Mercurial > repos > mvdbeek > damidseq_findpeaks

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author mvdbeek
date Thu, 14 Jun 2018 11:14:52 -0400
parents c851dab0d2d9
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be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324
mvdbeek
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1 <tool id="damidseq_find_peaks" name="damidseq find peaks" version="0.1.3">
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2 <description>Simple FDR random permutation peak caller</description>
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324
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3 <requirements>
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4 <requirement type="package" version="5.26">perl</requirement>
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5 </requirements>
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6 <version_command><![CDATA[perl '$__tool_directory__/find_peaks' --help 2>&1| grep find_peaks]]></version_command>
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7 <command detect_errors="aggressive"><![CDATA[
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8 perl '$__tool_directory__/find_peaks'
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9 --fdr=$fdr
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10 --frac=$frac
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11 --min_count=$min_count
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12 --min_quant=$min_quant
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324
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13 --n=$n
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14 --step=$step
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15 --unified_peaks=$unified_peaks
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16 '$input_file' 2>&1 | LC_ALL=C sed -e 's/[^A-Za-z0-9._-]/ /g' > log.txt &&
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17 mv peak_analysis*/*.gff peaks.gff &&
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18 cat peak_analysis*/*data >> log.txt
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19 ]]></command>
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324
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20 <inputs>
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21 <param name="input_file" type="data" format="gff,bed,bedgraph" label="Select dam-fusion/dam ratio files" help="You can use damidseq_core to produce this file."/>
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324
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22 <param argument="--fdr" type="float" min="0" max="1" value="0.01" label="Set the False Discovery Rate (FDR)"/>
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23 <param argument="--frac" type="integer" min="0" value="0" label="Number of random fragments to consider per iteration"/>
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24 <param argument="--min_count" type="integer" min="1" value="2" label="Minimum number of fragments to consider as a peak"/>
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25 <param argument="--min_quant" type="float" min="0" max="1" value="0.95" label="Minimum quantile for considering peaks"/>
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324
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26 <param argument="--n" type="integer" min="1" value="100" label="Number of iterations"/>
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324
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27 <param argument="--step" type="float" min="0" max="1" value="0.01" label="Stepping for quantiles"/>
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324
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28 <param argument="--unified_peaks" type="select" label="Set the False Discovery Rate (FDR)">
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324
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29 <option value="max">call maximum overlap as peak</option>
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324
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30 <option value="min">call minimum overlap as peak</option>
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324
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31 </param>
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32 </inputs>
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33 <outputs>
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34 <data name="peaks" format="gff3" from_work_dir="peaks.gff" label="${tool.name} GFF on ${on_string}"/>
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35 <data name="logs" format="txt" hidden="true" from_work_dir="log.txt" label="${tool.name} logs on ${on_string}"/>
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324
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36 </outputs>
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37 <tests>
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38 <test>
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39 <param name="input_file" value="hp1.bed" ftype="bed"/>
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40 <param name="min_count" value="1"/>
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41 <param name="fdr" value="0.1"/>
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42 <output name="peaks" value="peaks.gff"/>
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43 </test>
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44 </tests>
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45 <help><![CDATA[
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46
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47 Options:
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48 --fdr False discovery rate value
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49 [Current value: 0.01]
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50 --frac Number of random fragments to consider per iteration
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51 --min_count Minimum number of fragments to consider as a peak
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52 [Current value: 2]
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53 --min_quant Minimum quantile for considering peaks
be830200e987 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_findpeaks commit 87c99a97cb2ce55640afdd2e55c8b3ae5ad99324
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54 [Current value: 0.95]
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55 --n Number of iterations
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56 [Current value: 100]
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57 --step Stepping for quantiles
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58 [Current value: 0.01]
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59 --unified_peaks Method for calling peak overlaps (two options):
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60 'min': call minimum overlapping peak area
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61 'max': call maximum overlap as peak
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62 [Current value: max]
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63
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64 ]]></help>
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65 <citations>
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66 <citation type="doi">10.1093/bioinformatics/btv386</citation>
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67 </citations>
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68 </tool>