Mercurial > repos > iuc > presto_parselog

annotate presto_parselog.xml @ 3:fd8f1ac582bd draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit d52e3c9c53dd358e14e65a3a083e7d5c102f8697"
author iuc
date Sat, 25 Sep 2021 18:35:27 +0000
parents fc1fd003bc80
children 7f93403bc705
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fd8f1ac582bd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit d52e3c9c53dd358e14e65a3a083e7d5c102f8697"
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1 <tool id="presto_parselog" name="pRESTO ParseLog" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>Create tabular report from pRESTO log file</description>
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fd8f1ac582bd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit d52e3c9c53dd358e14e65a3a083e7d5c102f8697"
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3 <expand macro="bio_tools"/>
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4 <macros>
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5 <import>presto_macros.xml</import>
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6 </macros>
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8 <expand macro="requirements"/>
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10 <version_command>ParseLog.py --version</version_command>
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11 <command detect_errors="exit_code"><![CDATA[
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12 ParseLog.py
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13 -l '$log_file'
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14 -f $fields
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15 --outdir=.
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16 --outname=tmp
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17 ]]></command>
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19 <inputs>
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20 <param argument="-l" name="log_file" type="data" format="txt" label="pRESTO log file" help="Detailed log file generated from a pRESTO tool."/>
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21 <param argument="-f" name="fields" type="text" label="Field(s)" help="Space-separated list of fields to extract.">
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22 <expand macro="text-regex-validator"/>
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23 </param>
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24 </inputs>
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26 <outputs>
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27 <data name="output" format="tsv" from_work_dir="tmp_table.tab"/>
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28 </outputs>
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30 <tests>
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31 <test>
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32 <param name="log_file" value="presto_parselog_test_in.txt"/>
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33 <param name="fields" value="ID QUALITY"/>
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34 <output name="output" file="presto_parselog_test_out.txt" sort="true"/>
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35 </test>
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36 </tests>
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38 <help><![CDATA[
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39 Creates tab-separated tabular reports from pRESTO detailed log files.
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41 See the `pRESTO online help <@PRESTO_BASE_URL@/en/stable>`_ for more information.
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43 @HELP_NOTE@
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44 ]]></help>
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45 <expand macro="citations" />
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46 </tool>