Mercurial > repos > thanhlv > biotradis
comparison biotradis_remove_tags.xml @ 7:09c1f97a5bcc draft
"planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 1c12becfd708c0635632ab92620a846764ec4559-dirty"
| author | thanhlv |
|---|---|
| date | Fri, 06 Dec 2019 10:11:20 -0500 |
| parents | afe9a515d145 |
| children |
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| 6:5506c4307812 | 7:09c1f97a5bcc |
|---|---|
| 4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
| 5 </macros> | 5 </macros> |
| 6 <expand macro="requirements" /> | 6 <expand macro="requirements" /> |
| 7 <command detect_errors="exit_code"><![CDATA[ | 7 <command detect_errors="exit_code"><![CDATA[ |
| 8 | 8 |
| 9 remove_tags -f $input_bam -t $tag -m $mismatches -o removed -v > $log | 9 remove_tradis_tags -f $input_bam -t $tag -m $mismatches -o removed -v > $log |
| 10 | 10 |
| 11 ]]></command> | 11 ]]> </command> |
| 12 <inputs> | 12 <inputs> |
| 13 <param name="input_fastq" type="data" format="fastq" label="Fastq file" help="" /> | 13 <param name="input_fastq" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" label="Fastq file"/> |
| 14 <param name="tag" type="text" label="Tags to remove" help="" /> | 14 <param name="tag" type="text" label="Tags to remove" /> |
| 15 <param name="mismatches" type="integer" value ="0" label="Number of mismatches to allow when matching tag" help="(optional. default = 0)" /> | 15 <param name="mismatches" type="integer" min="0" value ="0" label="Number of mismatches to allow when matching tag" /> |
| 16 </inputs> | 16 </inputs> |
| 17 | 17 |
| 18 <outputs> | 18 <outputs> |
| 19 <data name="log" format="txt" label="${tool.name} on ${on_string}: Log"/> | 19 <data name="log" format="txt" label="${tool.name} on ${on_string}: Log"/> |
| 20 <data name="filtered_tags" format="fastqsanger" label="${tool.name} on ${on_string}" from_work_dir="removed.rmtag.fatsq" /> | 20 <data name="filtered_tags" format="fastqsanger" label="${tool.name} on ${on_string}" from_work_dir="removed.rmtag.fatsq" /> |
| 21 </outputs> | 21 </outputs> |
| 22 | 22 |
| 23 <tests> | 23 <tests> |
| 24 </tests> | 24 </tests> |
| 25 <help><![CDATA[ | 25 <help><![CDATA[ |
| 29 Usage: add_tags -b file.bam [options] | 29 Usage: add_tags -b file.bam [options] |
| 30 | 30 |
| 31 Options: | 31 Options: |
| 32 -b : bam file with tradis tags | 32 -b : bam file with tradis tags |
| 33 -v : verbose debugging output | 33 -v : verbose debugging output |
| 34 ]]></help> | 34 ]]> </help> |
| 35 <expand macro="citations" /> | |
| 35 | 36 |
| 36 </tool> | 37 </tool> |