Mercurial > repos > iuc > deseq2

annotate deseq2_macros.xml @ 28:7ff33c2d525b draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit a3c52d23c261ef0bd0cc4c3d59900e108ca3f67e"
author iuc
date Fri, 19 Nov 2021 21:03:55 +0000
parents d027d1f4984e
children cd9874cb9019
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e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
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1 <macros>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
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2 <xml name="factor_repeat">
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
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3 <repeat name="rep_factorName" title="Factor" min="1">
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
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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"
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
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5 help="Only letters, numbers and underscores will be retained in this field">
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
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6 <sanitizer>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
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7 <valid initial="string.letters,string.digits"><add value="_" /></valid>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
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8 </sanitizer>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
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9 </param>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
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10 <repeat name="rep_factorLevel" title="Factor level" min="2" default="2">
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
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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'"
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
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12 help="Only letters, numbers and underscores will be retained in this field">
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
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13 <sanitizer>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
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14 <valid initial="string.letters,string.digits"><add value="_" /></valid>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
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15 </sanitizer>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
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16 </param>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
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17 <yield/>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
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18 </repeat>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
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19 </repeat>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
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20 </xml>
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21 <xml name="requirements">
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
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22 <requirements>
28
7ff33c2d525b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit a3c52d23c261ef0bd0cc4c3d59900e108ca3f67e"
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23 <requirement type="package" version="1.34.0">bioconductor-deseq2</requirement>
27
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
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24 <!-- Optional dependency of tximport, needed to import kallisto results https://github.com/galaxyproject/usegalaxy-playbook/issues/161 -->
28
7ff33c2d525b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit a3c52d23c261ef0bd0cc4c3d59900e108ca3f67e"
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25 <requirement type="package" version="2.38.0">bioconductor-rhdf5</requirement>
7ff33c2d525b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit a3c52d23c261ef0bd0cc4c3d59900e108ca3f67e"
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26 <requirement type="package" version="1.22.0">bioconductor-tximport</requirement>
7ff33c2d525b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit a3c52d23c261ef0bd0cc4c3d59900e108ca3f67e"
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27 <requirement type="package" version="1.46.1">bioconductor-genomicfeatures</requirement>
7ff33c2d525b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit a3c52d23c261ef0bd0cc4c3d59900e108ca3f67e"
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28 <requirement type="package" version="1.20.3">r-getopt</requirement>
7ff33c2d525b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit a3c52d23c261ef0bd0cc4c3d59900e108ca3f67e"
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29 <requirement type="package" version="0.9.1">r-ggrepel</requirement>
7ff33c2d525b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit a3c52d23c261ef0bd0cc4c3d59900e108ca3f67e"
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30 <requirement type="package" version="3.1.1">r-gplots</requirement>
7ff33c2d525b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit a3c52d23c261ef0bd0cc4c3d59900e108ca3f67e"
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31 <requirement type="package" version="1.0.12">r-pheatmap</requirement>
27
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32 <requirement type="package" version="0.2.20">r-rjson</requirement>
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
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33 </requirements>
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
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34 </xml>
28
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35 <token name="@TOOL_VERSION@">2.11.40.7</token>
7ff33c2d525b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit a3c52d23c261ef0bd0cc4c3d59900e108ca3f67e"
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36 <token name="@SUFFIX_VERSION@">0</token>
27
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
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37 <xml name="edam_ontology">
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
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38 <edam_topics>
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
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39 <edam_topic>topic_3308</edam_topic>
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
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40 </edam_topics>
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
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41 <edam_operations>
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
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42 <edam_operation>operation_3800</edam_operation>
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
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43 </edam_operations>
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
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44 </xml>
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
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45 <xml name="citations">
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
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46 <citations>
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
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47 <citation type="doi">10.1186/s13059-014-0550-8</citation>
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
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48 </citations>
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
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49 </xml>
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
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50 <xml name="xrefs">
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
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51 <xrefs>
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
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52 <xref type='bio.tools'>DESeq2</xref>
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
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53 </xrefs>
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
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54 </xml>
22
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
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55 </macros>