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annotate macs2_bdgdiff.xml @ 49:1b3f899ef044 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
author iuc
date Sat, 08 Apr 2017 08:28:38 -0400
parents e04fc51ee5e1
children 8f6b37d29df5
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1 <tool id="macs2_bdgdiff" name="MACS2 bdgdiff" version="@VERSION_STRING@.0">
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2 <description>Differential peak detection based on paired four bedgraph files</description>
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3 <macros>
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4 <import>macs2_macros.xml</import>
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5 </macros>
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6 <expand macro="requirements">
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7 <requirement type="package" version="4.1.3">gawk</requirement>
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8 </expand>
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9 <expand macro="stdio" />
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10 <expand macro="version_command" />
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11 <command>
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12 <![CDATA[
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13 macs2 bdgdiff
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14 --t1 '${ t1 }'
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15 --t2 '${ t2 }'
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16 --c1 '${ c1 }'
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17 --c2 '${ c2 }'
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18 --cutoff '${ cutoff }'
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19 --min-len '${ minlen }'
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20 --depth1 '${ depth.depth1 }'
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21 --depth2 '${ depth.depth2 }'
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22 --max-gap '${ maxgap }'
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23 -o c1.bed c2.bed both.bed &&
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25 awk '!/^track name/' "c1.bed" > '${ output_cond1 }' &&
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26 awk '!/^track name/' "c2.bed" > '${ output_cond1 }' &&
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27 awk '!/^track name/' "both.bed" > '${ output_both }'
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29 ]]>
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30 </command>
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31 <inputs>
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32 <param name="t1" type="data" format="bedgraph" label="BedGraph for Treatment experiment 1" />
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33 <param name="t2" type="data" format="bedgraph" label="BedGraph for Treatment experiment 2" />
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35 <param name="c1" type="data" format="bedgraph" label="BedGraph for Control experiment 1" />
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36 <param name="c2" type="data" format="bedgraph" label="Bedgraph for Control experiment 2" />
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38 <param name="cutoff" type="float" label="Cutoff of log10 likelihood ratio cutoff" value="1.0" help="Default=1.0 correspoinding to likelihood ratio of 1,000 (--cutoff)"/>
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39 <param name="minlen" type="integer" label="Minimum length of differential region" value="200" help=" Try bigger value to remove small regions. Default=200 (--min-len)"/>
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41 <section name="depth" title="Sequencing depth" expanded="True" help="Sequencing depths will be used to calculate scaling factor for each sample, to down-scale larger sample to the level of smaller one. For example, while comparing condition 1 (10 Million reads) and condition 2 (20 million reads), use --depth1 10 --depth2 20, then pileup value in bedGraph for condition 2 will be divided by 2.">
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42 <param name="depth1" type="integer" value="1" label="Sequence depth of condition 1 in million reads" help="Default=1 (--depth1)" />
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43 <param name="depth2" type="integer" value="1" label="Sequence depth of condition 2 in million reads" help="Default=1 (--depth2)" />
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44 </section>
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45 <param name="maxgap" type="integer" value="100" label="Maximum gap to merge nearby differential regions" help="Consider a wider gap for broad marks. Maximum gap should be smaller than minimum length. Default=100 (--max-gap)." />
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47
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48 </inputs>
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49 <outputs>
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50 <data name="output_cond1" format="bed" label="${tool.name} on ${on_string} (Condition 1)"/>
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51 <data name="output_cond2" format="bed" label="${tool.name} on ${on_string} (Condition 2)"/>
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52 <data name="output_both" format="bed" label="${tool.name} on ${on_string} (Common)"/>
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53 </outputs>
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54 <tests>
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55 <test>
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56
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57 <param name="t1" value="bdgdiff_t1.bdg" ftype="bedgraph"/>
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58 <param name="t2" value="bdgdiff_t2.bdg" ftype="bedgraph"/>
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59 <param name="c1" value="bdgdiff_c1.bdg" ftype="bedgraph"/>
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60 <param name="c2" value="bdgdiff_c2.bdg" ftype="bedgraph"/>
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61 <param name="cutoff" value="1.0"/>
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62 <param name="minlen" value="200"/>
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63 <param name="depth1" value="10"/>
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64 <param name="depth2" value="1"/>
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65 <param name="maxgap" value="100"/>
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66 <output name="output_cond1">
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67 <assert_contents>
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68 <has_text text="c2.bed1" />
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69 </assert_contents>
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70 </output>
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71 </test>
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72 </tests>
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73 <help>
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74 <![CDATA[
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75 **What it does**
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76
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77 This is **bdgdiff** utility from the MACS2_ Package. It performs differential peak detection based on paired four bedgraph files.
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78
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79 .. _MACS2: https://github.com/taoliu/MACS
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81 @citation@
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82 ]]>
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83 </help>
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84 <expand macro="citations" />
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85 </tool>