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1 <tool id="fastaptamer_enrich_1_0_2" name="FASTAptamer-Enrich" version="1.0.2">
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2
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3 <description>Calculate fold-enrichment of each sequence across populations</description>
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4
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5 <version_command>fastaptamer_enrich -v</version_command>
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6
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7 <command interpreter="perl">fastaptamer_enrich -x $input_x -y $input_y -o $output -f $filter
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8 # if str(input_z) != ''
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9 -z "${input_z}"
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10 # end if
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11 </command>
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12
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13 <inputs>
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14 <param name="input_x" type="data" format="fasta" label="Input file X" help="Must use FASTA output from FASTAptamer-Count or FASTAptamer-Cluster"></param>
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15 <param name="input_y" type="data" format="fasta" label="Input file Y" help="Must use FASTA output from FASTAptamer-Count or FASTAptamer-Cluster"></param>
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16 <param name="input_z" type="data" format="fasta" optional="true" label="Input file Z" help="Must use FASTA output from FASTAptamer-Count or FASTAptamer-Cluster"></param>
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17 <param name="filter" type="float" optional="true" value="0" label="RPM Threshold Filter" help="Sequences with an aggregate RPM (across all populations) less than supplied value will be excluded from analysis"></param>
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18 </inputs>
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19
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20 <outputs>
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21 <data name="output" format="tabular" label="FASTAptamer-Enrich output file"></data>
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22 </outputs>
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23
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24 <help>
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25
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26 .. class:: warningmark
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27
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28 FASTAptamer-Enrich requires FASTA formatted input files generated by FASTAptamer-Count or FASTAptamer-Cluster.
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29
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30 ------
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31
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32 **FASTAptamer-Enrich** rapidly calculates "fold-enrichment" values for each sequence across two or three input files. Output is provided as a tab-delimited file and is formatted to include sequence composition, length, rank, reads, reads per million (RPM), cluster information (if available) and enrichment values for each sequence.
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33
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34 An optional threshold filter can be applied to exclude sequences with total reads per million (across all input populations) less than the number supplied.
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35
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36 Enrichment is calculated by dividing reads per million of y/x (and z/y and z/x, if a third input file is specified).
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37
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38 ------
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39
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40 .. image::
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41 http://burkelab.missouri.edu/images/fastaptamer-logo-xs.png
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42 :height: 98
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43 :width: 300
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44
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45 For more information on FASTAptamer, visit our website_.
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46
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47 FASTAptamer is distributed under a GNU GPL v3.0 license. For complete license click here_.
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48
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49 .. _here: http://burkelab.missouri.edu/fastaptamer/LICENSE.txt
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50 .. _website: http://burkelab.missouri.edu/fastaptamer.html
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51
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52 </help>
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53
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54 <citations>
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55 <citation type="doi">doi:10.1038/mtna.2015.4</citation>
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56 </citations>
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57
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58 </tool>
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