Mercurial > repos > lparsons > rseqc

annotate bam2wig.xml @ 1:cd2daa987b69 draft default tip

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planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit 2400cce6e3918648fda8f2a8d8485ab251a58827
author lparsons
date Tue, 07 Jul 2015 14:14:04 -0400
parents 306127635959
children
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306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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1 <tool id="rseqc_bam2wig" name="BAM to Wiggle" version="2.4galaxy1">
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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2 <description>
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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3 converts all types of RNA-seq data from .bam to .wig
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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4 </description>
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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5
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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6 <macros>
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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7 <import>rseqc_macros.xml</import>
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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8 </macros>
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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9
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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10 <requirements>
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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11 <expand macro="requirement_package_r" />
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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12 <expand macro="requirement_package_numpy" />
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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13 <expand macro="requirement_package_rseqc" />
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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14 </requirements>
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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15
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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16 <expand macro="stdio" />
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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18 <version_command><![CDATA[bam2wig.py --version]]></version_command>
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19
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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20 <command><![CDATA[
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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21 ln -sfn '${input}' 'input.bam' &&
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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22 ln -sfn '${input.metadata.bam_index}' 'input.bam.bai' &&
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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23 bam2wig.py -i input.bam -s $chromsize -o outfile
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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24
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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25 #if str($strand_type.strand_specific) == "pair"
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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26 -d
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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27 #if str($strand_type.pair_type) == "sd"
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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28 '1++,1--,2+-,2-+'
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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29 #else
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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30 '1+-,1-+,2++,2--'
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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31 #end if
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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32 #end if
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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33
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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34 #if str($strand_type.strand_specific) == "single"
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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35 -d
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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36 #if str($strand_type.single_type) == "s"
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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37 '++,--'
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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38 #else
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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39 '+-,-+'
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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40 #end if
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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41 #end if
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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42
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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43 #if $wigsum.wigsum_type
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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44 -t $wigsum.totalwig
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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45 #end if
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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46 #if $multihits.skipmultihits
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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47 --skip-multi-hits
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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48 --mapq=$multihits.mapq
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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49 #end if
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50 2>&1
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51 ]]>
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52 </command>
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53 <inputs>
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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54 <param name="input" type="data" label="Input .bam File" format="bam" help="(--input-file)"/>
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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55 <param name="chromsize" type="data" label="Chromosome size file (tab or space separated)" format="txt,tabular" help="(--chromSize)"/>
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56
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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57 <conditional name="multihits">
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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58 <param name="skipmultihits" type="boolean" label="Skip Multiple Hit Reads/Only Use Uniquely Mapped Reads" value="false" help="(--skip-multi-hits)" />
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59 <when value="true">
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60 <param name="mapq" value="30" type="integer" label="Minimum mapping quality for an alignment to be called 'uniquly mapped'" help="(--mapq)" />
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61 </when>
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62 <when value="false" />
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63 </conditional>
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64
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65 <conditional name="wigsum">
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66 <param name="wigsum_type" type="boolean" label="Specify wigsum?" value="false">
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67 </param>
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68 <when value="true">
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69 <param name="totalwig" value="0" type="integer" label="specified wigsum" help="(--wigsum)"/>
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70 </when>
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71 <when value="false"/>
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72 </conditional>
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73
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74 <conditional name="strand_type">
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75 <param name="strand_specific" type="select" label="Strand-specific?" value="none">
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76 <option value="none">none</option>
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77 <option value="pair">Pair-End RNA-seq</option>
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78 <option value="single">Single-End RNA-seq</option>
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79 </param>
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80 <when value="pair">
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81 <param name="pair_type" type="select" display="radio" label="Pair-End Read Type (format: mapped --> parent)" value="sd" help="(--strand)">
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82 <option value="sd"> read1 (positive --> positive; negative --> negative), read2 (positive --> negative; negative --> positive)</option>
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83 <option value="ds">read1 (positive --> negative; negative --> positive), read2 (positive --> positive; negative --> negative)</option>
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84 </param>
