Mercurial > repos > thanhlv > biotradis
comparison biotradis_filter_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="filter_tradis_tags" name="filter tradis tags" version="@VERSION@"> | |
| 2 <description>Filters a BAM file and outputs reads with tag matching -t option.</description> | |
| 3 <macros> | |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements" /> | |
| 7 <command detect_errors="exit_code"><![CDATA[ | |
| 8 | |
| 9 filter_tradis_tags -b $input_bam -t $tag -m $mismatches -o filtered | |
| 10 | |
| 11 ]]></command> | |
| 12 <inputs> | |
| 13 <param name="input_bam" type="data" format="bam" label="BAM file" help="" /> | |
| 14 <param name="tag" type="text" label="Tags to filter" help="" /> | |
| 15 <param name="mismatches" type="integer" value ="0" label="Number of mismatches to allow when matching tag" help="(optional. default = 0)" /> | |
| 16 <param argument="--verbose" type="boolean" truevalue="-v" falsevalue="" checked="false" label="verbose debugging output" help="(Default:No)" /> | |
| 17 </inputs> | |
| 18 | |
| 19 <outputs> | |
| 20 <data name="filtered_tags" format="fastq" label="${tool.name} on ${on_string}" from_work_dir="filtered.tag.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> |