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annotate macros.xml @ 1:0d54f161b0d5 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 74c403057350af3dde81aea154414a0d6a84d2a3"
author galaxyp
date Wed, 23 Sep 2020 17:01:00 +0000
parents 2bfd8e0a138d
children bbf9637d83cc
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2bfd8e0a138d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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1 <macros>
1
0d54f161b0d5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 74c403057350af3dde81aea154414a0d6a84d2a3"
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2 <token name="@VERSION@">2.0.0</token>
0d54f161b0d5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 74c403057350af3dde81aea154414a0d6a84d2a3"
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3 <token name="@GVERSION@">2.0.0-0</token>
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2bfd8e0a138d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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4 <xml name="requirements">
2bfd8e0a138d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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5 <requirements>
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6 <requirement type="package" version="@VERSION@">metaquantome</requirement>
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7 <yield/>
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8 </requirements>
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9 </xml>
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10 <xml name="db">
2bfd8e0a138d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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11 <param argument="db_tar" type="data" label="Database Archive File"/>
2bfd8e0a138d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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12 </xml>
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13 <xml name="ONTOLOGY_ARGS">
2bfd8e0a138d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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14 <conditional name="ontology_args">
2bfd8e0a138d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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15 <param name="ontology" type="select" label="Ontology">
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16 <option value="go">Gene Ontology (GO terms)</option>
2bfd8e0a138d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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17 <option value="ec">Enzyme Commission (EC) numbers</option>
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18 <option value="cog">Clusters of Orthologous Groups (COG categories)</option>
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19 </param>
2bfd8e0a138d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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20 <when value="go">
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21 <param argument="--slim_down" type="boolean" label="Use slim GO"/>
2bfd8e0a138d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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22 </when>
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23 <when value="ec">
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24 <!-- do nothing -->
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25 </when>
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26 <when value="cog">
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27 <!-- do nothing -->
2bfd8e0a138d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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28 </when>
2bfd8e0a138d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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29 </conditional>
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30 </xml>
2bfd8e0a138d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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31 <token name="@COMMON_PARAMS@"><![CDATA[
2bfd8e0a138d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a
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32 --samps '$samps'
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33 --mode '$mode_args.mode'
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34 #if $mode_args.mode == 'f'
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35 --ontology='$mode_args.ontology_args.ontology'
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36 #end if
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37 #if $mode_args.mode == 'ft'
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38 --ontology='$mode_args.ontology_args.ontology'
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39 #end if
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40 ]]>
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41 </token>
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42 <xml name="SAMPS">
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43 <param name="samps" type="data" format="tabular" label="Samples file"
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44 help="must be created by 'metaQuantome: create samples file'"/>
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45 </xml>
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46 <xml name="citations">
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47 <citations>
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48 <yield />
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49 </citations>
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50 </xml>
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51 </macros>