Mercurial > repos > nilesh > rseqc

annotate FPKM_count.xml @ 51:09846d5169fa draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
author iuc
date Tue, 14 Mar 2017 10:23:21 -0400
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51
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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1 <tool id="rseqc_FPKM_count" name="FPKM Count" version="@WRAPPER_VERSION@">
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2 <description>calculates raw read count, FPM, and FPKM for each gene</description>
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3
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4 <macros>
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5 <import>rseqc_macros.xml</import>
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6 </macros>
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8 <expand macro="requirements" />
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9
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10 <expand macro="stdio" />
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12 <version_command><![CDATA[FPKM_count.py --version]]></version_command>
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13
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14 <command><![CDATA[
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15 ln -sf '${input}' 'local_input.bam' &&
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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16 ln -sf '${input.metadata.bam_index}' 'local_input.bam.bai' &&
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17 FPKM_count.py -i 'local_input.bam' -o output -r '${refgene}'
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18
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19 #if str($strand_type.strand_specific) == "pair"
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20 -d
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21 #if str($strand_type.pair_type) == "sd"
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22 '1++,1--,2+-,2-+'
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23 #else
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24 '1+-,1-+,2++,2--'
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25 #end if
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26 #end if
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28 #if str($strand_type.strand_specific) == "single"
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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29 -d
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30 #if str($strand_type.single_type) == "s"
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31 '++,--'
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32 #else
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33 '+-,-+'
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34 #end if
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35 #end if
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36
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37 @MULTIHITS@
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38
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39 $onlyexonic
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40 --single-read="${singleread}"
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41 ]]>
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42 </command>
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43
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44 <inputs>
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45 <expand macro="bam_param" />
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46 <expand macro="refgene_param" />
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47 <expand macro="strand_type_param" />
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48 <expand macro="multihits_param" />
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49 <param name="onlyexonic" type="boolean" value="false" truevalue="--only-exonic" falsevalue="" label="Only use exonic (UTR exons and CDS exons) reads, otherwise use all reads" help="(--only-exonic)"/>
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50 <param name="singleread" type="select" label="How should read-pairs that only have one end mapped be counted?" help="(--single-read)">
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51 <option value="1" selected="true">Treat it as a whole fragment (1)</option>
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52 <option value="0.5">Treat it as a half fragment (0.5)</option>
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53 <option value="0">Ignore it (0)</option>
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54 </param>
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55 </inputs>
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56
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57 <outputs>
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58 <data format="xls" name="outputxls" from_work_dir="output.FPKM.xls"/>
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59 </outputs>
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60
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61 <tests>
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62 <test>
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63 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
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64 <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed"/>
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65 <output name="outputxls" file="output.FPKM.xls"/>
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66 </test>
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67 </tests>
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68
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69 <help><![CDATA[
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70 FPKM_count.py
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71 +++++++++++++
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72
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73 Given a BAM file and reference gene model, this program will calculate the raw
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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74 read count, FPM (fragments per million), and FPKM (fragments per million
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75 mapped reads per kilobase exon) for each gene in a BED file. For strand
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76 specific RNA-seq data, program will assign read to its parental gene according
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77 to strand rule, if you don't know the strand rule, run infer_experiment.py.
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78 Please note that chromosome ID, genome cooridinates should be concordant
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79 between BAM and BED files.
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80
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81 Inputs
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82 ++++++++++++++
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83
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84 Input BAM/SAM file
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85 Alignment file in BAM/SAM format.
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86
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87 Reference gene model
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88 Gene model in BED format.
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89
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90 Strand sequencing type (default=none)
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91 See Infer Experiment tool if uncertain.
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92
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93 Options
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94 ++++++++++++++
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95
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96 Skip Multiple Hit Reads
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97 Use Multiple hit reads or use only uniquely mapped reads.
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98
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99 Minimum mapping quality
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100 Minimum mapping quality (phred scaled) for an alignment to be called
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101 "uniquely mapped". default=30
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102
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103 Only use exonic reads
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104 Renders program only used exonic (UTR exons and CDS exons) reads,
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105 otherwise use all reads.
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106
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107 Single Reads
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108 How to count read-pairs that only have one end mapped. 0: ignore it. 0.5:
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109 treat it as half fragment. 1: treat it as whole fragment. default=1
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110
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111 Sample Output
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112 ++++++++++++++
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113
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114 ====== ========= ========= ========= ========= =========== ========== ============ ============
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115 #chrom st end accession mRNA_size gene_strand Frag_count FPM FPKM
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116 ====== ========= ========= ========= ========= =========== ========== ============ ============
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117 chr1 100652477 100715409 NM_001918 10815.0 ‘-‘ 5498.0 191.73788949 17.728884835
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118 chr1 175913961 176176380 NM_022457 2789.0 ‘-‘ 923.0 32.188809021 11.541344217
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119 chr1 150980972 151008189 NM_021222 2977.0 ‘+’ 687.0 23.958517657 8.0478729115
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120 chr1 6281252 6296044 NM_012405 4815.0 ‘-‘ 1396.0 48.684265866 10.11095864
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121 chr1 20959947 20978004 NM_032409 2660.0 ‘+’ 509.0 17.750925018 6.6732800821
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122 chr1 32479294 32509482 NM_006559 2891.0 ‘+’ 2151.0 75.014223408 25.947500314
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123 ====== ========= ========= ========= ========= =========== ========== ============ ============
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124
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125 @ABOUT@
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126
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127 ]]>
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128 </help>
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129
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130 <expand macro="citations" />
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131
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132 </tool>