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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/zerone commit 537bbf2e3ae9e7dcc619354911caf774338d7a0e
author iuc
date Thu, 06 Sep 2018 09:34:29 -0400
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886248a1cc7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/zerone commit 537bbf2e3ae9e7dcc619354911caf774338d7a0e
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1 <tool id="zerone" name="zerone" version="1.0">
886248a1cc7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/zerone commit 537bbf2e3ae9e7dcc619354911caf774338d7a0e
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2 <requirements>
886248a1cc7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/zerone commit 537bbf2e3ae9e7dcc619354911caf774338d7a0e
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3 <requirement type="package" version="1.0">zerone</requirement>
886248a1cc7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/zerone commit 537bbf2e3ae9e7dcc619354911caf774338d7a0e
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4 </requirements>
886248a1cc7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/zerone commit 537bbf2e3ae9e7dcc619354911caf774338d7a0e
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5 <version_command>zerone --version</version_command>
886248a1cc7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/zerone commit 537bbf2e3ae9e7dcc619354911caf774338d7a0e
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6 <command detect_errors="exit_code"><![CDATA[
886248a1cc7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/zerone commit 537bbf2e3ae9e7dcc619354911caf774338d7a0e
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7 #set $mock_args = []
886248a1cc7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/zerone commit 537bbf2e3ae9e7dcc619354911caf774338d7a0e
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8 #set $chip_args = []
886248a1cc7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/zerone commit 537bbf2e3ae9e7dcc619354911caf774338d7a0e
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9 #for i,mock_input in enumerate($mock):
886248a1cc7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/zerone commit 537bbf2e3ae9e7dcc619354911caf774338d7a0e
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10 #silent mock_args.append("'mock_%i.%s'" % ($i, $mock_input.ext))
886248a1cc7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/zerone commit 537bbf2e3ae9e7dcc619354911caf774338d7a0e
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11 ln -s '$mock_input' 'mock_${i}.${mock_input.ext}' &&
886248a1cc7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/zerone commit 537bbf2e3ae9e7dcc619354911caf774338d7a0e
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12 #end for
886248a1cc7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/zerone commit 537bbf2e3ae9e7dcc619354911caf774338d7a0e
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13 #for i,chip_input in enumerate($chip):
886248a1cc7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/zerone commit 537bbf2e3ae9e7dcc619354911caf774338d7a0e
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14 #silent chip_args.append("'chip_%i.%s'" % ($i, $mock_input.ext))
886248a1cc7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/zerone commit 537bbf2e3ae9e7dcc619354911caf774338d7a0e
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15 ln -s '$chip_input' 'chip_${i}.${chip_input.ext}' &&
886248a1cc7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/zerone commit 537bbf2e3ae9e7dcc619354911caf774338d7a0e
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16 #end for
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17
886248a1cc7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/zerone commit 537bbf2e3ae9e7dcc619354911caf774338d7a0e
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18 zerone
886248a1cc7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/zerone commit 537bbf2e3ae9e7dcc619354911caf774338d7a0e
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19 --mock #echo ",".join($mock_args)#
886248a1cc7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/zerone commit 537bbf2e3ae9e7dcc619354911caf774338d7a0e
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20 --chip #echo ",".join($chip_args)#
886248a1cc7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/zerone commit 537bbf2e3ae9e7dcc619354911caf774338d7a0e
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21 --window $window
886248a1cc7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/zerone commit 537bbf2e3ae9e7dcc619354911caf774338d7a0e
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22 --quality $quality
886248a1cc7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/zerone commit 537bbf2e3ae9e7dcc619354911caf774338d7a0e
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23 $list_output
886248a1cc7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/zerone commit 537bbf2e3ae9e7dcc619354911caf774338d7a0e
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24 $confidence > '$output'
886248a1cc7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/zerone commit 537bbf2e3ae9e7dcc619354911caf774338d7a0e
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25 ]]></command>
886248a1cc7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/zerone commit 537bbf2e3ae9e7dcc619354911caf774338d7a0e
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26 <inputs>
886248a1cc7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/zerone commit 537bbf2e3ae9e7dcc619354911caf774338d7a0e
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27 <param argument="--chip" type="data" format="sam,bam" multiple="true" label="ChIP alignment file(s)"/>
886248a1cc7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/zerone commit 537bbf2e3ae9e7dcc619354911caf774338d7a0e
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28 <param argument="--mock" type="data" format="sam,bam" multiple="true" label="Control alignment file(s)"/>
886248a1cc7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/zerone commit 537bbf2e3ae9e7dcc619354911caf774338d7a0e
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29 <param argument="--window" type="integer" value="300" min="1" label="Window size in bp (default 300)"/>
886248a1cc7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/zerone commit 537bbf2e3ae9e7dcc619354911caf774338d7a0e
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30 <param argument="--quality" type="integer" value="20" min="1" label="Minimum mapping quality (default 20)"/>
886248a1cc7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/zerone commit 537bbf2e3ae9e7dcc619354911caf774338d7a0e
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31 <param argument="--list_output" type="boolean" truevalue="--list-output" falsevalue="" label="Output list of targets (default table)"/>
886248a1cc7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/zerone commit 537bbf2e3ae9e7dcc619354911caf774338d7a0e
