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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit b'1f42c4a241d1a9baaadcdc58d22701bd55700537\n'-dirty
author dave
date Thu, 07 Jun 2018 15:15:14 -0400
parents 962b0ae5939f
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962b0ae5939f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit b'1f42c4a241d1a9baaadcdc58d22701bd55700537\n'-dirty
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1 <?xml version="1.0"?>
962b0ae5939f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit b'1f42c4a241d1a9baaadcdc58d22701bd55700537\n'-dirty
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2 <macros>
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3 <macro name="replicates_checkbox">
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4 <param name="replicates" type="boolean" truevalue="--replicates" falsevalue="" checked="True" label="Replicates?"/>
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5 </macro>
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6 <macro name="log10_checkbox">
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7 <param name="log10" type="boolean" truevalue="--log10" falsevalue="" checked="True" label="Apply log10 transformation on FPKM values?"/>
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8 </macro>
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9 <macro name="xy_selector">
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10 <param name="x" type="select" label="Sample name for x axis">
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11 <options from_dataset="input_database" />
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12 </param>
962b0ae5939f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit b'1f42c4a241d1a9baaadcdc58d22701bd55700537\n'-dirty
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13 <param name="y" type="select" label="Sample name for y axis">
962b0ae5939f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit b'1f42c4a241d1a9baaadcdc58d22701bd55700537\n'-dirty
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14 <options>
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15 <filter type="data_meta" ref="input_database" key="samples" />
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16 </options>
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17 </param>
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18 </macro>
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19 <macro name="genes_selector">
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20 <repeat name="genes" title="Genes" min="2">
962b0ae5939f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit b'1f42c4a241d1a9baaadcdc58d22701bd55700537\n'-dirty
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21 <!-- Cannot create a heatmap for less than two genes -->
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22 <param name="gene_id" type="select" label="Gene ID">
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23 <options>
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24 <filter type="data_meta" ref="input_database" key="genes" />
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25 </options>
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26 </param>
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27 </repeat>
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28 </macro>
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29 <macro name="features_selector">
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30 <param name="features" type="select" label="Expression levels to plot?">
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31 <option value="gene" selected="true">Genes</option>
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32 <option value="isoforms">Isoforms</option>
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33 <option value="tss">TSS</option>
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34 <option value="cds">CDS</option>
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35 </param>
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36 </macro>
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37 <macro name="multiple_genes_conditional">
962b0ae5939f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit b'1f42c4a241d1a9baaadcdc58d22701bd55700537\n'-dirty
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38 <conditional name="multiple_genes">
962b0ae5939f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit b'1f42c4a241d1a9baaadcdc58d22701bd55700537\n'-dirty
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39 <param name="multiple_genes_selector" type="select" label="Limit plot to genes">
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40 <option value="no" selected="true">Do not limit</option>
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41 <option value="yes">Select genes</option>
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42 </param>
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43 <when value="yes">
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44 <expand macro="features_selector" />
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45 <expand macro="genes_selector" />
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46 </when>
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47 <when value="no" />
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48 </conditional>
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49 </macro>
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50 </macros>