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annotate macros.xml @ 0:eb115eb8f25c draft

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"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
author workflow4metabolomics
date Thu, 17 Jun 2021 07:42:55 +0000
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eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
workflow4metabolomics
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1 <?xml version="1.0"?>
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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2 <macros>
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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3 <xml name="stdio">
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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4 <stdio>
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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5 <exit_code range="1" level="fatal" />
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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6 </stdio>
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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7 </xml>
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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9 <!-- COMMAND -->
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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10 <token name="@COMMAND_RSCRIPT@">LC_ALL=C Rscript $__tool_directory__/</token>
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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12 <token name="@COMMAND_LOG_EXIT@">
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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13 ;
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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14 return=\$?;
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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15 cat 'log.txt';
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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16 sh -c "exit \$return"
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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17 </token>
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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19 <!-- INPUT_VALIDATORS -->
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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20 <xml name="input_validator_range_integer">
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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21 <validator type="regex" message="The format is 'min,max'" >[0-9]+ *, *[0-9]+</validator>
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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22 </xml>
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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24 <xml name="input_validator_range_float">
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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25 <validator type="regex" message="The format is 'min,max'" >[0-9]+\.?[0-9]* *, *[0-9]+\.?[0-9]*</validator>
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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26 </xml>
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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28 <xml name="input_validator_list_integer">
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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29 <validator type="regex" message="The format is '1,2,4,6'" >[0-9, ]+</validator>
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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30 </xml>
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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33 <token name="@INPUT_IMAGE_LABEL@">RData file</token>
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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34 <token name="@INPUT_IMAGE_HELP@">It contains a xcms3::XCMSnExp object (named xdata)</token>
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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37 <!-- MISC -->
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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38 <token name="@HELP_AUTHORS_WRAPPERS@">
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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39
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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40 .. class:: infomark
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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41
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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42 **Galaxy integration** ABiMS TEAM - SU/CNRS - Station biologique de Roscoff and Yann Guitton - LABERCA
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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43 Part of Workflow4Metabolomics.org [W4M]
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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44
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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45 | Contact support@workflow4metabolomics.org for any questions or concerns about the Galaxy implementation of this tool.
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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47 </token>
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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48
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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49 <xml name="citation_w4m">
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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50 <citation type="doi">10.1093/bioinformatics/btu813</citation>
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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51 </xml>
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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52 </macros>