Mercurial > repos > lparsons > rseqc

annotate geneBody_coverage.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
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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_geneBody_coverage" name="Gene Body Converage (BAM)" version="2.4galaxy1">
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2 <description>
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3 Read coverage over gene body.
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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4 </description>
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6 <macros>
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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>
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9
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10 <requirements>
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11 <expand macro="requirement_package_r" />
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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" />
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14 </requirements>
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16 <expand macro="stdio" />
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18 <version_command><![CDATA[geneBody_coverage.py --version]]></version_command>
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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 #set $safename = ''.join(c in '_0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ' and c or '_' for c in $input.display_name)
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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22 #set $fname = "d1_" + str($safename) + ".bam"
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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23 ln -s '${input}' '${fname}' &&
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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24 ln -s '${input.metadata.bam_index}' '${fname}.bai' &&
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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25 echo '${fname}' > input_list.txt &&
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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26 #for $i, $additional_input in enumerate($additionalinputs):
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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27 #set $index = $i+2
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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28 #set $safename = ''.join(c in '_0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ' and c or '_' for c in $additional_input.file.display_name)
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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29 #set $fname = 'd' + str($index) + '_' + str($safename) + ".bam"
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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30 ln -s '$additional_input.file' '${fname}' &&
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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31 ln -s '$additional_input.file.metadata.bam_index' '${fname}.bai' &&
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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32 echo '${fname}' >> input_list.txt &&
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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33 #end for
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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34 geneBody_coverage.py -i input_list.txt -r $refgene --minimum_length $minimum_length -o output
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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35 ]]>
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36 </command>
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38 <inputs>
1
cd2daa987b69 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit 2400cce6e3918648fda8f2a8d8485ab251a58827
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39 <param name="input" type="data" label="Input .bam File" format="bam" help="(--input-file)"/>
cd2daa987b69 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit 2400cce6e3918648fda8f2a8d8485ab251a58827
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40 <repeat name="additionalinputs" title="Additional input .bam files">
cd2daa987b69 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit 2400cce6e3918648fda8f2a8d8485ab251a58827
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41 <param name="file" type="data" label="Additional input .bam file" format="bam" />
0
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42 </repeat>
1
cd2daa987b69 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit 2400cce6e3918648fda8f2a8d8485ab251a58827
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43 <param name="refgene" type="data" format="bed" label="reference gene model" help="(--refgene)"/>
cd2daa987b69 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit 2400cce6e3918648fda8f2a8d8485ab251a58827
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44 <param name="minimum_length" type="integer" value="100" label="Minimum mRNA length in bp (default: 100)" help="mRNA that are shorter than this value will be skipped (--minimum_length)." />
0
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45 </inputs>
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46
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47 <outputs>
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48 <data name="outputcurvespdf" format="pdf" from_work_dir="output.geneBodyCoverage.curves.pdf" label="${tool.name} on ${on_string} (Curves PDF)" />
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49 <data name="outputheatmappdf" format="pdf" from_work_dir="output.geneBodyCoverage.heatMap.pdf" label="${tool.name} on ${on_string} (HeatMap PDF)">
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50 <filter>len(additionalinputs) >= 2</filter>
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51 </data>
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52 <data name="outputr" format="txt" from_work_dir="output.geneBodyCoverage.r" label="${tool.name} on ${on_string} (R Script)" />
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53 <data name="outputtxt" format="txt" from_work_dir="output.geneBodyCoverage.txt" label="${tool.name} on ${on_string} (Text)" />
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54 </outputs>
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55
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56 <tests>
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57 <test>
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58 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
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59 <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed"/>
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60 <output name="outputcurvespdf" file="output.geneBodyCoverage.curves.pdf"/>
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61 <output name="outputr" file="output.geneBodyCoverage.r"/>
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62 <output name="outputtxt" file="output.geneBodyCoverage.txt"/>
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63 </test>
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64 <test>
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65 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
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66 <param name="file_0" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
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67 <param name="file_1" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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68 <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed"/>
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69 <output name="outputcurvespdf" file="output2.geneBodyCoverage.curves.pdf"/>
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70 <output name="outputcurvespdf" file="output2.geneBodyCoverage.heatMap.pdf"/>
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71 <output name="outputr" file="output2.geneBodycoverage.r"/>
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72 <output name="outputtxt" file="output2.geneBodyCoverage.txt"/>
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73 </test>
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74
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75 </tests>
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77 <help><![CDATA[
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78 geneBody_coverage.py
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79 ++++++++++++++++++++
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81 Read coverage over gene body. This module is used to check if read coverage is uniform and if there is any 5\'/3\' bias. This module scales all transcripts to 100 nt and calculates the number of reads covering each nucleotide position. Finally, it generates plots illustrating the coverage profile along the gene body.
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82
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83 If 3 or more BAM files were provided. This program generates a lineGraph and a heatmap. If fewer than 3 BAM files were provided, only lineGraph is generated. See below for examples.
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84
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85 When heatmap is generated, samples are ranked by the "skewness" of the coverage: Sample with best (worst) coverage will be displayed at the top (bottom) of the heatmap.
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86 Coverage skewness was measured by `Pearson’s skewness coefficients <http://en.wikipedia.org/wiki/Skewness#Pearson.27s_skewness_coefficients>`_
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87
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88 .. image:: http://rseqc.sourceforge.net/_images/geneBody_workflow.png
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89 :width: 800 px
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90 :scale: 80 %
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91
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92
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93 Inputs
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94 ++++++++++++++
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95
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96 Input BAM/SAM file
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97 Alignment file in BAM/SAM format.
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98
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99 Reference gene model
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100 Gene Model in BED format.
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101
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102 Minimum mRNA length
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103 Minimum mRNA length (bp). mRNA that are shorter than this value will be skipped (default is 100).
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104
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105 Outputs
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106 ++++++++++++++
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107 Text
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108 Table that includes the data used to generate the plots
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109
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110 R Script
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111 R script file that reads the data and generates the plot
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112
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113 PDF
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114 The final plot, in PDF format
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115
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116 Example plots:
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117 .. image:: http://rseqc.sourceforge.net/_images/Aug_26.geneBodyCoverage.curves.png
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118 :height: 600 px
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119 :width: 600 px
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120 :scale: 80 %
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121
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122 .. image:: http://rseqc.sourceforge.net/_images/Aug_26.geneBodyCoverage.heatMap.png
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123 :height: 600 px
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124 :width: 600 px
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125 :scale: 80 %
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126
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127 -----
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128
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129 About RSeQC
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130 +++++++++++
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131
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132 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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133
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134 The RSeQC package is licensed under the GNU GPL v3 license.
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135
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136 .. image:: http://rseqc.sourceforge.net/_static/logo.png
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137
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138 .. _RSeQC: http://rseqc.sourceforge.net/
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139 ]]>
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140 </help>
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141
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142 <expand macro="citations" />
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143
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144 </tool>