Mercurial > repos > petr-novak > repeatexplorer2_testing

comparison repex_full_clustering.xml @ 10:3c121bee9253 draft

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author petr-novak
date Thu, 27 Jul 2023 08:34:54 +0000
parents 319156f85093
children 1eefa5b3e8b9
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9:319156f85093 10:3c121bee9253
38 /opt/repex_tarean/stderr_filter.py stderr.log && 38 /opt/repex_tarean/stderr_filter.py stderr.log &&
39 cd tarean_output && 39 cd tarean_output &&
40 zip -r ${ReportArchive}.zip * && 40 zip -r ${ReportArchive}.zip * &&
41 mv ${ReportArchive}.zip ${ReportArchive} && 41 mv ${ReportArchive}.zip ${ReportArchive} &&
42 cp index.html ${ReportFile} && 42 cp index.html ${ReportFile} &&
43 mkdir -p ${ReportFile.files_path} && 43 mkdir -p ${ReportFile.extra_files_path} &&
44 cp -r --parents libdir ${ReportFile.files_path} && 44 cp -r --parents libdir ${ReportFile.extra_files_path} &&
45 cp -r --parents seqclust/clustering/superclusters ${ReportFile.files_path} && 45 cp -r --parents seqclust/clustering/superclusters ${ReportFile.extra_files_path} &&
46 cp -r --parents seqclust/clustering/clusters ${ReportFile.files_path} && 46 cp -r --parents seqclust/clustering/clusters ${ReportFile.extra_files_path} &&
47 cp seqclust/clustering/hitsort.cls ${ReportFile.files_path}/seqclust/clustering/hitsort.cls && 47 cp seqclust/clustering/hitsort.cls ${ReportFile.extra_files_path}/seqclust/clustering/hitsort.cls &&
48 cp *.png ${ReportFile.files_path}/ && 48 cp *.png ${ReportFile.extra_files_path}/ &&
49 cp *.csv ${ReportFile.files_path}/ && 49 cp *.csv ${ReportFile.extra_files_path}/ &&
50 cp *.html ${ReportFile.files_path}/ && 50 cp *.html ${ReportFile.extra_files_path}/ &&
51 cp *.css ${ReportFile.files_path}/ && 51 cp *.css ${ReportFile.extra_files_path}/ &&
52 cp *.fasta ${ReportFile.files_path}/ 2>>$log && rm -r ../tarean_output || : 52 cp *.fasta ${ReportFile.extra_files_path}/ 2>>$log && rm -r ../tarean_output || :
53 53
54 </command> 54 </command>
55 <inputs> 55 <inputs>
56 <param name="FastaFile" label="NGS reads" type="data" format="fasta" 56 <param name="FastaFile" label="NGS reads" type="data" format="fasta"
57 help="Input file must contain FASTA-formatted NGS reads. Illumina paired-end reads are recommended."/> 57 help="Input file must contain FASTA-formatted NGS reads. Illumina paired-end reads are recommended."/>