Mercurial > repos > chrisd > coverage_sampler

annotate gene_fraction.xml @ 0:72901052a829 draft

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planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit 3a1ac4b58e77fb6fba076c679ee7e317a79d1f8b
author chrisd
date Wed, 23 Mar 2016 17:54:53 -0400
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72901052a829 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit 3a1ac4b58e77fb6fba076c679ee7e317a79d1f8b
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1 <tool id="gene_fraction" name="Coverage Sampler" version="0.1.0">
72901052a829 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit 3a1ac4b58e77fb6fba076c679ee7e317a79d1f8b
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2 <requirements>
72901052a829 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit 3a1ac4b58e77fb6fba076c679ee7e317a79d1f8b
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3 <requirement type="package" version="0.1">csa</requirement>
72901052a829 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit 3a1ac4b58e77fb6fba076c679ee7e317a79d1f8b
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4 </requirements>
72901052a829 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit 3a1ac4b58e77fb6fba076c679ee7e317a79d1f8b
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5 <stdio>
72901052a829 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit 3a1ac4b58e77fb6fba076c679ee7e317a79d1f8b
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6 <exit_code range="1:" />
72901052a829 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit 3a1ac4b58e77fb6fba076c679ee7e317a79d1f8b
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7 </stdio>
72901052a829 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit 3a1ac4b58e77fb6fba076c679ee7e317a79d1f8b
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8 <description>Calculates the amount of a gene that is covered from a sample of reads</description>
72901052a829 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit 3a1ac4b58e77fb6fba076c679ee7e317a79d1f8b
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9 <command><![CDATA[
72901052a829 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit 3a1ac4b58e77fb6fba076c679ee7e317a79d1f8b
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10 csa
72901052a829 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit 3a1ac4b58e77fb6fba076c679ee7e317a79d1f8b
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11 -amr_fp $input1
72901052a829 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit 3a1ac4b58e77fb6fba076c679ee7e317a79d1f8b
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12 -sam_fp $input2
72901052a829 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit 3a1ac4b58e77fb6fba076c679ee7e317a79d1f8b
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13 -min $min
72901052a829 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit 3a1ac4b58e77fb6fba076c679ee7e317a79d1f8b
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14 -max $max
72901052a829 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit 3a1ac4b58e77fb6fba076c679ee7e317a79d1f8b
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15 -t $threshold
72901052a829 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit 3a1ac4b58e77fb6fba076c679ee7e317a79d1f8b
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16 -skip $skip
72901052a829 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit 3a1ac4b58e77fb6fba076c679ee7e317a79d1f8b
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17 -samples $samples
72901052a829 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit 3a1ac4b58e77fb6fba076c679ee7e317a79d1f8b
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18 -out_fp $output1
72901052a829 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit 3a1ac4b58e77fb6fba076c679ee7e317a79d1f8b
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19 ]]></command>
72901052a829 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit 3a1ac4b58e77fb6fba076c679ee7e317a79d1f8b
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20 <inputs>
72901052a829 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit 3a1ac4b58e77fb6fba076c679ee7e317a79d1f8b
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21 <param type="data" name="input1" format="fasta" label="Reference sequence" />
72901052a829 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit 3a1ac4b58e77fb6fba076c679ee7e317a79d1f8b
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22 <param type="data" name="input2" format="sam" label="SAM file" />
72901052a829 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit 3a1ac4b58e77fb6fba076c679ee7e317a79d1f8b
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23 <param name="min" type="integer" label="Starting sample level"
72901052a829 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit 3a1ac4b58e77fb6fba076c679ee7e317a79d1f8b
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24 value="1" min="1" max="100" help="(-min)" />
72901052a829 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit 3a1ac4b58e77fb6fba076c679ee7e317a79d1f8b
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25 <param name="max" type="integer" label="Ending sample level"
72901052a829 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit 3a1ac4b58e77fb6fba076c679ee7e317a79d1f8b
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26 value="1" min="1" max="100" help="(-max)" />
72901052a829 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit 3a1ac4b58e77fb6fba076c679ee7e317a79d1f8b
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27 <param name="threshold" type="integer" label="Gene threshold"
72901052a829 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit 3a1ac4b58e77fb6fba076c679ee7e317a79d1f8b
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28 value="0" min="0" max="100" help="(-t)" />
72901052a829 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit 3a1ac4b58e77fb6fba076c679ee7e317a79d1f8b
