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annotate gene_fraction/src/gene_fraction.xml @ 0:f95150c37d38 draft default tip

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planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
author chrisd
date Sun, 21 Feb 2016 23:31:55 -0500
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0
f95150c37d38 planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
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1 <tool id="gene_fraction" name="Coverage sampler" version="0.1.0">
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2 <requirements>
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3 </requirements>
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4 <stdio>
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5 <exit_code range="1:" />
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6 </stdio>
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7 <command><![CDATA[
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8 csa
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9 -amr_fp $input1
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10 -sam_fp $input2
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11 -min $min
f95150c37d38 planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
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12 -max $max
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13 -skip $skip
f95150c37d38 planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
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14 -t $threshold
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15 -samples $samples
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16 -out_fp $output1
f95150c37d38 planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
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17 ]]></command>
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18 <inputs>
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19 <param type="data" name="input1" format="fasta" />
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20 <param type="data" name="input2" format="sam" />
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21 <param name="min" type="integer" label="Minimum sample value"
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22 value="1" min="1" max="100" help="(-min)" />
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23 <param name="max" type="integer" label="Maximum sample value"
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24 value="1" min="1" max="100" help="(-max)" />
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25 <param name="skip" type="integer" label="Amount of levels to skip"
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26 value="1" min="1" max="100" help="(-skip)" />
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27 <param name="threshold" type="integer" label="Gene fraction threshold"
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28 value="1" min="1" max="100" help="(-t)" />
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29 <param name="samples" type="integer" label="Amount of samples per level"
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30 value="1" min="1" max="100" help="(-samples)" />
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31 </inputs>
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32 <outputs>
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33 <data name="output1" format="tabular" />
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34 </outputs>
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35 <help><![CDATA[
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36
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37 Program: Coverage Sampler
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38 Contact: Chris Dean <cdean11@rams.colostate.edu
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39
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40 Usage: csa [options]
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41
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42 Options:
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43
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44 -amr_fp amr database path
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45 -sam_fp sam file path
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46 -min starting level
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47 -max ending level
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48 -skip amount of levels to skip
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49 -t gene fraction threshold
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50 -samples amount of samples per level
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51 -d directory parsing
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52 -bam bam file parsing
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53 -out_fp output file path
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54
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55
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56 ]]></help>
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57 </tool>