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32 <param argument="--confidence" type="boolean" truevalue="--confidence" falsevalue="" label="Print targets only with higher confidence" help="Restricts intervals accordingly in list output"/>
886248a1cc7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/zerone commit 537bbf2e3ae9e7dcc619354911caf774338d7a0e
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33 </inputs>
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34 <outputs>
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35 <data name="output" format="interval" label="Zerone on $on_string"/>
886248a1cc7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/zerone commit 537bbf2e3ae9e7dcc619354911caf774338d7a0e
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36 </outputs>
886248a1cc7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/zerone commit 537bbf2e3ae9e7dcc619354911caf774338d7a0e
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37 <tests>
886248a1cc7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/zerone commit 537bbf2e3ae9e7dcc619354911caf774338d7a0e
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38 <test>
886248a1cc7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/zerone commit 537bbf2e3ae9e7dcc619354911caf774338d7a0e
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39 <param name="chip" value="ctcf1.bam,ctcf2.bam"/>
886248a1cc7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/zerone commit 537bbf2e3ae9e7dcc619354911caf774338d7a0e
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40 <param name="mock" value="mock.bam"/>
886248a1cc7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/zerone commit 537bbf2e3ae9e7dcc619354911caf774338d7a0e
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41 <output name="output">
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42 <assert_contents>
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43 <has_line line="# QC score: 0.478"/>
886248a1cc7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/zerone commit 537bbf2e3ae9e7dcc619354911caf774338d7a0e
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44 <has_line line="# features: 0.025, 10.000, 0.000, 0.018, 0.924"/>
886248a1cc7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/zerone commit 537bbf2e3ae9e7dcc619354911caf774338d7a0e
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45 <has_line line="# advice: accept discretization."/>
886248a1cc7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/zerone commit 537bbf2e3ae9e7dcc619354911caf774338d7a0e
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46 <has_line_matching expression="chrX\t1\t300\t0\t0\t0\t0\t0.33332"/>
886248a1cc7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/zerone commit 537bbf2e3ae9e7dcc619354911caf774338d7a0e
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47 </assert_contents>
886248a1cc7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/zerone commit 537bbf2e3ae9e7dcc619354911caf774338d7a0e
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48 </output>
886248a1cc7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/zerone commit 537bbf2e3ae9e7dcc619354911caf774338d7a0e
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49 </test>
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50 <test>
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51 <param name="chip" value="ctcf1.bam,ctcf2.bam"/>
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52 <param name="mock" value="mock.bam"/>
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53 <param name="list_output" value="true"/>
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54 <output name="output" file="list_output.tab"/>
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55 </test>
886248a1cc7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/zerone commit 537bbf2e3ae9e7dcc619354911caf774338d7a0e
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56 </tests>
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57 <help><![CDATA[
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58 **What it does**
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59
886248a1cc7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/zerone commit 537bbf2e3ae9e7dcc619354911caf774338d7a0e
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60 Zerone discretizes several ChIP-seq replicates simultaneously and resolves conflicts between them. After the job is done, Zerone checks the results and tells you whether it passes the quality control.
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61
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62 **Results**
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63
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64 The first three lines contain the result of the quality control. It consists of a quality score followed by the numeric values of 5 features, and an advice to either accept or reject the discretization. The recommendation is to accept if the score is positive and reject if it is negative. If the score is higher than 1 (or lower than -1), the advice is considered extremely reliable.
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65
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66 The rest of the lines contain the discretization proper. The first three columns specify the chromosome, start and end positions of each window.
886248a1cc7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/zerone commit 537bbf2e3ae9e7dcc619354911caf774338d7a0e
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67 The fourth column represents the enrichment. Zerone classifies each window into one of two possible states. State 0 represents background signal and state 1 represents an enriched window.
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68
886248a1cc7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/zerone commit 537bbf2e3ae9e7dcc619354911caf774338d7a0e
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69 The fifth column contains the read counts of all the control profiles summed together per window. The following columns show the number of reads per window in the ChIP-seq files, in the order they were provided. The final column is the estimated probability that the window is a target (it is a confidence score for the call).
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70
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71 If you select "Output list of targets" Zerone produces an alternative output in which only the targets are shown after merging consecutive windows.
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72 The first three columns are the same as in window output i.e. chromosome or sequence name, start and end. The last column is the confidence score of the called target. It is the highest confidence of the windows merged in the same target region.
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73 ]]></help>
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74 <citations>
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75 <citation type="doi">10.1093/bioinformatics/btw33</citation>
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76 </citations>
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77 </tool>