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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit ec66b5b0627e7cf15b6e67e90d82ba8e0743b761
author galaxyp
date Mon, 18 Mar 2024 12:35:03 +0000
parents a1daafbf5233
children
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2ee495a1fc84 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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1 <macros>
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a1daafbf5233 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 12499da76192d2a61bfd475bc6e21dbe6f23643a"
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2 <token name="@TOOL_VERSION@">2.0.2</token>
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deaf035bbe9f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 9204193c3442e427c149b90f15fe3a56fc9802e9"
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3 <token name="@VERSION_SUFFIX@">0</token>
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35cc7ca0bdc7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit ec66b5b0627e7cf15b6e67e90d82ba8e0743b761
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4 <xml name="xrefs">
35cc7ca0bdc7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit ec66b5b0627e7cf15b6e67e90d82ba8e0743b761
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5 <xrefs>
35cc7ca0bdc7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit ec66b5b0627e7cf15b6e67e90d82ba8e0743b761
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6 <xref type="bio.tools">metaQuantome</xref>
35cc7ca0bdc7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit ec66b5b0627e7cf15b6e67e90d82ba8e0743b761
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7 </xrefs>
35cc7ca0bdc7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit ec66b5b0627e7cf15b6e67e90d82ba8e0743b761
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8 </xml>
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2ee495a1fc84 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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9 <xml name="requirements">
2ee495a1fc84 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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10 <requirements>
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35cc7ca0bdc7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit ec66b5b0627e7cf15b6e67e90d82ba8e0743b761
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11 <requirement type="package" version="@TOOL_VERSION@">metaquantome</requirement>
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2ee495a1fc84 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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12 <yield/>
2ee495a1fc84 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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13 </requirements>
2ee495a1fc84 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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14 </xml>
2ee495a1fc84 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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15 <xml name="db">
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35cc7ca0bdc7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit ec66b5b0627e7cf15b6e67e90d82ba8e0743b761
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16 <param argument="db_tar" type="data" label="Database Archive File"/>
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17 </xml>
2ee495a1fc84 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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18 <xml name="ONTOLOGY_ARGS">
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19 <conditional name="ontology_args">
35cc7ca0bdc7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit ec66b5b0627e7cf15b6e67e90d82ba8e0743b761
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20 <param name="ontology" type="select" label="Ontology">
35cc7ca0bdc7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit ec66b5b0627e7cf15b6e67e90d82ba8e0743b761
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21 <option value="go">Gene Ontology (GO terms)</option>
35cc7ca0bdc7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit ec66b5b0627e7cf15b6e67e90d82ba8e0743b761
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22 <option value="ec">Enzyme Commission (EC) numbers</option>
35cc7ca0bdc7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit ec66b5b0627e7cf15b6e67e90d82ba8e0743b761
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23 <option value="cog">Clusters of Orthologous Groups (COG categories)</option>
35cc7ca0bdc7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit ec66b5b0627e7cf15b6e67e90d82ba8e0743b761
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24 </param>
35cc7ca0bdc7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit ec66b5b0627e7cf15b6e67e90d82ba8e0743b761
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25 <when value="go">
35cc7ca0bdc7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit ec66b5b0627e7cf15b6e67e90d82ba8e0743b761
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26 <param argument="--slim_down" type="boolean" label="Use slim GO"/>
35cc7ca0bdc7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit ec66b5b0627e7cf15b6e67e90d82ba8e0743b761
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27 </when>
35cc7ca0bdc7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit ec66b5b0627e7cf15b6e67e90d82ba8e0743b761
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28 <when value="ec">
35cc7ca0bdc7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit ec66b5b0627e7cf15b6e67e90d82ba8e0743b761
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29 <!-- do nothing -->
35cc7ca0bdc7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit ec66b5b0627e7cf15b6e67e90d82ba8e0743b761
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30 </when>
35cc7ca0bdc7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit ec66b5b0627e7cf15b6e67e90d82ba8e0743b761
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31 <when value="cog">
35cc7ca0bdc7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit ec66b5b0627e7cf15b6e67e90d82ba8e0743b761
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32 <!-- do nothing -->
35cc7ca0bdc7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit ec66b5b0627e7cf15b6e67e90d82ba8e0743b761
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33 </when>
35cc7ca0bdc7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit ec66b5b0627e7cf15b6e67e90d82ba8e0743b761
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34 </conditional>
0
2ee495a1fc84 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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35 </xml>
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36 <token name="@COMMON_PARAMS@"><![CDATA[
2ee495a1fc84 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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37 --samps '$samps'
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38 --mode '$mode_args.mode'
2ee495a1fc84 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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39 #if $mode_args.mode == 'f'
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40 --ontology='$mode_args.ontology_args.ontology'
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41 #end if
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42 #if $mode_args.mode == 'ft'
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43 --ontology='$mode_args.ontology_args.ontology'
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44 #end if
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45 ]]>
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46 </token>
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47 <xml name="SAMPS">
6
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48 <param name="samps" type="data" format="tabular" label="Samples file" help="must be created by 'metaQuantome: create samples file'"/>
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49 </xml>
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50 <xml name="citations">
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51 <citations>
6
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52 <citation type="doi">10.1021/ACS.JPROTEOME.0C00960</citation>
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53 <yield/>
0
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54 </citations>
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55 </xml>
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56 </macros>