Mercurial > repos > nilesh > rseqc

annotate FPKM_count.xml @ 60:1421603cc95b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 1dfe55ca83685cadb0ce8f6ebbd8c13232376d1d
author iuc
date Sat, 26 Nov 2022 15:19:14 +0000
parents dbedfc5f5a3c
children 5968573462fa
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1 <tool id="rseqc_FPKM_count" name="FPKM Count" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@">
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2 <description>calculates raw read count, FPM, and FPKM for each gene</description>
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3 <expand macro="bio_tools"/>
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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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10 <expand macro="stdio" />
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12 <version_command><![CDATA[FPKM_count.py --version]]></version_command>
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14 <command><![CDATA[
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15 @BAM_SAM_INPUTS@
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16 FPKM_count.py -i 'input.${extension}' -o output -r '${refgene}'
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18 #if str($strand_type.strand_specific) == "pair"
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19 -d
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20 #if str($strand_type.pair_type) == "sd"
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21 '1++,1--,2+-,2-+'
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22 #else
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23 '1+-,1-+,2++,2--'
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24 #end if
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25 #end if
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27 #if str($strand_type.strand_specific) == "single"
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28 -d
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29 #if str($strand_type.single_type) == "s"
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30 '++,--'
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31 #else
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32 '+-,-+'
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33 #end if
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34 #end if
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36 @MULTIHITS@
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38 $onlyexonic
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39 --single-read="${singleread}"
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40 ]]>
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41 </command>
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43 <inputs>
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44 <expand macro="bam_param" />
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45 <expand macro="refgene_param" />
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46 <expand macro="strand_type_param" />
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47 <expand macro="multihits_param" />
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48 <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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49 <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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50 <option value="1" selected="true">Treat it as a whole fragment (1)</option>
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51 <option value="0.5">Treat it as a half fragment (0.5)</option>
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52 <option value="0">Ignore it (0)</option>
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53 </param>
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54 </inputs>
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56 <outputs>
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57 <data format="xls" name="outputxls" from_work_dir="output.FPKM.xls"/>
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58 </outputs>
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60 <tests>
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61 <test>
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62 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
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63 <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" ftype="bed12"/>
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64 <output name="outputxls" file="output.FPKM.xls"/>
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65 </test>
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66 </tests>
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67
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68 <help><![CDATA[
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69 FPKM_count.py
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70 +++++++++++++
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71
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72 Given a BAM file and reference gene model, this program will calculate the raw
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73 read count, FPM (fragments per million), and FPKM (fragments per million
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74 mapped reads per kilobase exon) for each gene in a BED file. For strand
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75 specific RNA-seq data, program will assign read to its parental gene according
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76 to strand rule, if you don't know the strand rule, run infer_experiment.py.
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77 Please note that chromosome ID, genome cooridinates should be concordant
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78 between BAM and BED files.
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79
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80 Inputs
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81 ++++++++++++++
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82
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83 Input BAM/SAM file
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84 Alignment file in BAM/SAM format.
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85
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86 Reference gene model
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87 Gene model in BED format.
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88
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89 Strand sequencing type (default=none)
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90 See Infer Experiment tool if uncertain.
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91
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92 Options
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93 ++++++++++++++
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94
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95 Skip Multiple Hit Reads
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96 Use Multiple hit reads or use only uniquely mapped reads.
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97
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98 Minimum mapping quality
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99 Minimum mapping quality (phred scaled) for an alignment to be called
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100 "uniquely mapped". default=30
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101
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102 Only use exonic reads
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103 Renders program only used exonic (UTR exons and CDS exons) reads,
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104 otherwise use all reads.
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105
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106 Single Reads
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107 How to count read-pairs that only have one end mapped. 0: ignore it. 0.5:
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108 treat it as half fragment. 1: treat it as whole fragment. default=1
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109
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110 Sample Output
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111 ++++++++++++++
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112
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113 ====== ========= ========= ========= ========= =========== ========== ============ ============
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114 #chrom st end accession mRNA_size gene_strand Frag_count FPM FPKM
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115 ====== ========= ========= ========= ========= =========== ========== ============ ============
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116 chr1 100652477 100715409 NM_001918 10815.0 ‘-‘ 5498.0 191.73788949 17.728884835
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117 chr1 175913961 176176380 NM_022457 2789.0 ‘-‘ 923.0 32.188809021 11.541344217
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118 chr1 150980972 151008189 NM_021222 2977.0 ‘+’ 687.0 23.958517657 8.0478729115
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119 chr1 6281252 6296044 NM_012405 4815.0 ‘-‘ 1396.0 48.684265866 10.11095864
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120 chr1 20959947 20978004 NM_032409 2660.0 ‘+’ 509.0 17.750925018 6.6732800821
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121 chr1 32479294 32509482 NM_006559 2891.0 ‘+’ 2151.0 75.014223408 25.947500314
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122 ====== ========= ========= ========= ========= =========== ========== ============ ============
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123
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124 @ABOUT@
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125
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126 ]]>
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127 </help>
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128
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129 <expand macro="citations" />
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130
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131 </tool>