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annotate macros.xml @ 45:702bdf59d6c8 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deseq2 commit 2bcb448af8311320be0a970be37aa8ea4eed66b9
author iuc
date Fri, 19 Dec 2025 08:09:31 +0000
parents 1cb33de18af5
children
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621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
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1 <macros>
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
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2 <xml name="factor_repeat">
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
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3 <repeat name="rep_factorName" title="Factor" min="1">
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
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4 <param name="factorName" type="text" value="FactorName" label="Specify a factor name, e.g. effects_drug_x or cancer_markers"
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
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5 help="Only letters, numbers and underscores will be retained in this field">
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
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6 <sanitizer>
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
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7 <valid initial="string.letters,string.digits"><add value="_" /></valid>
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
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8 </sanitizer>
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
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9 </param>
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10 <repeat name="rep_factorLevel" title="Factor level" min="2" default="2">
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
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11 <param name="factorLevel" type="text" value="FactorLevel" label="Specify a factor level, typical values could be 'tumor', 'normal', 'treated' or 'control'"
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
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12 help="Only letters, numbers and underscores will be retained in this field">
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
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13 <sanitizer>
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
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14 <valid initial="string.letters,string.digits"><add value="_" /></valid>
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
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15 </sanitizer>
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
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16 </param>
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17 <yield/>
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
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18 </repeat>
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
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19 </repeat>
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
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20 </xml>
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21 <xml name="reference_target_levels">
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22 <param name="reference_level" type="text" label="Reference level for primary factor" help="Specify the reference level for the primary factor. If left blank, the first encountered level of the primary factor will be used as reference." optional="true"/>
702bdf59d6c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deseq2 commit 2bcb448af8311320be0a970be37aa8ea4eed66b9
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23 <param name="target_level" type="text" label="Target level for primary factor" help="Specify the target level for the primary factor. If left blank, all levels will be compared against the primary factor." optional="true"/>
702bdf59d6c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deseq2 commit 2bcb448af8311320be0a970be37aa8ea4eed66b9
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24 </xml>
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25 <xml name="requirements">
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
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26 <requirements>
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
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27 <requirement type="package" version="@DESEQ2_VERSION@">bioconductor-deseq2</requirement>
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28 <!-- Optional dependency of tximport, needed to import kallisto results https://github.com/galaxyproject/usegalaxy-playbook/issues/161 -->
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29 <requirement type="package" version="2.44.0">bioconductor-rhdf5</requirement>
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
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30 <requirement type="package" version="1.28.0">bioconductor-tximport</requirement>
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
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31 <requirement type="package" version="1.52.1">bioconductor-genomicfeatures</requirement>
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32 <requirement type="package" version="1.20.3">r-getopt</requirement>
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33 <requirement type="package" version="0.9.3">r-ggrepel</requirement>
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34 <requirement type="package" version="3.1.3">r-gplots</requirement>
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35 <requirement type="package" version="1.0.12">r-pheatmap</requirement>
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36 <requirement type="package" version="0.2.21">r-rjson</requirement>
45
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37 <requirement type="package" version="0.1_3">r-base64enc</requirement>
43
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38 </requirements>
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39 </xml>
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
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40 <token name="@TOOL_VERSION@">2.11.40.8</token>
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41 <token name="@DESEQ2_VERSION@">1.40.2</token>
44
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42 <token name="@VERSION_SUFFIX@">1</token>
43
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43 <token name="@PROFILE@">22.01</token>
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44 <xml name="edam_ontology">
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45 <edam_topics>
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46 <edam_topic>topic_3308</edam_topic>
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47 </edam_topics>
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48 <edam_operations>
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49 <edam_operation>operation_3800</edam_operation>
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50 </edam_operations>
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51 </xml>
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52 <xml name="citations">
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53 <citations>
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54 <citation type="doi">10.1186/s13059-014-0550-8</citation>
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55 </citations>
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56 </xml>
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57 <xml name="xrefs">
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58 <xrefs>
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59 <xref type="bio.tools">DESeq2</xref>
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60 <xref type="bioconductor">deseq2</xref>
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61 </xrefs>
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62 </xml>
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63 </macros>