Mercurial > repos > thanhlv > biotradis
comparison biotradis_remove_tags.xml @ 0:afe9a515d145 draft
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
| author | thanhlv |
|---|---|
| date | Thu, 25 Jul 2019 06:03:12 -0400 |
| parents | |
| children | 09c1f97a5bcc |
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| -1:000000000000 | 0:afe9a515d145 |
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| 1 <tool id="remove_tradis_tags" name="remove tradis tags" version="@VERSION@"> | |
| 2 <description>Removes transposon sequence and quality tags from the read strings</description> | |
| 3 <macros> | |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements" /> | |
| 7 <command detect_errors="exit_code"><![CDATA[ | |
| 8 | |
| 9 remove_tags -f $input_bam -t $tag -m $mismatches -o removed -v > $log | |
| 10 | |
| 11 ]]></command> | |
| 12 <inputs> | |
| 13 <param name="input_fastq" type="data" format="fastq" label="Fastq file" help="" /> | |
| 14 <param name="tag" type="text" label="Tags to remove" help="" /> | |
| 15 <param name="mismatches" type="integer" value ="0" label="Number of mismatches to allow when matching tag" help="(optional. default = 0)" /> | |
| 16 </inputs> | |
| 17 | |
| 18 <outputs> | |
| 19 <data name="log" format="txt" label="${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" /> | |
| 21 </outputs> | |
| 22 | |
| 23 <tests> | |
| 24 </tests> | |
| 25 <help><![CDATA[ | |
| 26 Adds transposon sequence and quality tags to the read strings and | |
| 27 outputs a BAM. | |
| 28 | |
| 29 Usage: add_tags -b file.bam [options] | |
| 30 | |
| 31 Options: | |
| 32 -b : bam file with tradis tags | |
| 33 -v : verbose debugging output | |
| 34 ]]></help> | |
| 35 | |
| 36 </tool> |