Mercurial > repos > nilesh > rseqc

annotate FPKM_count.xml @ 14:b21f0167e197 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit ccb6f7edba5492f4750ef8a59c4f91eb67fdbbec
author iuc
date Wed, 22 Feb 2023 15:05:13 +0000
parents a7f9084572fe
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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 <macros>
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4 <import>rseqc_macros.xml</import>
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5 </macros>
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7 <expand macro="bio_tools"/>
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8
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9 <expand macro="requirements" />
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11 <expand macro="stdio" />
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13 <version_command><![CDATA[FPKM_count.py --version]]></version_command>
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15 <command><![CDATA[
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16 @BAM_SAM_INPUTS@
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17 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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26 #if str($strand_type.strand_specific) == "single"
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27 -d
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28 #if str($strand_type.single_type) == "s"
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29 '++,--'
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30 #else
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31 '+-,-+'
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32 #end if
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33 #end if
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34 @MULTIHITS@
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35 $onlyexonic
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36 --single-read="${singleread}"
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37 ]]>
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38 </command>
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40 <inputs>
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41 <expand macro="bam_param" />
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42 <expand macro="refgene_param" />
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43 <expand macro="strand_type_param" />
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44 <expand macro="multihits_param" />
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45 <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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46 <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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47 <option value="1" selected="true">Treat it as a whole fragment (1)</option>
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48 <option value="0.5">Treat it as a half fragment (0.5)</option>
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49 <option value="0">Ignore it (0)</option>
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50 </param>
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51 </inputs>
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52
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53 <outputs>
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54 <data format="tabular" name="output" from_work_dir="output.FPKM.xls" label="${tool.name} on ${on_string}: FPKM counts"/>
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55 </outputs>
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57 <tests>
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58 <test>
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59 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
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60 <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" ftype="bed12"/>
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61 <output name="output" file="output01.tab"/>
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62 </test>
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63 <test>
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64 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
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65 <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" ftype="bed12"/>
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66 <conditional name="multihits_type">
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67 <param name="multihits_type_selector" value="skip_multihits"/>
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68 <param name="mapq" value="20"/>
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69 </conditional>
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70 <output name="output" file="output02.tab"/>
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71 <assert_command>
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72 <has_text text="--mapq=20" />
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73 </assert_command>
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74 </test>
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75 </tests>
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77 <help><![CDATA[
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78 FPKM_count.py
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79 +++++++++++++
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80
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81 Given a BAM file and reference gene model, this program will calculate the raw
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82 read count, FPM (fragments per million), and FPKM (fragments per million
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83 mapped reads per kilobase exon) for each gene in a BED file. For strand
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84 specific RNA-seq data, program will assign read to its parental gene according
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85 to strand rule, if you don't know the strand rule, run infer_experiment.py.
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86 Please note that chromosome ID, genome cooridinates should be concordant
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87 between BAM and BED files.
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88
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89 Inputs
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90 ++++++++++++++
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91
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92 Input BAM/SAM file
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93 Alignment file in BAM/SAM format.
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94
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95 Reference gene model
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96 Gene model in BED format.
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97
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98 Strand sequencing type (default=none)
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99 See Infer Experiment tool if uncertain.
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100
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101 Options
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102 ++++++++++++++
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103
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104 Skip Multiple Hit Reads
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105 Use Multiple hit reads or use only uniquely mapped reads.
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106
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107 Minimum mapping quality
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108 Minimum mapping quality (phred scaled) for an alignment to be called
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109 "uniquely mapped". default=30
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110
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111 Only use exonic reads
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112 Renders program only used exonic (UTR exons and CDS exons) reads,
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113 otherwise use all reads.
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114
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115 Single Reads
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116 How to count read-pairs that only have one end mapped. 0: ignore it. 0.5:
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117 treat it as half fragment. 1: treat it as whole fragment. default=1
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118
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119 Sample Output
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120 ++++++++++++++
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121
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122 ====== ========= ========= ========= ========= =========== ========== ============ ============
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123 #chrom st end accession mRNA_size gene_strand Frag_count FPM FPKM
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124 ====== ========= ========= ========= ========= =========== ========== ============ ============
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125 chr1 100652477 100715409 NM_001918 10815.0 ‘-‘ 5498.0 191.73788949 17.728884835
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126 chr1 175913961 176176380 NM_022457 2789.0 ‘-‘ 923.0 32.188809021 11.541344217
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127 chr1 150980972 151008189 NM_021222 2977.0 ‘+’ 687.0 23.958517657 8.0478729115
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128 chr1 6281252 6296044 NM_012405 4815.0 ‘-‘ 1396.0 48.684265866 10.11095864
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129 chr1 20959947 20978004 NM_032409 2660.0 ‘+’ 509.0 17.750925018 6.6732800821
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130 chr1 32479294 32509482 NM_006559 2891.0 ‘+’ 2151.0 75.014223408 25.947500314
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131 ====== ========= ========= ========= ========= =========== ========== ============ ============
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132
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133 @ABOUT@
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134
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135 ]]>
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136 </help>
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137
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138 <expand macro="citations" />
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139
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140 </tool>