Mercurial > repos > trinity_ctat > ctat_clean_headers
comparison ctat_clean_headers.xml @ 0:78547514909d draft default tip
Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool.
| author | trinity_ctat |
|---|---|
| date | Thu, 12 Apr 2018 10:12:18 -0400 |
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| -1:000000000000 | 0:78547514909d |
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| 1 <tool id="ctat_clean_headers" name="ctat_clean_headers" version="1.0.0" profile="17.05"> | |
| 2 <description>Clean read headers of fastq files</description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="5">perl</requirement> | |
| 5 </requirements> | |
| 6 <command detect_errors="exit_code"> | |
| 7 perl -lpe 'if (m/^[@+]/){ s/ //g}' "$input" > "$output" | |
| 8 </command> | |
| 9 <macros> | |
| 10 </macros> | |
| 11 <stdio> | |
| 12 <exit_code range="1:" level="fatal" description="Error returned from pipeline" /> | |
| 13 </stdio> | |
| 14 <regex match="Must investigate error above." | |
| 15 source="stderr" | |
| 16 level="fatal" | |
| 17 description="Unknown error encountered" /> | |
| 18 <inputs> | |
| 19 <param format="fastq" name="input" type="data" label="Fastq file with reads to be cleaned" help=""/> | |
| 20 </inputs> | |
| 21 <outputs> | |
| 22 <data format="fastq" name="output" label="Cleaned ${on_string}" /> | |
| 23 </outputs> | |
| 24 <tests> | |
| 25 </tests> | |
| 26 <help> | |
| 27 Removes whitespace from the header of each read in a fastq file. If your Trinity run gives you errors with dying threads during the normalization step, try this tool on each input first. | |
| 28 </help> | |
| 29 <citations> | |
| 30 </citations> | |
| 31 </tool> |