
diff changeset
75 9;B889FFFFFFDDBDBDDD=8844231..,,,-,,,,,,,,1133..---17111,,,,,22555131121.--.,333
0
e018cfd2dc02 Imported from capsule None
devteam
parents:
diff changeset
76 11,.,,3--,,.,,--,3511123..--!,,,,--,----9,,,,8=,,-,,,-,,,,---26:9:5-..1,,,,11//,
3
a63d1aa8e829 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
77 ,,,!,,1917--,,,,-3.,--,,17,,,,---+11113.030000,,,044400036;96662.//;7><;!!!
0
e018cfd2dc02 Imported from capsule None
devteam
parents:
diff changeset
78 @FSRRS4401BRRTC [length=145] [gc=38.62] [flows=800] [phred_min=0] [phred_max=38] [trimmed_length=74]
e018cfd2dc02 Imported from capsule None
devteam
parents:
diff changeset
79 tcagCCAGCAATTCCGACTTAATTGTTCTTCTTCCATCATTCATCTCGACTAACAGTTCTACGATTAATGAGTTTGGCtt
e018cfd2dc02 Imported from capsule None
devteam
parents:
diff changeset
80 taatttgttgttcattattgtcacaattacactactgagactgccaaggcacncagggataggnn
e018cfd2dc02 Imported from capsule None
devteam
parents:
diff changeset
81 +FSRRS4401BRRTC [length=145] [gc=38.62] [flows=800] [phred_min=0] [phred_max=38] [trimmed_length=74]
3
a63d1aa8e829 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
82 FFFFFFFFFDDDDFFFFGFDDDDBAAAAA=<4444@@B=555:BBBBB@@?8:8<?<89898<84442;==3,,,514,,
a63d1aa8e829 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
83 ,11,,,.,,21777555513,..--1115758.//34488><<;;;;9944/!/4,,,57855!!
0
e018cfd2dc02 Imported from capsule None
devteam
parents:
diff changeset
84
e018cfd2dc02 Imported from capsule None
devteam
parents:
diff changeset
85 By default this is converted into a 3 column tabular file, with the full FASTQ title used as column 1:
e018cfd2dc02 Imported from capsule None
devteam
parents:
diff changeset
86
e018cfd2dc02 Imported from capsule None
devteam
parents:
diff changeset
87 =================================================================================================== ============== ==============
e018cfd2dc02 Imported from capsule None
devteam
parents:
diff changeset
88 FSRRS4401BE7HA [length=395] [gc=36.46] [flows=800] [phred_min=0] [phred_max=40] [trimmed_length=95] tcagTTAA...nnn FFFDDDDD...!!!
e018cfd2dc02 Imported from capsule None
devteam
parents:
diff changeset
89 FSRRS4401BRRTC [length=145] [gc=38.62] [flows=800] [phred_min=0] [phred_max=38] [trimmed_length=74] tcagCCAG...gnn FFFFFFFF...5!!
e018cfd2dc02 Imported from capsule None
devteam
parents:
diff changeset
90 =================================================================================================== ============== ==============
e018cfd2dc02 Imported from capsule None
devteam
parents:
diff changeset
91
e018cfd2dc02 Imported from capsule None
devteam
parents:
diff changeset
92 If you specified the title should be turned into 2 columns, you'd get 4 columns in total:
e018cfd2dc02 Imported from capsule None
devteam
parents:
diff changeset
93
e018cfd2dc02 Imported from capsule None
devteam
parents:
diff changeset
94 ============== ==================================================================================== ============== ==============
e018cfd2dc02 Imported from capsule None
devteam
parents:
diff changeset
95 FSRRS4401BE7HA [length=395] [gc=36.46] [flows=800] [phred_min=0] [phred_max=40] [trimmed_length=95] tcagTTAA...nnn FFFDDDDD...!!!
e018cfd2dc02 Imported from capsule None
devteam
parents:
diff changeset
96 FSRRS4401BRRTC [length=145] [gc=38.62] [flows=800] [phred_min=0] [phred_max=38] [trimmed_length=74] tcagCCAG...gnn FFFFFFFF...5!!
e018cfd2dc02 Imported from capsule None
devteam
parents:
diff changeset
97 ============== ==================================================================================== ============== ==============
e018cfd2dc02 Imported from capsule None
devteam
parents:
diff changeset
98
e018cfd2dc02 Imported from capsule None
devteam
parents:
diff changeset
99 Similarly, for this example treating the title string as 7 columns makes sense:
e018cfd2dc02 Imported from capsule None
devteam
parents:
diff changeset
100
e018cfd2dc02 Imported from capsule None
devteam
parents:
diff changeset
101 ============== ============ ========== =========== ============= ============== =================== ============== ==============
e018cfd2dc02 Imported from capsule None
devteam
parents:
diff changeset
102 FSRRS4401BE7HA [length=395] [gc=36.46] [flows=800] [phred_min=0] [phred_max=40] [trimmed_length=95] tcagTTAA...nnn FFFDDDDD...!!!
e018cfd2dc02 Imported from capsule None
devteam
parents:
diff changeset
103 FSRRS4401BRRTC [length=145] [gc=38.62] [flows=800] [phred_min=0] [phred_max=38] [trimmed_length=74] tcagCCAG...gnn FFFFFFFF...5!!
e018cfd2dc02 Imported from capsule None
devteam
parents:
diff changeset
104 ============== ============ ========== =========== ============= ============== =================== ============== ==============
e018cfd2dc02 Imported from capsule None
devteam
parents:
diff changeset
105
e018cfd2dc02 Imported from capsule None
devteam
parents:
diff changeset
106 Note the sequences and quality strings have been truncated for display purposes in the above tables.
3
a63d1aa8e829 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
107 ]]></help>
a63d1aa8e829 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
108 <citations>
a63d1aa8e829 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
109 <citation type="doi">10.1093/bioinformatics/btq281</citation>
a63d1aa8e829 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular commit f2582539542b33240234e8ea6093e25d0aee9b6a
devteam
parents: 1
diff changeset
110 </citations>
0
e018cfd2dc02 Imported from capsule None
devteam
parents:
diff changeset
111 </tool>