Mercurial > repos > thanhlv > biotradis
comparison biotradis_plot.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="add_tradis_tags" name="add tradis tags" version="@VERSION@"> | |
| 2 <description>Create insertion site plot for Artemis</description> | |
| 3 <macros> | |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements" /> | |
| 7 <command detect_errors="exit_code"><![CDATA[ | |
| 8 | |
| 9 tradis_plot -b $input_bam -m $mapping_quality | |
| 10 | |
| 11 ]]></command> | |
| 12 <inputs> | |
| 13 <param name="input_bam" type="data" format="bam" label="BAM file" help="" /> | |
| 14 <param name="mapping_quality" type="integer" value="30" label="mapping quality must be greater than X " help="(optional. default: 30)" /> | |
| 15 </inputs> | |
| 16 | |
| 17 <outputs> | |
| 18 <data name="output_bam" format="bam" label="${tool.name} on ${on_string}" from_work_dir="added.tr.bam" /> | |
| 19 </outputs> | |
| 20 | |
| 21 <tests> | |
| 22 </tests> | |
| 23 <help><![CDATA[ | |
| 24 Adds transposon sequence and quality tags to the read strings and | |
| 25 outputs a BAM. | |
| 26 | |
| 27 Usage: add_tags -b file.bam [options] | |
| 28 | |
| 29 Options: | |
| 30 -b : bam file with tradis tags | |
| 31 -v : verbose debugging output | |
| 32 ]]></help> | |
| 33 | |
| 34 </tool> |