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85 </when>
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86 <when value="single">
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87 <param name="single_type" type="select" display="radio" label="Single-End Read Type (format: mapped --> parent)" value="s" help="(--strand)">
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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88 <option value="s">positive --> positive; negative --> negative</option>
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89 <option value="d">positive --> negative; negative --> positive</option>
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90 </param>
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91 </when>
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92 <when value="none"></when>
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93 </conditional>
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94 </inputs>
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95
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96 <outputs>
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97 <data format="wig" name="output" from_work_dir="outfile.wig">
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98 <filter>strand_type['strand_specific'] == 'none'</filter>
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99 </data>
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100 <data format="wig" name="outputfwd" from_work_dir="outfile.Forward.wig" label="${tool.name} on ${on_string} (Forward Reads)">
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101 <filter>strand_type['strand_specific'] != 'none'</filter>
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102 </data>
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103 <data format="wig" name="outputrv" from_work_dir="outfile.Reverse.wig" label="${tool.name} on ${on_string} (Reverse Reads)">
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104 <filter>strand_type['strand_specific'] != 'none'</filter>
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105 </data>
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106 </outputs>
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107
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108 <tests>
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109 <test>
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110 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
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111 <param name="chromsize" value="hg19.chrom.sizes"/>
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112 <output name="output" file="testwig.wig"/>
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113 </test>
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114 <test>
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115 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
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116 <param name="chromsize" value="hg19.chrom.sizes"/>
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117 <param name="skipmultihits" value="True"/>
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118 <param name="mapq" value="20"/>
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119 <output name="output" file="testwig.wig"/>
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120 </test>
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121 <test>
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122 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
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123 <param name="chromsize" value="hg19.chrom.sizes"/>
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124 <param name="strand_specific" value="pair"/>
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125 <param name="pair_type" value="sd"/>
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126 <output name="outputfwd" file="testwig.Forward.wig"/>
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127 <output name="outputrv" file="testwig.Reverse.wig"/>
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128 </test>
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129 </tests>
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130
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131 <help><![CDATA[
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132 bam2wig.py
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133 ++++++++++
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134
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135 Visualization is the most straightforward and effective way to QC your RNA-seq
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136 data. For example, change of expression or new splicing can be easily checked
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137 by visually comparing two RNA-seq tracks using genome browser such as UCSC_,
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138 IGB_ and IGV_. `bam2wig.py` converts all types of RNA-seq data from BAM_
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139 format into wiggle_ format in one-stop. wiggle_ files can then be easily
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140 converted into bigwig_. Bigwig is indexed, binary format of wiggle file, and
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141 it's particular useful to display large, continuous dataset on genome
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142 browser.
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143
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144 Inputs
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145 ++++++++++++++
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146
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147 Input BAM file
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148 Alignment file in BAM format (SAM is not supported). BAM file will be sorted and indexed using samTools.
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149
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150 Chromosome size file
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151 Tab or space separated text file with 2 columns: first column is chromosome name, second column is size of the chromosome. Chromosome names (such as "chr1") should be consistent between this file and BAM file.
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152
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153 Specified wigsum (default=none)
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154 Specified wigsum. Wigsum of 100000000 equals to coverage achieved by 1 million 100nt reads. Ignore this option to disable normalization.
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155
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156 Skip multiple Hit reads
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157 skips multiple hit reads or only use uniquely mapped reads
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158
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159 Strand-specific (default=none)
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160 How read(s) were stranded during sequencing. If you are not sure about the strand rule, run infer_experiment.py
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161
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162 Outputs
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163 ++++++++++++++
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164
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165 If RNA-seq is not strand specific, one wig file will be generated, if RNA-seq
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166 is strand specific, two wig files corresponding to Forward and Reverse will be generated.
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167
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168 -----
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169
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170 About RSeQC
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171 +++++++++++
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172
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173 The RSeQC_ package provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. "Basic modules" quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while "RNA-seq specific modules" investigate sequencing saturation status of both splicing junction detection and expression estimation, mapped reads clipping profile, mapped reads distribution, coverage uniformity over gene body, reproducibility, strand specificity and splice junction annotation.
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174
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175 The RSeQC package is licensed under the GNU GPL v3 license.
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176
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177 .. image:: http://rseqc.sourceforge.net/_static/logo.png
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178
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179 .. _RSeQC: http://rseqc.sourceforge.net/
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180
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181 .. _UCSC: http://genome.ucsc.edu/index.html
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182 .. _IGB: http://bioviz.org/igb/
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183 .. _IGV: http://www.broadinstitute.org/igv/home
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184 .. _BAM: http://genome.ucsc.edu/goldenPath/help/bam.html
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185 .. _wiggle: http://genome.ucsc.edu/goldenPath/help/wiggle.html
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186 .. _bigwig: http://genome.ucsc.edu/FAQ/FAQformat.html#format6.1
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187 ]]>
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188 </help>
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306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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190 <expand macro="citations" />
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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192 </tool>