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comparison fastq_paired_end_joiner.xml @ 4:080a058abf1e draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner commit f2582539542b33240234e8ea6093e25d0aee9b6a
author devteam
date Sat, 30 Sep 2017 14:59:13 -0400
parents 6a7f5da7c76d
children 822cc1e6274e
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3:6a7f5da7c76d 4:080a058abf1e
1 <tool id="fastq_paired_end_joiner" name="FASTQ joiner" version="2.0.1"> 1 <tool id="fastq_paired_end_joiner" name="FASTQ joiner" version="2.0.1.0">
2 <description>on paired end reads</description> 2 <description>on paired end reads</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.0.1">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_joiner.py '$input1_file' '${input1_file.extension[len( 'fastq' ):]}' '$input2_file' '${input2_file.extension[len( 'fastq' ):]}' '$output_file' '$style' '${paste_sequence}'</command> 6 <command><![CDATA[
7 <inputs> 7 gx-fastq-paired-end-joiner '$input1_file' '${input1_file.extension[len('fastq'):]}' '$input2_file' '${input2_file.extension[len('fastq'):]}' '$output_file' $style '${paste_sequence}'
8 <param name="input1_file" type="data" format="fastqsanger,fastqcssanger" label="Left-hand Reads" /> 8 ]]></command>
9 <param name="input2_file" type="data" format="fastqsanger,fastqcssanger" label="Right-hand Reads" /> 9 <inputs>
10 <param name="style" type="select" label="FASTQ Header Style"> 10 <param name="input1_file" type="data" format="fastqsanger,fastqcssanger,fastqsanger.gz,fastqcssanger.gz,fastqsanger.bz2,fastqcssanger.bz2" label="Left-hand Reads" />
11 <option value="old" selected="true">old</option> 11 <param name="input2_file" type="data" format="fastqsanger,fastqcssanger,fastqsanger.gz,fastqcssanger.gz,fastqsanger.bz2,fastqcssanger.bz2" label="Right-hand Reads" />
12 <option value="new">new</option> 12 <param name="style" type="select" label="FASTQ Header Style">
13 </param> 13 <option value="old" selected="true">old</option>
14 <param name="paste_sequence" type="text" label="Bases to insert between joined reads" value="" help="Values are in Base-space and quality scores of maximal value will be used"/> 14 <option value="new">new</option>
15 </inputs> 15 </param>
16 <outputs> 16 <param name="paste_sequence" type="text" value="" label="Bases to insert between joined reads" help="Values are in Base-space and quality scores of maximal value will be used"/>
17 <data name="output_file" format="input" /> 17 </inputs>
18 </outputs> 18 <outputs>
19 <tests> 19 <data name="output_file" format_source="input1_file" />
20 <test> 20 </outputs>
21 <param name="input1_file" value="split_pair_reads_1.fastqsanger" ftype="fastqsanger" /> 21 <tests>
22 <param name="input2_file" value="split_pair_reads_2.fastqsanger" ftype="fastqsanger" /> 22 <test>
23 <output name="output_file" file="3.fastqsanger" /> 23 <param name="input1_file" value="split_pair_reads_1.fastqsanger" ftype="fastqsanger" />
24 </test> 24 <param name="input2_file" value="split_pair_reads_2.fastqsanger" ftype="fastqsanger" />
25 </tests> 25 <output name="output_file" file="3.fastqsanger" ftype="fastqsanger" />
26 <help> 26 </test>
27 </tests>
28 <help><![CDATA[
27 **What it does** 29 **What it does**
28 30
29 This tool joins paired end FASTQ reads from two separate files into a 31 This tool joins paired end FASTQ reads from two separate files into a
30 single read in one file. The join is performed using sequence 32 single read in one file. The join is performed using sequence
31 identifiers, allowing the two files to contain differing ordering. If 33 identifiers, allowing the two files to contain differing ordering. If
79 81
80 ------ 82 ------
81 83
82 **Credits** 84 **Credits**
83 85
84 This is an extended version (adds support for "new" style FASTQ headers) 86 New style header support added by Simone Leo <simone.leo@crs4.it> .
85 of D. Blankenberg's fastq joiner: 87 ]]></help>
86 88 <citations>
87 `Blankenberg D, Gordon A, Von Kuster G, Coraor N, Taylor J, Nekrutenko A; Galaxy Team. Manipulation of FASTQ data with Galaxy. Bioinformatics. 2010 Jul 15;26(14):1783-5. &lt;http://www.ncbi.nlm.nih.gov/pubmed/20562416&gt;`_ 89 <citation type="doi">10.1093/bioinformatics/btq281</citation>
88 90 </citations>
89 New style header support added by Simone Leo &lt;simone.leo@crs4.it&gt;
90 </help>
91
92 <citations>
93 <citation type="doi">10.1093/bioinformatics/btq281</citation>
94 </citations>
95
96 </tool> 91 </tool>