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comparison presto_alignsets.xml @ 0:d813bf6ede83 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
author iuc
date Wed, 30 May 2018 15:31:11 -0400
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1 <tool id="presto_alignsets" name="pRESTO AlignSets" version="@PRESTO_VERSION@">
2 <description>Multiple-align sequences with the same barcodes.</description>
3
4 <macros>
5 <import>presto_macros.xml</import>
6 </macros>
7
8 <expand macro="requirements"/>
9
10 <version_command>AlignSets.py --version</version_command>
11 <command detect_errors="exit_code"><![CDATA[
12 ln -s '$fastq_in' in.fastq &&
13 AlignSets.py muscle
14 --nproc "\${GALAXY_SLOTS:-1}"
15 -s in.fastq
16 --bf '$bf'
17 $div
18 --outname=tmp
19 #if $capture_log
20 --log '$log_out'
21 #end if
22 ]]></command>
23
24 <inputs>
25 <param argument="-s" name="fastq_in" type="data" format="fastq" label="Input FASTQ file" help="FASTQ file of sequences with barcodes/UMIs in an annotation."/>
26 <param argument="--bf" type="text" value="BARCODE" label="Barcode Field" help="Name of the annotation field which contains the barcode/UMI sequence."/>
27 <param argument="--div" type="boolean" value="false" truevalue="--div" falsevalue="" label="Calculate Nucleotide Diversity" help="Specify to calculate nucleotide diversity of each set."/>
28 <expand macro="presto-log-param"/>
29 </inputs>
30
31 <outputs>
32 <data name="fastq_out" format="fastq" from_work_dir="tmp_align-pass.fastq"/>
33 <expand macro="presto-log-output"/>
34 </outputs>
35
36 <tests>
37 <test>
38 <param name="fastq_in" value="presto_alignsets_test_in.fastq"/>
39 <output name="fastq_out" file="presto_alignsets_test_out.fastq" compare="sim_size" delta="15"/>
40 </test>
41 </tests>
42
43 <help><![CDATA[
44 Multiple aligns sequences with the same barcode to correct for any misalignments due to either different primer usage or insertions/deletions in the sequences.
45
46 Only supports the "muscle" sub-command of pRESTO's AlignSets.py.
47
48 See the `pRESTO online help <@PRESTO_URL_BASE@/AlignSets.html>`_ for more information.
49
50 @HELP_NOTE@
51 ]]></help>
52 <expand macro="citations" />
53 </tool>