Mercurial > repos > iuc > presto_parselog

comparison presto_parselog.xml @ 0:488cd05be723 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 15:35:52 -0400
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1 <tool id="presto_parselog" name="pRESTO ParseLog" version="@PRESTO_VERSION@">
2 <description>Create tabular report from pRESTO log file</description>
3
4 <macros>
5 <import>presto_macros.xml</import>
6 </macros>
7
8 <expand macro="requirements"/>
9
10 <version_command>ParseLog.py --version</version_command>
11 <command detect_errors="exit_code"><![CDATA[
12 ParseLog.py
13 -l '$log_file'
14 -f $fields
15 --outdir=.
16 --outname=tmp
17 ]]></command>
18
19 <inputs>
20 <param argument="-l" name="log_file" type="data" format="txt" label="pRESTO log file" help="Detailed log file generated from a pRESTO tool."/>
21 <param argument="-f" name="fields" type="text" label="Field(s)" help="Space-separated list of fields to extract.">
22 <expand macro="text-regex-validator"/>
23 </param>
24 </inputs>
25
26 <outputs>
27 <data name="output" format="tsv" from_work_dir="tmp_table.tab"/>
28 </outputs>
29
30 <tests>
31 <test>
32 <param name="log_file" value="presto_parselog_test_in.txt"/>
33 <param name="fields" value="ID QUALITY"/>
34 <output name="output" file="presto_parselog_test_out.txt" sort="true"/>
35 </test>
36 </tests>
37
38 <help><![CDATA[
39 Creates tab-separated tabular reports from pRESTO detailed log files.
40
41 See the `pRESTO online help <@PRESTO_URL_BASE@/ParseLog.html>`_ for more information.
42
43 @HELP_NOTE@
44 ]]></help>
45 <expand macro="citations" />
46 </tool>