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comparison prestor_abseq3.xml @ 0:ef917c03493c 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 15:35:10 -0400
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1 <tool id="prestor_abseq3" name="pRESTOr AbSeq3 Report" version="@PRESTO_VERSION@">
2 <description>Create HTML QC report from pRESTO outputs</description>
3
4 <macros>
5 <import>presto_macros.xml</import>
6 </macros>
7
8 <requirements>
9 <requirement type="package" version="07f9c7caeb60">prestor</requirement>
10 </requirements>
11
12 <command detect_errors="exit_code"><![CDATA[
13 ln -s '$qual1' ./quality-1_table.tab &&
14 ln -s '$qual2' ./quality-2_table.tab &&
15 ln -s '$primer1' ./primers-1_table.tab &&
16 ln -s '$primer2' ./primers-2_table.tab &&
17 ln -s '$cons1' ./consensus-1_table.tab &&
18 ln -s '$cons2' ./consensus-2_table.tab &&
19 ln -s '$assemble' ./assemble_table.tab &&
20 ln -s '$maskqual' ./maskqual_table.tab &&
21 ln -s '$cregion' ./cregion_table.tab &&
22 Rscript '${prestor_script}'
23 ]]></command>
24
25 <configfiles>
26 <configfile name="prestor_script"><![CDATA[
27 library(prestor)
28 report_abseq3('.', sample='${sample}', output_dir='.', output_file='report.html', format='html')
29 ]]>
30 </configfile>
31 </configfiles>
32
33 <inputs>
34 <param name="sample" type="text" label="Sample Name" help="Sample Name. Must not contain spaces.">
35 <validator type="regex" message="Value may include alphanumeric characters, underscores and spaces.">[^\s]+</validator>
36 </param>
37 <param name="qual1" type="data" format="txt" label="ParseLog of FilterSeq(R1)" help="Output of running ParseLog on the log file from FilterSeq on Read 1."/>
38 <param name="qual2" type="data" format="txt" label="ParseLog of FilterSeq(R2)" help="Output of running ParseLog on the log file from FilterSeq on Read 2."/>
39 <param name="primer1" type="data" format="txt" label="ParseLog of MaskPrimers(R1)" help="Output of running ParseLog on the log file from MaskPrimers on Read 1."/>
40 <param name="primer2" type="data" format="txt" label="ParseLog of MaskPrimers(R2)" help="Output of running ParseLog on the log file from MaskPrimers on Read 2."/>
41 <param name="cons1" type="data" format="txt" label="ParseLog of BuildConsensus(R1)" help="Output of running ParseLog on the log file from BuildConsensus on Read 1."/>
42 <param name="cons2" type="data" format="txt" label="ParseLog of BuildConsensus(R2)" help="Output of running ParseLog on the log file from BuildConsensus on Read 2."/>
43 <param name="assemble" type="data" format="txt" label="ParseLog of AssemblePairs" help="Output of running ParseLog on the log file from AssemblePairs."/>
44 <param name="maskqual" type="data" format="txt" label="ParseLog of FilterSeq(pairs)" help="Output of running ParseLog on the log file from FilterSeq on the consensus reads."/>
45 <param name="cregion" type="data" format="txt" label="ParseLog of MaskPrimers(pairs)" help="Output of running ParseLog on the log file from MaskPrimers for the C Region."/>
46 </inputs>
47
48 <outputs>
49 <data name="output" format="html" from_work_dir="report.html"/>
50 </outputs>
51
52 <tests>
53 <test>
54 <param name="sample" value="TestSample"/>
55 <param name="qual1" value="prestor_logs/quality-1_table.tab"/>
56 <param name="qual2" value="prestor_logs/quality-2_table.tab"/>
57 <param name="primer1" value="prestor_logs/primers-1_table.tab"/>
58 <param name="primer2" value="prestor_logs/primers-2_table.tab"/>
59 <param name="cons1" value="prestor_logs/consensus-1_table.tab"/>
60 <param name="cons2" value="prestor_logs/consensus-2_table.tab"/>
61 <param name="assemble" value="prestor_logs/assemble_table.tab"/>
62 <param name="maskqual" value="prestor_logs/maskqual_table.tab"/>
63 <param name="cregion" value="prestor_logs/cregion_table.tab"/>
64 <output name="output">
65 <assert_contents>
66 <has_text text="pRESTO Report"/>
67 </assert_contents>
68 </output>
69 </test>
70 </tests>
71
72 <help><![CDATA[
73 Creates an HTML QC report from the log files generated when running pRESTO.
74
75 See the `Prestor project page <https://bitbucket.org/javh/prototype-prestor/src>`_ for more information.
76 ]]></help>
77
78 <expand macro="citations" />
79 </tool>