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annotate macros.xml @ 0:c2bd59d24f41 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
author iuc
date Sat, 16 Nov 2024 18:43:39 +0000
parents
children f1a958f3e3f6
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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0
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>
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
iuc
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2 <token name="@TOOL_VERSION@">3.0.0</token>
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
iuc
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3 <token name="@VERSION_SUFFIX@">0</token>
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
iuc
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5 <requirements>
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
iuc
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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
iuc
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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
iuc
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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
iuc
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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
iuc
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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
iuc
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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
iuc
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15 $group_by_experiment
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
iuc
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16 $group_by_sample
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
iuc
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17 &&
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
iuc
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18 mv fastq-run-info.tsv logs/"\$accessionid"-fastq-run-info.tsv > /dev/null 2>&1 || true;
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
iuc
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19 done
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
iuc
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20 ]]></token>
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
iuc
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21 <xml name="citations">
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
iuc
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22 <citations>
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
iuc
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23 <citation type="bibtex">
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
iuc
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24 <![CDATA[
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
iuc
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25 @software{petit2024fastq-dl,
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
iuc
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26 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
iuc
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27 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
iuc
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28 version = {2.0.2},
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
iuc
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29 year = {2024},
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
iuc
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30 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
iuc
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31 note = {Accessed: 2024-10-31}
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
iuc
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32 }
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
iuc
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33 ]]>
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
iuc
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34 </citation>
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
iuc
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35 </citations>
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
iuc
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36 </xml>
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
iuc
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37 <xml name="creators">
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
iuc
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38 <creator>
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
iuc
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39 <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
iuc
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40 </creator>
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
iuc
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41 </xml>
c2bd59d24f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl commit 8da9481e027494c5fd881564d01d9e2ab55fe305
iuc
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42 </macros>