Mercurial > repos > jjohnson > cistrome_beta

annotate beta_minus.xml @ 5:c119110a5b47 draft default tip

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planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/cistrome_beta commit d824634e1b43fd7f2628631d2d4443ca1cd1ecce-dirty
author jjohnson
date Thu, 22 Mar 2018 11:17:52 -0400
parents 52ed4957ace9
children
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1 <tool id="beta_minus" name="BETA-minus: Targets prediction with binding only" version="@VERSION@.0">
2
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2 <description>Predict the factors (TFs or CRs) direct target genes by only binding data</description>
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3 <macros>
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4 <import>beta_macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <expand macro="stdio" />
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8 <command><![CDATA[
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9 BETA minus
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10 #include source=$common_opts#
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11 #include source=$genome_opts#
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12 #include source=$write_log#
2
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13 ]]></command>
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14 <inputs>
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15 <expand macro="common_params" />
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16 <expand macro="genome_params" />
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17 </inputs>
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18 <outputs>
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19 <data format="txt" name="log" label="Log of BETA minus"/>
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20 <data format="tabular" name="targetsoutput" label="BETA predicted Targets" from_work_dir="BETA_OUTPUT/NA_targets.txt"/>
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21 <data format="tabular" name="targetpeaks" label="BETA Target gene's associated peaks" from_work_dir="BETA_OUTPUT/NA_targets_associated_peaks.txt"/>
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22 </outputs>
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23 <tests>
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24 <test>
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25 <param name='peakfile' value="peaks.bed" ftype="bed" dbkey="hg19"/>
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26 <param name="distance" value="100000"/>
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27 <param name="peaknumber" value="10000"/>
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28 <param name="genomeName" value="hg19"/>
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29 <output name="log">
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30 <assert_contents>
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31 <has_text_matching expression="Finished" />
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32 </assert_contents>
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33 </output>
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34 <output name="targetsoutput">
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35 <assert_contents>
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36 <has_text_matching expression="chr19\t4675243\t4723855\tNM_139159\t1.1.*\t-\tDPP" />
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37 </assert_contents>
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38 </output>
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39 <output name="targetpeaks">
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40 <assert_contents>
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41 <has_text_matching expression="chr19\t4723422\t4724314\tregion_9\tNM_139159\tDPP9\t13\t0.6.*" />
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42 </assert_contents>
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43 </output>
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44 </test>
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45 </tests>
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46 <help><![CDATA[
0
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47 ** BETA minus **
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48
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49 @EXTERNAL_DOCUMENTATION@
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50
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51 @CITATION_SECTION@
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52
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53 This tool annotates the given intervals and scores with genome
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54 features such as gene body. It's the major module in CEAS package
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55 which is written by Hyunjin Gene Shin, published in Bioinformatics
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56 (pubmed id:19689956).
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57
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58 .. class:: warningmark
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59
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60 **NEED IMPROVEMENT**
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61
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62 -----
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63
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64 **Parameters**
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65
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66 - **PEAKFILE file** contains peaks for the experiment in a bed
2
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67 format file. Normally, it's produced by the peak calling tool. It's
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68 required.
0
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69 - **genome** hg19 for human and mm9 for mouse. Others, don't set this parameter.
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70 - **REFERENCE** is the refgene info file downloaded from UCSC genome browser.
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71 It is a tab delimited text file with gene annotation with refseq and gene symbol.
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72 Input this file only if your genome is neither hg19 nor mm9.
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73 profiling
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74 - **OUTPUT** to specify the output files directory
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75 - **bl** Whether or not to use CTCF boundary file to get the contributed peaks
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76 - **NAME** specify the name of the output files.
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77 - **DISTANCE** specify the distance wich peaks within it will be considered.
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78
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79
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80 -----
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81
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82 **script parameter list of BETA minus**
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83
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84 ::
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85
2
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86 -h, --help show this help message and exit
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87 -p PEAKFILE, --peakfile PEAKFILE
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88 The bed format of peaks binding sites.
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89 BETA supports 3 or 5 columns bed format: CHROM, START, END [NAME, SCORE]
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90 -g {hg19,mm9}, --genome {hg19,mm9}
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91 Specify your species, {hg19, mm9}
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92 -r REFERENCE, --reference REFERENCE
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93 the refgene info file downloaded from UCSC genome
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94 browser.input this file only if your genome is neither
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95 hg19 nor mm9
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96 -o OUTPUT, --output OUTPUT
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97 the directory to store all the output files, if you
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98 don't set this, files will be output into the current
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99 directory
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100 --bl whether or not use CTCF boundary to filter peaks
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101 around a gene, DEFAULT=FALSE
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102 --pn PEAKNUMBER the number of peaks you want to consider, DEFAULT=10000
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103 -n NAME, --name NAME this argument is used to name the result file.If not
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104 set, the peakfile name will be used instead
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105 -d DISTANCE, --distance DISTANCE
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106 Set a number which unit is 'base'. It will get peaks
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107 within this distance from gene TSS. default:100000 (100kb)
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108
2
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109 ]]></help>
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110 <expand macro="citations" />
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111 </tool>