Mercurial > repos > devteam > fastq_paired_end_interlacer
comparison fastq_paired_end_interlacer.xml @ 2:1adeef975783 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer commit 28c441e8aa66a55d276b0f6325d34086eb715872
| author | devteam |
|---|---|
| date | Sat, 07 Oct 2017 10:00:35 -0400 |
| parents | e0a8fba7ed2f |
| children | a59c6f7b14c3 |
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| 1:e0a8fba7ed2f | 2:1adeef975783 |
|---|---|
| 1 <tool id="fastq_paired_end_interlacer" name="FASTQ interlacer" version="1.2.0"> | 1 <tool id="fastq_paired_end_interlacer" name="FASTQ interlacer" version="1.2.0.1"> |
| 2 <description>on paired end reads</description> | 2 <description>on paired end reads</description> |
| 3 <requirements> | 3 <requirements> |
| 4 <requirement type="package" version="1.1.1">galaxy_sequence_utils</requirement> | 4 <requirement type="package" version="1.1.2">galaxy_sequence_utils</requirement> |
| 5 </requirements> | 5 </requirements> |
| 6 <command><![CDATA[ | 6 <command><![CDATA[ |
| 7 gx-fastq-paired-end-interlacer | 7 gx-fastq-paired-end-interlacer |
| 8 #if $reads.reads_selector == 'paired' | 8 #if $reads.reads_selector == 'paired' |
| 9 '${reads.input1_file}' ${reads.input1_file.extension[len('fastq'):]} '${reads.input2_file}' ${reads.input2_file.extension[len('fastq'):]} | 9 '${reads.input1_file}' ${reads.input1_file.extension[len('fastq'):]} '${reads.input2_file}' ${reads.input2_file.extension[len('fastq'):]} |
| 59 <param name="input2_file" value="paired_end_2_errors.fastqsanger" ftype="fastqsanger" /> | 59 <param name="input2_file" value="paired_end_2_errors.fastqsanger" ftype="fastqsanger" /> |
| 60 <output name="outfile_pairs" file="paired_end_merged_cleaned.fastqsanger" ftype="fastqsanger" /> | 60 <output name="outfile_pairs" file="paired_end_merged_cleaned.fastqsanger" ftype="fastqsanger" /> |
| 61 <output name="outfile_singles" file="paired_end_merged_cleaned_singles.fastqsanger" ftype="fastqsanger" /> | 61 <output name="outfile_singles" file="paired_end_merged_cleaned_singles.fastqsanger" ftype="fastqsanger" /> |
| 62 </test> | 62 </test> |
| 63 <test> | 63 <test> |
| 64 <param name="reads_selector" value="paired" /> | |
| 65 <param name="input1_file" value="paired_end_1_errors.fastqsanger.gz" ftype="fastqsanger.gz" /> | |
| 66 <param name="input2_file" value="paired_end_2_errors.fastqsanger.gz" ftype="fastqsanger.gz" /> | |
| 67 <output name="outfile_pairs" file="paired_end_merged_cleaned.fastqsanger" ftype="fastqsanger.gz" decompress="true" /> | |
| 68 <output name="outfile_singles" file="paired_end_merged_cleaned_singles.fastqsanger" ftype="fastqsanger.gz" decompress="true" /> | |
| 69 </test> | |
| 70 <test> | |
| 71 <param name="reads_selector" value="paired" /> | |
| 72 <param name="input1_file" value="paired_end_1_errors.fastqsanger.bz2" ftype="fastqsanger.bz2" /> | |
| 73 <param name="input2_file" value="paired_end_2_errors.fastqsanger.bz2" ftype="fastqsanger.bz2" /> | |
| 74 <output name="outfile_pairs" file="paired_end_merged_cleaned.fastqsanger" ftype="fastqsanger.bz2" decompress="true" /> | |
| 75 <output name="outfile_singles" file="paired_end_merged_cleaned_singles.fastqsanger" ftype="fastqsanger.bz2" decompress="true" /> | |
| 76 </test> | |
| 77 <test> | |
| 64 <param name="reads_selector" value="paired_collection" /> | 78 <param name="reads_selector" value="paired_collection" /> |
| 65 <param name="reads_coll"> | 79 <param name="reads_coll"> |
| 66 <collection type="paired"> | 80 <collection type="paired"> |
| 67 <element name="forward" value="paired_end_1.fastqsanger" ftype="fastqsanger" /> | 81 <element name="forward" value="paired_end_1.fastqsanger" ftype="fastqsanger" /> |
| 68 <element name="reverse" value="paired_end_2.fastqsanger" ftype="fastqsanger" /> | 82 <element name="reverse" value="paired_end_2.fastqsanger" ftype="fastqsanger" /> |