Mercurial > repos > iuc > fastq_dl

annotate macros.xml @ 2:0095a278a085 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 3253434cee1e88dcab77c1cc99264900c78eadb9
author iuc
date Thu, 13 Nov 2025 13:33:35 +0000
parents f1a958f3e3f6
children
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c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
iuc
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1 <macros>
1
f1a958f3e3f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 4f31c74918fc999e01c3e8bc1156ecd79efbc39b
iuc
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2 <token name="@TOOL_VERSION@">3.0.1</token>
2
0095a278a085 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 3253434cee1e88dcab77c1cc99264900c78eadb9
iuc
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3 <token name="@VERSION_SUFFIX@">1</token>
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c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
iuc
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4 <xml name="requirements">
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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5 <requirements>
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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6 <requirement type="package" version="@TOOL_VERSION@">fastq-dl</requirement>
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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7 </requirements>
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
iuc
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8 </xml>
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
iuc
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9 <token name="@FASTQ_DL_FOR_LOOP@"><![CDATA[
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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10 for accessionid in "\${accessionsarr[@]}"; do
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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11 fastq-dl --accession "\$accessionid"
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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12 --provider ena
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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13 --only-provider
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
iuc
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14 $only_download_metadata
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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15 $group_by_experiment
2
0095a278a085 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 3253434cee1e88dcab77c1cc99264900c78eadb9
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16 $group_by_sample;
0095a278a085 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 3253434cee1e88dcab77c1cc99264900c78eadb9
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17 exit_code=\$? ;
0095a278a085 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 3253434cee1e88dcab77c1cc99264900c78eadb9
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18 if [ \$exit_code -ne 0 ]; then
0095a278a085 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 3253434cee1e88dcab77c1cc99264900c78eadb9
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19 echo "fastq-dl failed for accession: \${accessionid}" >&2 ;
0095a278a085 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 3253434cee1e88dcab77c1cc99264900c78eadb9
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20 exit \$exit_code ;
0095a278a085 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 3253434cee1e88dcab77c1cc99264900c78eadb9
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21 break ;
0095a278a085 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 3253434cee1e88dcab77c1cc99264900c78eadb9
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22 else
0
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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23 mv fastq-run-info.tsv logs/"\$accessionid"-fastq-run-info.tsv > /dev/null 2>&1 || true;
2
0095a278a085 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 3253434cee1e88dcab77c1cc99264900c78eadb9
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24 fi ;
0
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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25 done
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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26 ]]></token>
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
iuc
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27 <xml name="citations">
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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28 <citations>
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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29 <citation type="bibtex">
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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30 <![CDATA[
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
iuc
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31 @software{petit2024fastq-dl,
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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32 author = {Robert A. Petit III and Micheal B. Hall and Gerry Tonkin-Hill and Jie Zhu and Timothy D. Read},
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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33 title = {{fastq-dl}: efficiently download FASTQ files from SRA or ENA repositories},
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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34 version = {2.0.2},
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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35 year = {2024},
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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36 url = {https://github.com/rpetit3/fastq-dl},
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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37 note = {Accessed: 2024-10-31}
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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38 }
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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39 ]]>
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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40 </citation>
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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41 </citations>
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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42 </xml>
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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43 <xml name="creators">
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44 <creator>
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45 <person givenName="Rand" familyName="Zoabi" url="https://github.com/RZ9082" identifier="https://orcid.org/0009-0000-2501-8053" />
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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46 </creator>
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47 </xml>
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
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48 </macros>