Mercurial > repos > devteam > fastq_paired_end_deinterlacer
diff fastq_paired_end_deinterlacer.xml @ 1:462abc5618ba 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 14:58:47 -0400 |
| parents | f0949bc49926 |
| children | b7ce72b00e62 |
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--- a/fastq_paired_end_deinterlacer.xml Mon Jan 27 09:27:16 2014 -0500 +++ b/fastq_paired_end_deinterlacer.xml Sat Sep 30 14:58:47 2017 -0400 @@ -1,35 +1,37 @@ -<tool id="fastq_paired_end_deinterlacer" name="FASTQ de-interlacer" version="1.1"> - <description>on paired end reads</description> - <requirements> - <requirement type="package" version="1.0.0">galaxy_sequence_utils</requirement> - </requirements> - <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> - <inputs> - <param name="input_file" type="data" format="fastqsanger,fastqcssanger" label="FASTQ reads" /> - </inputs> - <outputs> - <data name="output1_pairs_file" format="input" label="FASTQ de-interlacer left mates from data ${input_file.hid}" /> - <data name="output2_pairs_file" format="input" label="FASTQ de-interlacer right mates from data ${input_file.hid}"/> - <data name="output1_singles_file" format="input" label="FASTQ de-interlacer left singles from data ${input_file.hid}"/> - <data name="output2_singles_file" format="input" label="FASTQ de-interlacer right singles from data ${input_file.hid}"/> - </outputs> - <tests> - <test> - <param name="input_file" value="paired_end_merged.fastqsanger" ftype="fastqsanger" /> - <output name="output1_pairs_file" file="paired_end_1.fastqsanger" /> - <output name="output2_pairs_file" file="paired_end_2.fastqsanger" /> - <output name="output1_singles_file" file="paired_end_1_singles.fastqsanger" /> - <output name="output2_singles_file" file="paired_end_2_singles.fastqsanger" /> - </test> - <test> - <param name="input_file" value="paired_end_merged_errors.fastqsanger" ftype="fastqsanger" /> - <output name="output1_pairs_file" file="paired_end_1_cleaned.fastqsanger" /> - <output name="output2_pairs_file" file="paired_end_2_cleaned.fastqsanger" /> - <output name="output1_singles_file" file="paired_end_1_cleaned_singles.fastqsanger" /> - <output name="output2_singles_file" file="paired_end_2_cleaned_singles.fastqsanger" /> - </test> - </tests> - <help> +<tool id="fastq_paired_end_deinterlacer" name="FASTQ de-interlacer" version="1.1.1"> + <description>on paired end reads</description> + <requirements> + <requirement type="package" version="1.1.1">galaxy_sequence_utils</requirement> + </requirements> + <command><![CDATA[ +gx-fastq-paired-end-deinterlacer '$input_file' '${input_file.extension[len('fastq'):]}' '$output1_pairs_file' '$output2_pairs_file' '$output1_singles_file' '$output2_singles_file' + ]]></command> + <inputs> + <param name="input_file" type="data" format="fastqsanger,fastqcssanger,fastqsanger.gz,fastqcssanger.gz,fastqsanger.bz2,fastqcssanger.bz2" label="FASTQ reads" /> + </inputs> + <outputs> + <data name="output1_pairs_file" format_source="input_file" label="FASTQ de-interlacer left mates from data ${input_file.hid}" /> + <data name="output2_pairs_file" format_source="input_file" label="FASTQ de-interlacer right mates from data ${input_file.hid}"/> + <data name="output1_singles_file" format_source="input_file" label="FASTQ de-interlacer left singles from data ${input_file.hid}"/> + <data name="output2_singles_file" format_source="input_file" label="FASTQ de-interlacer right singles from data ${input_file.hid}"/> + </outputs> + <tests> + <test> + <param name="input_file" value="paired_end_merged.fastqsanger" ftype="fastqsanger" /> + <output name="output1_pairs_file" file="paired_end_1.fastqsanger" ftype="fastqsanger" /> + <output name="output2_pairs_file" file="paired_end_2.fastqsanger" ftype="fastqsanger" /> + <output name="output1_singles_file" file="paired_end_1_singles.fastqsanger" ftype="fastqsanger" /> + <output name="output2_singles_file" file="paired_end_2_singles.fastqsanger" ftype="fastqsanger" /> + </test> + <test> + <param name="input_file" value="paired_end_merged_errors.fastqsanger" ftype="fastqsanger" /> + <output name="output1_pairs_file" file="paired_end_1_cleaned.fastqsanger" ftype="fastqsanger" /> + <output name="output2_pairs_file" file="paired_end_2_cleaned.fastqsanger" ftype="fastqsanger" /> + <output name="output1_singles_file" file="paired_end_1_cleaned_singles.fastqsanger" ftype="fastqsanger" /> + <output name="output2_singles_file" file="paired_end_2_cleaned_singles.fastqsanger" ftype="fastqsanger" /> + </test> + </tests> + <help><![CDATA[ **What it does** 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. @@ -68,6 +70,8 @@ CGCCATTCCGAATCGTAGTTGTCGGCGTCTTCCAGTGCGGCAAGGCATCGT +1539:931/2 WNUUZ\P^`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB - - </help> + ]]></help> + <citations> + <citation type="doi">10.1093/bioinformatics/btq281</citation> + </citations> </tool>