Mercurial > repos > iuc > chira_collapse
comparison chira_collapse.xml @ 0:872249f5495a draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
| author | iuc |
|---|---|
| date | Sun, 19 Jan 2020 16:32:04 -0500 |
| parents | |
| children | 00187b27f5e5 |
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| -1:000000000000 | 0:872249f5495a |
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| 1 <tool id="chira_collapse" name="ChiRA collapse" version="@WRAPPER_VERSION@0"> | |
| 2 <description>deduplicate fastq reads</description> | |
| 3 <macros> | |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements" /> | |
| 7 <command><![CDATA[ | |
| 8 chira_collapse.py | |
| 9 -i '$in' | |
| 10 -u '$umi_len' | |
| 11 -o '$out' | |
| 12 ]]></command> | |
| 13 | |
| 14 <inputs> | |
| 15 <param format="fastq" name="in" type="data" label="Input FASTQ file"/> | |
| 16 <param name="umi_len" type="integer" value="0" | |
| 17 label="Length of the UMI if present at the 5' end of your reads"/> | |
| 18 </inputs> | |
| 19 <outputs> | |
| 20 <data format="fasta" name="out" label="ChiRA collapse FASTQ on ${on_string}"/> | |
| 21 </outputs> | |
| 22 | |
| 23 <tests> | |
| 24 <test expect_num_outputs="1"> | |
| 25 <param name="in" value="reads.fastq" /> | |
| 26 <output name="out" file="reads.fasta" /> | |
| 27 </test> | |
| 28 </tests> | |
| 29 | |
| 30 <help> | |
| 31 | |
| 32 .. class:: infomark | |
| 33 | |
| 34 **What it does** | |
| 35 | |
| 36 This tool deduplicates the reads from the FASTQ file and writes into a fasta each read once with it's read count. | |
| 37 | |
| 38 **Inputs** | |
| 39 | |
| 40 * Quality and adapter trimmed FASTQ file | |
| 41 | |
| 42 **Outputs** | |
| 43 | |
| 44 * FASTA file with unique sequences. The headers of the sequence are in the following format: >sequence_id|UMI|read_count | |
| 45 | |
| 46 </help> | |
| 47 <expand macro="citations" /> | |
| 48 </tool> |