Mercurial > repos > iuc > ivar_removereads
comparison ivar_removereads.xml @ 0:bd2a7d1316b9 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
| author | iuc |
|---|---|
| date | Mon, 30 Mar 2020 07:13:18 -0400 |
| parents | |
| children | ee2beb764a7b |
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| -1:000000000000 | 0:bd2a7d1316b9 |
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| 1 <tool id="ivar_removereads" name="ivar removereads" version="@VERSION@+galaxy0"> | |
| 2 <description>Remove reads from trimmed BAM file</description> | |
| 3 <macros> | |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements" /> | |
| 7 <expand macro="version_command" /> | |
| 8 <command detect_errors="exit_code"><![CDATA[ | |
| 9 ln -s '$input_bam' sorted.bam && | |
| 10 ln -s '$primer_index' primers.txt && | |
| 11 ln -s '$input_bed' bed.bed && | |
| 12 ivar removereads | |
| 13 -i sorted.bam | |
| 14 -p removed_reads.bam | |
| 15 -t primers.txt | |
| 16 -b bed.bed | |
| 17 ]]> </command> | |
| 18 <inputs> | |
| 19 <param name="input_bam" argument="-i" type="data" format="bam" label="Bam file" help="Aligned reads, to trim primers and quality"/> | |
| 20 <param name="primer_index" argument="-t" type="data" format="txt" label="Text file with primer indices separated by spaces" help="This is the output of getmasked command"/> | |
| 21 <param name="input_bed" argument="-b" type="data" format="bed" label="BED file with primer sequences and positions"/> | |
| 22 </inputs> | |
| 23 <outputs> | |
| 24 <data name="output_bam" format="bam" label="${tool.name} on ${on_string}" from_work_dir="removed_reads.bam"/> | |
| 25 </outputs> | |
| 26 <tests> | |
| 27 <test> | |
| 28 <param name="input_bam" value="zika/Z52_a.trimmed.sorted.bam"/> | |
| 29 <param name="primer_index" value="zika/primer_mismatchers_indices.txt"/> | |
| 30 <param name="input_bed" value="zika/db/zika_primers.bed"/> | |
| 31 <output name="output_bam" file="zika/Z52_a.masked.bam" compare="sim_size" delta="100000" /> | |
| 32 </test> | |
| 33 </tests> | |
| 34 <help><![CDATA[ | |
| 35 This command accepts an aligned and sorted BAM file trimmed using ivar trim | |
| 36 and removes the reads corresponding to the supplied primer indices, which is | |
| 37 the output of ivar getmasked command. Under the hood, ivar trim adds the | |
| 38 zero based primer index (based on the BED file) to the BAM auxillary data for | |
| 39 every read. Hence, ivar removereads will only work on BAM files that have | |
| 40 been trimmed using ivar trim. | |
| 41 | |
| 42 Documentation can be found at `<https://andersen-lab.github.io/ivar/html/manualpage.html>`_. | |
| 43 ]]> </help> | |
| 44 <expand macro="citations" /> | |
| 45 </tool> |