comparison fastq_paired_end_deinterlacer.xml @ 1:64fa25e9b916 draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
author devteam
date Sat, 30 Sep 2017 14:56:49 -0400
parents e6e6498bf63c
children f408707593be
comparison
equal deleted inserted replaced
0:e6e6498bf63c 1:64fa25e9b916
1 <tool id="fastq_paired_end_deinterlacer" name="FASTQ de-interlacer" version="1.1"> 1 <tool id="fastq_paired_end_deinterlacer" name="FASTQ de-interlacer" version="1.1.1">
2 <description>on paired end reads</description> 2 <description>on paired end reads</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.0.0">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_deinterlacer.py '$input_file' '${input_file.extension[len( 'fastq' ):]}' '$output1_pairs_file' '$output2_pairs_file' '$output1_singles_file' '$output2_singles_file'</command> 6 <command><![CDATA[
7 <inputs> 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'
8 <param name="input_file" type="data" format="fastqsanger,fastqcssanger" label="FASTQ reads" /> 8 ]]></command>
9 </inputs> 9 <inputs>
10 <outputs> 10 <param name="input_file" type="data" format="fastqsanger,fastqcssanger,fastqsanger.gz,fastqcssanger.gz,fastqsanger.bz2,fastqcssanger.bz2" label="FASTQ reads" />
11 <data name="output1_pairs_file" format="input" label="FASTQ de-interlacer left mates from data ${input_file.hid}" /> 11 </inputs>
12 <data name="output2_pairs_file" format="input" label="FASTQ de-interlacer right mates from data ${input_file.hid}"/> 12 <outputs>
13 <data name="output1_singles_file" format="input" label="FASTQ de-interlacer left singles from data ${input_file.hid}"/> 13 <data name="output1_pairs_file" format_source="input_file" label="FASTQ de-interlacer left mates from data ${input_file.hid}" />
14 <data name="output2_singles_file" format="input" label="FASTQ de-interlacer right singles from data ${input_file.hid}"/> 14 <data name="output2_pairs_file" format_source="input_file" label="FASTQ de-interlacer right mates from data ${input_file.hid}"/>
15 </outputs> 15 <data name="output1_singles_file" format_source="input_file" label="FASTQ de-interlacer left singles from data ${input_file.hid}"/>
16 <tests> 16 <data name="output2_singles_file" format_source="input_file" label="FASTQ de-interlacer right singles from data ${input_file.hid}"/>
17 <test> 17 </outputs>
18 <param name="input_file" value="paired_end_merged.fastqsanger" ftype="fastqsanger" /> 18 <tests>
19 <output name="output1_pairs_file" file="paired_end_1.fastqsanger" /> 19 <test>
20 <output name="output2_pairs_file" file="paired_end_2.fastqsanger" /> 20 <param name="input_file" value="paired_end_merged.fastqsanger" ftype="fastqsanger" />
21 <output name="output1_singles_file" file="paired_end_1_singles.fastqsanger" /> 21 <output name="output1_pairs_file" file="paired_end_1.fastqsanger" ftype="fastqsanger" />
22 <output name="output2_singles_file" file="paired_end_2_singles.fastqsanger" /> 22 <output name="output2_pairs_file" file="paired_end_2.fastqsanger" ftype="fastqsanger" />
23 </test> 23 <output name="output1_singles_file" file="paired_end_1_singles.fastqsanger" ftype="fastqsanger" />
24 <test> 24 <output name="output2_singles_file" file="paired_end_2_singles.fastqsanger" ftype="fastqsanger" />
25 <param name="input_file" value="paired_end_merged_errors.fastqsanger" ftype="fastqsanger" /> 25 </test>
26 <output name="output1_pairs_file" file="paired_end_1_cleaned.fastqsanger" /> 26 <test>
27 <output name="output2_pairs_file" file="paired_end_2_cleaned.fastqsanger" /> 27 <param name="input_file" value="paired_end_merged_errors.fastqsanger" ftype="fastqsanger" />
28 <output name="output1_singles_file" file="paired_end_1_cleaned_singles.fastqsanger" /> 28 <output name="output1_pairs_file" file="paired_end_1_cleaned.fastqsanger" ftype="fastqsanger" />
29 <output name="output2_singles_file" file="paired_end_2_cleaned_singles.fastqsanger" /> 29 <output name="output2_pairs_file" file="paired_end_2_cleaned.fastqsanger" ftype="fastqsanger" />
30 </test> 30 <output name="output1_singles_file" file="paired_end_1_cleaned_singles.fastqsanger" ftype="fastqsanger" />
31 </tests> 31 <output name="output2_singles_file" file="paired_end_2_cleaned_singles.fastqsanger" ftype="fastqsanger" />
32 <help> 32 </test>
33 </tests>
34 <help><![CDATA[
33 **What it does** 35 **What it does**
34 36
35 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. 37 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.
36 38
37 Sequence identifiers for paired-end reads must follow the /1 and /2 convention. 39 Sequence identifiers for paired-end reads must follow the /1 and /2 convention.
66 68
67 @1539:931/2 69 @1539:931/2
68 CGCCATTCCGAATCGTAGTTGTCGGCGTCTTCCAGTGCGGCAAGGCATCGT 70 CGCCATTCCGAATCGTAGTTGTCGGCGTCTTCCAGTGCGGCAAGGCATCGT
69 +1539:931/2 71 +1539:931/2
70 WNUUZ\P^`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 72 WNUUZ\P^`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
71 73 ]]></help>
72 </help> 74 <citations>
75 <citation type="doi">10.1093/bioinformatics/btq281</citation>
76 </citations>
73 </tool> 77 </tool>