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29 <param name="skip" type="integer" label="Amount of levels to skip"
72901052a829 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit 3a1ac4b58e77fb6fba076c679ee7e317a79d1f8b
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30 value="1" min="1" max="100" help="(-skip)" />
72901052a829 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit 3a1ac4b58e77fb6fba076c679ee7e317a79d1f8b
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31 <param name="samples" type="integer" label="Amount of samples per level"
72901052a829 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit 3a1ac4b58e77fb6fba076c679ee7e317a79d1f8b
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32 value="1" min="1" max="100" help="(-samples)" />
72901052a829 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit 3a1ac4b58e77fb6fba076c679ee7e317a79d1f8b
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33 </inputs>
72901052a829 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit 3a1ac4b58e77fb6fba076c679ee7e317a79d1f8b
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34 <outputs>
72901052a829 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit 3a1ac4b58e77fb6fba076c679ee7e317a79d1f8b
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35 <data name="output1" format="tabular" />
72901052a829 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit 3a1ac4b58e77fb6fba076c679ee7e317a79d1f8b
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36 </outputs>
72901052a829 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit 3a1ac4b58e77fb6fba076c679ee7e317a79d1f8b
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37 <tests>
72901052a829 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit 3a1ac4b58e77fb6fba076c679ee7e317a79d1f8b
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38 <test>
72901052a829 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit 3a1ac4b58e77fb6fba076c679ee7e317a79d1f8b
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39 <param name="input1" value="ref.fa"/>
72901052a829 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit 3a1ac4b58e77fb6fba076c679ee7e317a79d1f8b
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40 <param name="input2" value="test.sam"/>
72901052a829 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit 3a1ac4b58e77fb6fba076c679ee7e317a79d1f8b
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41 <output name="outfil1" file="out.txt"/>
72901052a829 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit 3a1ac4b58e77fb6fba076c679ee7e317a79d1f8b
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42 </test>
72901052a829 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit 3a1ac4b58e77fb6fba076c679ee7e317a79d1f8b
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43 </tests>
72901052a829 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit 3a1ac4b58e77fb6fba076c679ee7e317a79d1f8b
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44 <help><![CDATA[
72901052a829 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit 3a1ac4b58e77fb6fba076c679ee7e317a79d1f8b
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45 This program takes iterative samples from a SAM file with the goal of identifying the amount of a gene that is covered by a sample of reads.
72901052a829 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit 3a1ac4b58e77fb6fba076c679ee7e317a79d1f8b
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46
72901052a829 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit 3a1ac4b58e77fb6fba076c679ee7e317a79d1f8b
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47 Program: Coverage Sampler
72901052a829 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit 3a1ac4b58e77fb6fba076c679ee7e317a79d1f8b
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48
72901052a829 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit 3a1ac4b58e77fb6fba076c679ee7e317a79d1f8b
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49 Contact: Chris Dean <cdean11@rams.colostate.edu>
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50
72901052a829 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit 3a1ac4b58e77fb6fba076c679ee7e317a79d1f8b
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51 Usage: csa [options]
72901052a829 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit 3a1ac4b58e77fb6fba076c679ee7e317a79d1f8b
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52
72901052a829 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit 3a1ac4b58e77fb6fba076c679ee7e317a79d1f8b
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53 Options:
72901052a829 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit 3a1ac4b58e77fb6fba076c679ee7e317a79d1f8b
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54 -amr_fp amr database path
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55 -sam_fp sam file path
72901052a829 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit 3a1ac4b58e77fb6fba076c679ee7e317a79d1f8b
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56 -min starting level
72901052a829 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit 3a1ac4b58e77fb6fba076c679ee7e317a79d1f8b
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57 -max ending level
72901052a829 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit 3a1ac4b58e77fb6fba076c679ee7e317a79d1f8b
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58 -skip amount of levels to skip
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59 -t gene fraction threshold
72901052a829 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit 3a1ac4b58e77fb6fba076c679ee7e317a79d1f8b
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60 -samples amount of samples per level
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61 -out_fp output file path
72901052a829 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit 3a1ac4b58e77fb6fba076c679ee7e317a79d1f8b
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62 ]]></help>
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63 </tool>