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annotate cummeRbund_macros.xml @ 0:587c425b4e76 draft

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Initial commit with version 1.0.0 of the cummeRbund wrapper.
author devteam
date Tue, 23 Dec 2014 15:58:27 -0500
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children 78fcfc04fcfe
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587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
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1 <?xml version="1.0"?>
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2 <macros>
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3 <macro name="stdio">
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4 <stdio>
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5 <exit_code range="1:" />
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6 <exit_code range=":-1" />
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7 <regex match="Error:" />
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8 <regex match="Exception:" />
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9 </stdio>
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10 </macro>
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11 <macro name="replicates_checkbox">
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12 <param name="replicates" type="boolean" truevalue="--replicates" falsevalue="" checked="True" label="Replicates?"/>
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13 </macro>
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14 <macro name="log10_checkbox">
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15 <param name="log10" type="boolean" truevalue="--log10" falsevalue="" checked="True" label="Apply log10 transformation on FPKM values?"/>
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16 </macro>
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17 <macro name="xy_selector">
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18 <param name="x" type="select" label="Sample name for x axis" dynamic_options="get_samples(input_database.dataset.file_name)" />
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19 <param name="y" type="select" label="Sample name for y axis" dynamic_options="get_samples(input_database.dataset.file_name)" />
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20 </macro>
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21 <macro name="genes_selector">
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22 <repeat name="genes" title="Genes">
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23 <param name="gene_id" type="select" label="Gene ID" dynamic_options="get_genes(input_database.dataset.file_name)" />
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24 </repeat>
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25 </macro>
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26 <macro name="features_selector">
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27 <param name="features" type="select" label="Expression levels to plot?">
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28 <option value="gene" selected="true">Genes</option>
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29 <option value="isoforms">Isoforms</option>
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30 <option value="tss">TSS</option>
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31 <option value="cds">CDS</option>
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32 </param>
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33 </macro>
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34 <macro name="multiple_genes_conditional">
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35 <conditional name="multiple_genes">
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36 <param name="multiple_genes_selector" type="select" label="Limit plot to genes">
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37 <option value="no" selected="true">Do not limit</option>
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38 <option value="yes">Select genes</option>
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39 </param>
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40 <when value="yes">
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41 <expand macro="features_selector" />
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42 <expand macro="genes_selector" />
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43 </when>
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44 <when value="no" />
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45 </conditional>
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46 </macro>
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47 </macros>