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comparison presto_partition.xml @ 0:0b103d43a2c7 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 15:35:32 -0400
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1 <tool id="presto_partition" name="pRESTO Partition" version="@PRESTO_VERSION@">
2 <description>Partition a file in two</description>
3
4 <macros>
5 <import>presto_macros.xml</import>
6 </macros>
7
8 <expand macro="requirements"/>
9
10 <version_command>SplitSeq.py --version</version_command>
11 <command detect_errors="exit_code"><![CDATA[
12 ln -s '$fastq_in' in.fastq &&
13 SplitSeq.py group
14 -s in.fastq
15 -f '$field'
16 --num '$threshold'
17 --outname=tmp_group &&
18 mv './tmp_group_under-${threshold}.fastq' '$lower_out' &&
19 mv './tmp_group_atleast-${threshold}.fastq' '$upper_out'
20 ]]></command>
21
22 <inputs>
23 <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."/>
24 <param argument="-f" name="field" type="text" value="" label="Annotation Field" help="Name of the numeric annotation field to partition by."/>
25 <param argument="--num" name="threshold" type="integer" value="0" label="Threshold" help="Numeric threshold. File will be partitions be into n &lt; threshold and n &gt;= threshold."/>
26 </inputs>
27
28 <outputs>
29 <data name="lower_out" format="fastq" label="Sequences with $field &lt; $threshold"/>
30 <data name="upper_out" format="fastq" label="Sequences with $field &gt;= $threshold"/>
31 </outputs>
32
33 <tests>
34 <test>
35 <param name="fastq_in" value="presto_splitseq_partition_test_in.fastq"/>
36 <param name="field" value="CONSCOUNT"/>
37 <param name="threshold" value="3"/>
38 <output name="lower_out" file="presto_splitseq_partition_test_out_under.fastq" sort="true"/>
39 <output name="upper_out" file="presto_splitseq_partition_test_out_atleast.fastq" sort="true"/>
40 </test>
41 </tests>
42
43 <help><![CDATA[
44 Uses pRESTO SplitSeq.py group to partition a file of sequences into two files. The input file is split based on a numeric
45 annotation field to yield one file which contains all sequences with the field value less than the provided threshold and
46 a second file with all sequences with the field value greater than or equal to the threshold.
47
48 See the `pRESTO online help <@PRESTO_URL_BASE@/SplitSeq.html>`_ for more information.
49
50 @HELP_NOTE@
51 ]]></help>
52 <expand macro="citations" />
53 </tool>