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
comparison
equal deleted inserted replaced
-1:000000000000 0:bd2a7d1316b9
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>