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comparison tools/fastq_paired_unpaired/fastq_paired_unpaired.xml @ 8:8cbc866b72ce draft

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"Update all the pico_galaxy tools on main Tool Shed"
author peterjc
date Fri, 16 Apr 2021 22:36:15 +0000
parents 2709a0f065c9
children 422724644e24
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7:2709a0f065c9 8:8cbc866b72ce
1 <tool id="fastq_paired_unpaired" name="Divide FASTQ file into paired and unpaired reads" version="0.1.4"> 1 <tool id="fastq_paired_unpaired" name="Divide FASTQ file into paired and unpaired reads" version="0.1.4">
2 <description>using the read name suffices</description> 2 <description>using the read name suffixes</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.0.1">galaxy_sequence_utils</requirement> 4 <requirement type="package" version="1.0.1">galaxy_sequence_utils</requirement>
5 <requirement type="package" version="1.67">biopython</requirement> 5 <requirement type="package" version="1.67">biopython</requirement>
6 </requirements> 6 </requirements>
7 <version_command> 7 <version_command>
15 '$output_paired' 15 '$output_paired'
16 #end if 16 #end if
17 $output_singles 17 $output_singles
18 </command> 18 </command>
19 <inputs> 19 <inputs>
20 <param name="input_fastq" type="data" format="fastq" label="FASTQ file to divide into paired and unpaired reads"/> 20 <param name="input_fastq" type="data" format="foobar" label="FASTQ file to divide into paired and unpaired reads"/>
21 <conditional name="output_choice_cond"> 21 <conditional name="output_choice_cond">
22 <param name="output_choice" type="select" label="How to output paired reads?"> 22 <param name="output_choice" type="select" label="How to output paired reads?">
23 <option value="separate">Separate (two FASTQ files, for the forward and reverse reads, in matching order).</option> 23 <option value="separate">Separate (two FASTQ files, for the forward and reverse reads, in matching order).</option>
24 <option value="interleaved">Interleaved (one FASTQ file, alternating forward read then partner reverse read).</option> 24 <option value="interleaved">Interleaved (one FASTQ file, alternating forward read then partner reverse read).</option>
25 </param> 25 </param>
63 paired reads, and orphan or single reads. 63 paired reads, and orphan or single reads.
64 64
65 The input file should be a valid FASTQ file which has been sorted so that 65 The input file should be a valid FASTQ file which has been sorted so that
66 any partner forward+reverse reads are consecutive. The output files all 66 any partner forward+reverse reads are consecutive. The output files all
67 preserve this sort order. Pairing are recognised based on standard name 67 preserve this sort order. Pairing are recognised based on standard name
68 suffices. See below or run the tool with no arguments for more details. 68 suffixes. See below or run the tool with no arguments for more details.
69 69
70 Any reads where the forward/reverse naming suffix used is not recognised 70 Any reads where the forward/reverse naming suffix used is not recognised
71 are treated as orphan reads. The tool supports the /1 and /2 convention 71 are treated as orphan reads. The tool supports the /1 and /2 convention
72 originally used by Illumina, .f and .r convention, the Sanger convention 72 originally used by Illumina, .f and .r convention, the Sanger convention
73 (see http://staden.sourceforge.net/manual/pregap4_unix_50.html for details), 73 (see http://staden.sourceforge.net/manual/pregap4_unix_50.html for details),
74 and the current Illumina convention where the reads get the same identifier 74 and the current Illumina convention where the reads get the same identifier
75 with the fragment number in the description, for example: 75 with the fragment number in the description, for example:
76 76
77 * @HWI-ST916:79:D04M5ACXX:1:1101:10000:100326 1:N:0:TGNCCA 77 * @HWI-ST916:79:D04M5ACXX:1:1101:10000:100326 1:N:0:TGNCCA
78 * @HWI-ST916:79:D04M5ACXX:1:1101:10000:100326 2:N:0:TGNCCA 78 * @HWI-ST916:79:D04M5ACXX:1:1101:10000:100326 2:N:0:TGNCCA
79 79
80 Note that this does support multiple forward and reverse reads per template 80 Note that this does support multiple forward and reverse reads per template
81 (which is quite common with Sanger sequencing), e.g. this which is sorted 81 (which is quite common with Sanger sequencing), e.g. this which is sorted
82 alphabetically: 82 alphabetically:
83 83
104 cite the following paper: 104 cite the following paper:
105 105
106 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013). 106 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013).
107 Galaxy tools and workflows for sequence analysis with applications 107 Galaxy tools and workflows for sequence analysis with applications
108 in molecular plant pathology. PeerJ 1:e167 108 in molecular plant pathology. PeerJ 1:e167
109 http://dx.doi.org/10.7717/peerj.167 109 https://doi.org/10.7717/peerj.167
110 110
111 This tool is available to install into other Galaxy Instances via the Galaxy 111 This tool is available to install into other Galaxy Instances via the Galaxy
112 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/fastq_paired_unpaired 112 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/fastq_paired_unpaired
113 </help> 113 </help>
114 <citations> 114 <citations>