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1 <tool id="dotplot_runner" name="Dotplot ProHits">
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2 <description></description>
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3 <command interpreter="python">dotplot_runner.py $saint_file $FDR1 $FDR2 $spec_max $dotplot $heatmap $estimated $stats \$INSTALL_RUN_PATH/</command>
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4 <requirements>
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5 <requirement type="set_environment">INSTALL_RUN_PATH</requirement>
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6 </requirements>
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7 <inputs>
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8 <param format="txt" name="saint_file" type="data" label="SAINT Output"/>
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9 <param type="float" name="FDR1" label="False Discovery Rate 1" value="0.01"/>
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10 <param type="float" name="FDR2" label="False Discovery Rate 2" value="0.025"/>
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11 <param type="integer" name="spec_max" label="Maximum spectral count" value="50"/>
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12 </inputs>
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13 <outputs>
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14 <data format="pdf" name="dotplot" label="DotPlot" />
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15 <data format="pdf" name="heatmap" label="Heatmap" />
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16 <data format="pdf" name="estimated" label="Estimated" />
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17 <data format="pdf" name="stats" label="Stats" />
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18 </outputs>
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19 <stdio>
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20 <regex match="Error|error"
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21 source="stdout"
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22 level="fatal"
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23 description="Unknown error"/>
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24 <regex match="Error|error"
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25 source="stderr"
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26 level="fatal"
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27 description="Unknown error"/>
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28 <regex match="Error: bad bait"
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29 source="stdout"
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30 level="fatal"
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31 description="Error: bad bait"/>
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32 </stdio>
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33
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34 <tests>
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35 <test>
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36 <param name="input" value="fa_gc_content_input.fa"/>
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37 <output name="out_file1" file="fa_gc_content_output.txt"/>
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38 </test>
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39 </tests>
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40 <help>
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41 </help>
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42 </tool> |
