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1 <tool id="plotheatmap" name="plotheatmap" version="1.0">
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2 <description>Make a count matrix for edgeR</description>
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3 <stdio>
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4 <exit_code range="1:" />
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5 </stdio>
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6 <command>
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7 <![CDATA[
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8 $__tool_directory__/tools/script.R $count_matrix $stats_matrix $log_fc $log_cpm $pvalue $fdr > $rscript_log 2> $rerror_log
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9
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10
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11
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12 ]]>
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13 </command>
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14 <inputs>
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15 <param name="count_matrix" type="data" format="data" label=""/>
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16 <param name="stats_matrix" type="data" format="data" label=""/>
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17 <param name="log_fc" type="float" value="0.5" label=""/>
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18 <param name="log_cpm" type="float" value="0.5" label=""/>
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19 <param name="pvalue" type="float" value="0.5" label=""/>
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20 <param name="fdr" type="float" value="0.5" label=""/>
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21
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22 </inputs>
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23 <outputs>
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24 <!-- <data name="output" format="data" /> -->
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25 <data format="pdf" name="haetamappdf" from_work_dir="heatmap.pdf" >
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26 <filter>(outftype == 'pdf')</filter>
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27 </data>
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28 <data name="rscript_log" format="data" />
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29 <data name="rerror_log" format="data" />
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30 </outputs>
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31 <tests>
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32
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33 <test>
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34 <param name="count_matrix" value="count.matrix"/>
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35 <param name="stats_matrix" value="stats.data"/>
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36 <param name="log_fc" value="1"/>
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37 <param name="log_cpm" value="2"/>
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38 <param name="pvalue" value="0.05"/>
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39 <param name="fdr" value="0.1"/>
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40 <!-- <output name="output" file="done"/> -->
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41 <output name="haetamappdf" file="heatmap.pdf" ftype="pdf" compare="sim_size" />
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42 <output name="rscript_log" file="rscript.log"/>
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43 <output name="rerror_log" file="rerror.log"/>
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44
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45 </test>
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46
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47 </tests>
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48 <help>
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49 <![CDATA[
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50
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51 tutaj cos bedzie
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52 ]]>
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53 </help>
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54 <citations>
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55
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56 </citations>
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57 </tool> |
